Interferon regulatory factor gene transcriptions

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Associate Editor(s)-in-Chief: Henry A. Hoff

Interferon regulatory factors (IRF) are proteins which regulate transcription of interferons (see regulation of gene expression).[1] They are used in the JAK-STAT signaling pathway.[2] Interferon regulatory factors contain a conserved N-terminal region of about 120 amino acids, which folds into a structure that binds specifically to the interferon consensus sequence (ICS), which is located upstream of the interferon genes.[3] The remaining parts of the interferon regulatory factor sequence vary depending on the precise function of the protein.[3] The Kaposi sarcoma herpesvirus, KSHV[4], is a cancer virus that encodes four different IRF-like genes[5]; including vIRF1[6], which is a transforming oncoprotein that inhibits type 1 interferon activity.[7] In addition, the expression of IRF genes is under epigenetic regulation by promoter DNA methylation. [8]

Gene expressions

Main article: Gene expressions

There "are totally 11 members (from IRF-1 to IRF-11) identified from vertebrates [10]. All the IRF members share a well-conserved N-terminal helix-turn-helix IRF superfamily domain (also called DNA-binding domain, DBD) with five conserved tryptophan (Trp) residues, which could recognize DNA sequences containing 5’-GAAA-3’ tetranucleotide, such as the IFN-stimulated response element (ISREs, GAAANNGAAA) [11, 12]. Moreover, it was reported that the IRS consensus (-78/-66, AANNGAAA), which existed in the promoter region of IFN-β, could be bound by the IRF family members [13]."[9] "As for the C-terminus, most of the IRFs share an IRF-3 superfamily domain, which was also named as IRF associated domain 1 (IAD1). IRF-1 and IRF-2 do not possess conserved IAD1 domain, but they contain non-conserved activation domain (the last 100 amino acids of IRF-1 were rich in tyrosine) or repression domain (the final 25 amino acids of IRF-2 were rich in histidine, arginine and lysine) in their C-terminus, respectively."[10]

IRF1

Interferon regulatory factor 1 is a protein that in humans is encoded by the IRF1 gene.[11][12]

Interferon regulatory factor 1 was the first member of the interferon regulatory transcription factor (IRF) family identified. Initially described as a transcription factor able to activate expression of the cytokine Interferon beta,[13] IRF-1 was subsequently shown to function as a transcriptional activator or repressor of a variety of target genes.

"IRF1 regulates expression of ISGs in response to IFN-I and IFN-II by directly binding the ISRE or IRF-responsive element."[14]

The IRF-1 protein binds to the ISRE via an N-terminal helix-turn-helix DNA binding domain,[15] which is highly conserved among all IRF proteins.

Beyond its function as a transcription factor, IRF-1 has also been shown to trans-activate the tumour suppressor protein p53 through the recruitment of its co-factor p300.[16]

IRF-1 has been shown to play roles in the immune response, regulating apoptosis, DNA damage and tumor suppression.[17]

It has been shown that the extreme C-terminus of IRF-1 regulates its ability to activate transcription, nanobodies targeting this domain (MF1) are able to increase IRF-1 activity.[18]

IRF2

Interferon regulatory factor 2 is a protein that in humans is encoded by the IRF2 gene.[19]

IRF2 encodes interferon regulatory factor 2, a member of the interferon regulatory transcription factor (IRF) family. IRF2 competitively inhibits the IRF1-mediated transcriptional activation of interferons alpha and beta, and presumably other genes that employ IRF1 for transcription activation. However, IRF2 also functions as a transcriptional activator of histone H4.[20]

IRF3

Interferon regulatory factor 3 (IRF3) is an interferon regulatory factor.[21]

IRF3 is a member of the interferon regulatory transcription factor (IRF) family.[21] IRF3 was originally discovered as a homolog of IRF1 and IRF2. IRF3 has been further characterized and shown to contain several functional domains including a nuclear export signal, a DNA-binding domain, a C-terminal IRF association domain and several regulatory phosphorylation sites.[22] IRF3 is found in an inactive cytoplasmic form that upon serine/threonine phosphorylation forms a complex with CREBBP.[23] This complex translocates to the nucleus and activates the transcription of interferons alpha and beta, as well as other interferon-induced genes.[24]

IRF3 plays an important role in the innate immune system's response to viral infection.[25] Aggregated MAVS have been found to activate IRF3 dimerization.[26] A 2015 study shows phosphorylation of innate immune adaptor proteins MAVS, STING and TRIF at a conserved pLxIS motif recruits and specifies IRF3 phosphorylation and activation by the Serine/threonine-protein kinase TBK1, thereby activating the production of type-I interferons.[27] Another study has shown that IRF3-/- knockouts protect from myocardial infarction.[28] The same study identified IRF3 and the type I IFN response as a potential therapeutic target for post-myocardial infarction cardioprotection.[28]

Gene ID: 3661 is IRF3 interferon regulatory factor 3 on 19q13.33: "This gene encodes a member of the interferon regulatory transcription factor (IRF) family. The encoded protein is found in an inactive cytoplasmic form that upon serine/threonine phosphorylation forms a complex with CREBBP. This complex translocates to the nucleus and activates the transcription of interferons alpha and beta, as well as other interferon-induced genes. The protein plays an important role in the innate immune response against DNA and RNA viruses. Mutations in this gene are associated with Encephalopathy, acute, infection-induced, herpes-specific, 7."[29]

IRF4

Interferon regulatory factor 4 also known as MUM1 is a protein that in humans is encoded by the IRF4 gene,[30][31][32] located at 6p25-p23.

In melanocytic cells the IRF4 gene may be regulated by MITF.[33] IRF4 is a transcription factor that has been implicated in acute leukemia.[34] This gene is strongly associated with pigmentation: sensitivity of skin to sun exposure, freckles, blue eyes, and brown hair color.[35] A variant has been implicated in greying of hair.[36]

IRF5

Interferon regulatory factor 5 is a protein that in humans is encoded by the IRF5 gene.[37]

IRF5 is a member of the interferon regulatory factor (IRF) family, a group of transcription factors with diverse roles, including virus-mediated activation of interferon, and modulation of cell growth, differentiation, apoptosis, and immune system activity. Members of the IRF family are characterized by a conserved N-terminal DNA-binding domain containing tryptophan (W) repeats. Alternative splice variants encoding different isoforms exist.[37]

An adaptor protein named TASL plays an important regulatory role in IRF5 activation by being phosphorylated at the pLxIS motif,[38] drawing a similar analogy to the IRF3 activation pathway through the adaptor proteins MAVS, STING and TRIF.[39]

IRF6

Interferon regulatory factor 6 (IRF6) is a protein that in humans is encoded by the IRF6 gene.[40]

This gene encodes a member of the interferon regulatory transcription factor (IRF) family. Family members share a highly conserved N-terminal helix-turn-helix DNA-binding domain and a less conserved C-terminal protein-binding domain.[41] The function of IRF6 is related to the formation of connective tissue, for example that of the palate.[42] This gene encodes a member of the interferon regulatory transcription factor (IRF) family. In addition, it has been observed that IRF6 gene is under epigenetic regulation by promoter methylation.[8]

IRF7

Interferon regulatory factor 7 (IRF7) is a member of the interferon regulatory factor family of transcription factors.

IRF7 encodes interferon regulatory factor 7, a member of the interferon regulatory transcription factor (IRF) family. IRF7 has been shown to play a role in the transcriptional activation of virus-inducible cellular genes, including the type I interferon genes. In particular, IRF7 regulates many interferon-alpha genes.[43] Constitutive expression of IRF7 is largely restricted to lymphoid tissue, largely plasmacytoid dendritic cells, whereas IRF7 is inducible in many tissues. Multiple IRF7 transcript variants have been identified, although the functional consequences of these have not yet been established.[44]

The IRF7 pathway was shown to be silenced in some metastatic breast cancer cell lines, which may help the cells avoid the host immune response.[45] Restoring IRF7 to these cell lines reduced metastases and increased host survival time in animal models.

The IRF7 gene and product were shown to be defective in a patient with severe susceptibility to H1N1 influenza, while susceptibility to other viral diseases such as CMV, RSV, and parainfluenza was unaffected.[46]

IRF8

Interferon regulatory factor 8 (IRF8) also known as the interferon consensus sequence-binding protein (ICSBP), is a protein that in humans is encoded by the IRF8 gene.[47][3][48] IRF8 is a transcription factor that plays critical roles in the regulation of lineage commitment and in myeloid cell maturation including the decision for a common myeloid progenitor (CMP) to differentiate into a monocyte precursor cell.

Interferon Consensus Sequence-binding protein (ICSBP) is a transcription factor of the interferon regulatory factor (IRF) family. Proteins of this family are composed of a conserved DNA-binding domain in the N-terminal region and a divergent C-terminal region that serves as the regulatory domain. The IRF family proteins bind to the IFN-stimulated response element (ISRE) and regulate expression of genes stimulated by type I IFNs, namely IFN-α and IFN-β. IRF family proteins also control expression of IFN-α and IFN-β-regulated genes that are induced by viral infection.[47]

Many "GAS-containing STAT1-target genes have been identified (40), including guanylate-binding protein (GBP), SOCS1, IRF1, and IRF8."[14]

IRF9

Interferon regulatory factor 9 is a protein that in humans is encoded by the IRF9 gene, previously known as ISGF3G.[49][50][51]

Gene ID: 10379 is IRF9 interferon regulatory factor 9 on 14q12: "This gene encodes a member of the interferon regulatory factor (IRF) family, a group of transcription factors with diverse roles, including virus-mediated activation of interferon, and modulation of cell growth, differentiation, apoptosis, and immune system activity. Members of the IRF family are characterized by a conserved N-terminal DNA-binding domain containing tryptophan (W) repeats. Mutations in this gene result in Immunodeficiency 65."[52]

"Interferon-I binding to [interferon α receptor] IFNAR results in receptor dimerization and increased [Janus kinase 1] JAK1 and [tyrosine kinase 2] TYK2 kinase activity via juxtapositioning and transphosphorylation (13). Subsequently, JAK1 and TYK2 phosphorylate IFNAR1 and IFNAR2 on target tyrosine residues that become docking sites for [signal transducer and activator of transcription 1] STAT1 and STAT2 (14). Receptor-bound STAT1 and STAT2 are thus phosphorylated on a critical tyrosine residue (pTyr) driving SH2-pTyr mediated dimer formation, nuclear translocation, and transcriptional activation. In the canonical pathway of IFN-I-mediated signaling, Tyr701 phosphorylation of STAT1 and Tyr690 of STAT2 leads to heterodimerization, interaction with [interferon regulatory factor 9] IRF9 and formation of [interferon-stimulated gene factor 3] ISGF3 [...]. After translocation to the nucleus, this complex binds the [interferon-stimulated response element] ISRE (consensus sequence AGTTTCN2TTTCN) of over 300 [interferon-stimulated genes] ISGs, such as ISG15, [2'-5'-oligoadenylate synthetase 1-3] OAS1-3, [interferon-induced protein with tetratricopeptide repeats 1-3] IFIT1-3, or MX1 and 2 that are instrumental in antiviral activity (13–15) [...]."[14]

"Most of the knowledge about the DNA responsive elements involved in IFN-I and IFN-II signaling dates from early experiments that focused on individual genes and their role in the antiviral response (83). Accordingly, the ISRE was shown to exist in proximal ISG promoters as a single element or in multiple copies, in either orientation with (minor) consensus sequence variations (AGTTTCN2TTTCN; [...]). Functional analysis of a selection of IFN-I-inducible genes (84, 85), [...] has revealed that ISRE is essential for IFN induction."[14]

Interactions

Main article: Interaction gene transcriptions

IRF1 has been shown to interact with:

IRF2 has been shown to interact with BRD7,[65] EP300[66] and PCAF.[66][60]

IRF3 has been shown to interact with IRF7.[67]

IRF4 has been shown to interact with:

IRF7 has been shown to interact with IRF3.[67] Also, IRF7 has been shown to interact with Aryl Hydrocarbon Receptor Interacting Protein (AIP), which is a negative regulator for the antiviral pathway.[72]

IRF8 has been shown to interact with IRF1[56][57] and COPS2.[73]

IRF9 has been shown to interact with STAT2[74][75] and STAT1.[74]

Consensus sequences

Main article: Consensus sequence gene transcriptions

Consensus sequence for IRF-3 is GCTTTCC.[76]

IRF-3 samplings

Main article: Model samplings

Copying a responsive elements consensus sequence GCTTTCC and putting the sequence in "⌘F" finds one between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence GCTTTCC (starting with SuccessablesIRF3.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand, negative direction, looking for GCTTTCC, 0.
  2. negative strand, positive direction, looking for GCTTTCC, 1, GCTTTCC at 1097.
  3. positive strand, negative direction, looking for GCTTTCC, 0.
  4. positive strand, positive direction, looking for GCTTTCC, 0.
  5. complement, negative strand, negative direction, looking for CGAAAGG, 0.
  6. complement, negative strand, positive direction, looking for CGAAAGG, 0.
  7. complement, positive strand, negative direction, looking for CGAAAGG, 0.
  8. complement, positive strand, positive direction, looking for CGAAAGG, 1, CGAAAGG at 1097.
  9. inverse complement, negative strand, negative direction, looking for GGAAAGC, 0.
  10. inverse complement, negative strand, positive direction, looking for GGAAAGC, 0.
  11. inverse complement, positive strand, negative direction, looking for GGAAAGC, 1, GGAAAGC at 1678.
  12. inverse complement, positive strand, positive direction, looking for GGAAAGC, 0.
  13. inverse negative strand, negative direction, looking for CCTTTCG, 1, CCTTTCG at 1678.
  14. inverse negative strand, positive direction, looking for CCTTTCG, 0.
  15. inverse positive strand, negative direction, looking for CCTTTCG, 0.
  16. inverse positive strand, positive direction, looking for CCTTTCG, 0.

IRF3 negative direction distal promoters

  1. Positive strand, negative direction: GGAAAGC at 1678

IRF3 positive direction distal promoters

  1. Negative strand, positive direction: GCTTTCC at 1097

IRF3 random dataset samplings

  1. IRF3r0: 0.
  2. IRF3r1: 1, GCTTTCC at 331.
  3. IRF3r2: 0.
  4. IRF3r3: 0.
  5. IRF3r4: 0.
  6. IRF3r5: 1, GCTTTCC at 2459.
  7. IRF3r6: 0.
  8. IRF3r7: 1, GCTTTCC at 590.
  9. IRF3r8: 0.
  10. IRF3r9: 1, GCTTTCC at 1692.
  11. IRF3r0ci: 3, GGAAAGC at 4511, GGAAAGC at 3277, GGAAAGC at 457.
  12. IRF3r1ci: 1, GGAAAGC at 3218.
  13. IRF3r2ci: 0.
  14. IRF3r3ci: 0.
  15. IRF3r4ci: 3, GGAAAGC at 4325, GGAAAGC at 4023, GGAAAGC at 2611.
  16. IRF3r5ci: 1, GGAAAGC at 4227.
  17. IRF3r6ci: 0.
  18. IRF3r7ci: 0.
  19. IRF3r8ci: 0.
  20. IRF3r9ci: 1, GGAAAGC at 2051.

IRF3r arbitrary UTRs

  1. IRF3r0ci: GGAAAGC at 4511, GGAAAGC at 3277.
  2. IRF3r4ci: 3GGAAAGC at 4325, GGAAAGC at 4023.

IRF3r alternate UTRs

  1. IRF3r1ci: GGAAAGC at 3218.
  2. IRF3r5ci: GGAAAGC at 4227.

IRF3r alternate positive direction core promoters

  1. IRF3r4ci: GGAAAGC at 4325.

IRF3r arbitrary negative direction proximal promoters

  1. IRF3r4ci: GGAAAGC at 2611.

IRF3r arbitrary positive direction proximal promoters

  1. IRF3r5ci: GGAAAGC at 4227.

IRF3r arbitrary negative direction distal promoters

  1. IRF3r0ci: GGAAAGC at 457.

IRF3r alternate negative direction distal promoters

  1. IRF3r1: GCTTTCC at 331.
  2. IRF3r5: GCTTTCC at 2459.
  3. IRF3r7: GCTTTCC at 590.
  4. IRF3r9: GCTTTCC at 1692.
  5. IRF3r9ci: GGAAAGC at 2051.

IRF3r arbitrary positive direction distal promoters

  1. IRF3r1: GCTTTCC at 331.
  2. IRF3r5: GCTTTCC at 2459.
  3. IRF3r7: GCTTTCC at 590.
  4. IRF3r9: GCTTTCC at 1692.
  5. IRF3r1ci: GGAAAGC at 3218.
  6. IRF3r9ci: GGAAAGC at 2051.

IRF3r alternate positive direction distal promoters

  1. IRF3r0ci: GGAAAGC at 3277, GGAAAGC at 457.
  2. IRF3r4ci: GGAAAGC at 4023, GGAAAGC at 2611.

IRF3 analysis and results

Main article: Complex locus A1BG and ZNF497 § IRF3s

Consensus sequence for IRF-3 is GCTTTCC.[76]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 0 2 0 0
Randoms UTR arbitrary negative 4 10 0.4 0.3
Randoms UTR alternate negative 2 10 0.2 0.3
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 0 10 0 0.05
Randoms Core alternate positive 1 10 0.1 0.05
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 1 10 0.1 0.05
Randoms Proximal alternate negative 0 10 0 0.05
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 1 10 0.1 0.05
Randoms Proximal alternate positive 0 10 0 0.05
Reals Distal negative 1 2 0.5 0.5 ± 0.5 (--0,+-1)
Randoms Distal arbitrary negative 1 10 0.1 0.3
Randoms Distal alternate negative 5 10 0.5 0.3
Reals Distal positive 1 2 0.5 0.5 ± 0.5 (-+1, ++0)
Randoms Distal arbitrary positive 6 10 0.6 0.4
Randoms Distal alternate positive 2 10 0.2 0.4

Comparison:

The occurrences of real IRF3s are greater than the randoms. This suggests that the real IRF3s are likely active or activable.

Interferon-stimulated response element samplings

Main article: Model samplings

Copying a responsive elements consensus sequence AGTTTCNNTTTCN and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence AGTTTCNNTTTCN (starting with SuccessablesISRE.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand, negative direction, looking for AGTTTCNNTTTCN, 0.
  2. positive strand, negative direction, looking for AGTTTCNNTTTCN, 0.
  3. positive strand, positive direction, looking for AGTTTCNNTTTCN, 0.
  4. negative strand, positive direction, looking for AGTTTCNNTTTCN, 0.
  5. complement, negative strand, negative direction, looking for TCAAAGNNAAAGN, 0.
  6. complement, positive strand, negative direction, looking for TCAAAGNNAAAGN, 0.
  7. complement, positive strand, positive direction, looking for TCAAAGNNAAAGN, 0.
  8. complement, negative strand, positive direction, looking for TCAAAGNNAAAGN, 0.
  9. inverse complement, negative strand, negative direction, looking for NGAAANNGAAACT, 0.
  10. inverse complement, positive strand, negative direction, looking for NGAAANNGAAACT, 0.
  11. inverse complement, positive strand, positive direction, looking for NGAAANNGAAACT, 0.
  12. inverse complement, negative strand, positive direction, looking for NGAAANNGAAACT, 0.
  13. inverse negative strand, negative direction, looking for NCTTTNNCTTTGA, 0.
  14. inverse positive strand, negative direction, looking for NCTTTNNCTTTGA, 0.
  15. inverse positive strand, positive direction, looking for NCTTTNNCTTTGA, 0.
  16. inverse negative strand, positive direction, looking for NCTTTNNCTTTGA, 0.

IFN-stimulated response element samplings

Main article: Model samplings

Copying a responsive elements consensus sequence GAAANNGAAA and putting the sequence in "⌘F" finds 15 GAAA but none with GAAANNGAAA between ZNF497 and A1BG or 17 GAAA but none with GAAANNGAAA between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence GAAANNGAAA (starting with SuccessablesIFN.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand, negative direction, looking for GAAANNGAAA, 0.
  2. positive strand, negative direction, looking for GAAANNGAAA, 0.
  3. positive strand, positive direction, looking for GAAANNGAAA, 0.
  4. negative strand, positive direction, looking for GAAANNGAAA, 1, GAAATAGAAA at 2629.
  5. complement, negative strand, negative direction, looking for CTTTNNCTTT, 0.
  6. complement, positive strand, negative direction, looking for CTTTNNCTTT, 0.
  7. complement, positive strand, positive direction, looking for CTTTNNCTTT, 1, CTTTATCTTT at 2629.
  8. complement, negative strand, positive direction, looking for CTTTNNCTTT, 0.
  9. inverse complement, negative strand, negative direction, looking for TTTCNNTTTC, 1, TTTCGTTTTC at 2477.
  10. inverse complement, positive strand, negative direction, looking for TTTCNNTTTC, 0.
  11. inverse complement, positive strand, positive direction, looking for TTTCNNTTTC, 0.
  12. inverse complement, negative strand, positive direction, looking for TTTCNNTTTC, 0.
  13. inverse negative strand, negative direction, looking for AAAGNNAAAG, 0.
  14. inverse positive strand, negative direction, looking for AAAGNNAAAG, 1, AAAGCAAAAG at 2477.
  15. inverse positive strand, positive direction, looking for AAAGNNAAAG, 0.
  16. inverse negative strand, positive direction, looking for AAAGNNAAAG, 0.

IFN negative direction distal promoters

  1. Negative strand, negative direction: TTTCGTTTTC at 2477.

IFN positive direction distal promoters

  1. Negative strand, positive direction: GAAATAGAAA at 2629.

IFN random dataset samplings

  1. IFNr0: 0.
  2. IFNr1: 0.
  3. IFNr2: 0.
  4. IFNr3: 0.
  5. IFNr4: 0.
  6. IFNr5: 0.
  7. IFNr6: 1, GAAACAGAAA at 1103.
  8. IFNr7: 1, GAAACTGAAA at 3530.
  9. IFNr8: 1, GAAAAAGAAA at 313.
  10. IFNr9: 1, GAAAAGGAAA at 591.
  11. IFNr0ci: 0.
  12. IFNr1ci: 1, TTTCACTTTC at 2203.
  13. IFNr2ci: 0.
  14. IFNr3ci: 0.
  15. IFNr4ci: 0.
  16. IFNr5ci: 0.
  17. IFNr6ci: 0.
  18. IFNr7ci: 0.
  19. IFNr8ci: 0.
  20. IFNr9ci: 0.

IFNr alternate UTRs

  1. IFNr7: GAAACTGAAA at 3530.

IFNr arbitrary negative direction distal promoters

  1. IFNr6: GAAACAGAAA at 1103.
  2. IFNr8: GAAAAAGAAA at 313.

IFNr alternate negative direction distal promoters

  1. IFNr9: GAAAAGGAAA at 591.
  2. IFNr1ci: TTTCACTTTC at 2203.

IFNr arbitrary positive direction distal promoters

  1. IFNr7: GAAACTGAAA at 3530.
  2. IFNr9: GAAAAGGAAA at 591.
  3. IFNr1ci: TTTCACTTTC at 2203.

IFNr alternate positive direction distal promoters

  1. IFNr6: GAAACAGAAA at 1103.
  2. IFNr8: GAAAAAGAAA at 313.

IFN analysis and results

Main article: Complex locus A1BG and ZNF497 § IFNs

"All the IRF members share a well-conserved N-terminal helix-turn-helix IRF superfamily domain (also called DNA-binding domain, DBD) with five conserved tryptophan (Trp) residues, which could recognize DNA sequences containing 5’-GAAA-3’ tetranucleotide, such as the IFN-stimulated response element (ISREs, GAAANNGAAA) [11, 12]."[9]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 0 2 0 0
Randoms UTR arbitrary negative 0 10 0 0.05
Randoms UTR alternate negative 1 10 0.1 0.05
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 0 10 0 0
Randoms Core alternate positive 0 10 0 0
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 0 10 0 0
Randoms Proximal alternate negative 0 10 0 0
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 0 10 0 0
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 1 2 0.5 0.5 ± 0.5 (--1,+-0)
Randoms Distal arbitrary negative 2 10 0.2 0.2
Randoms Distal alternate negative 2 10 0.2 0.2
Reals Distal positive 1 2 0.5 0.5 ± 0.5 (-+1,++0)
Randoms Distal arbitrary positive 3 10 0.3 0.25
Randoms Distal alternate positive 2 10 0.2 0.25

Comparison:

The occurrences of real IFNs are greater than the randoms. This suggests that the real IFNs are likely active or activable.

IRS consensus samplings

Copying a responsive elements consensus sequence AANNGAAA and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence AANNGAAA (starting with SuccessablesIRS.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand, negative direction, looking for AANNGAAA, 1, AATAGAAA at 1733.
  2. positive strand, negative direction, looking for AANNGAAA, 13, AAAAGAAA at 4394, AAAAGAAA at 4389, AAAAGAAA at 4382, AATAGAAA at 4081, AAAAGAAA at 2838, AAAAGAAA at 2821, AAAAGAAA at 2800, AAAAGAAA at 2055, AAGGGAAA at 1660, AAAGGAAA at 1642, AAAAGAAA at 1630, AAATGAAA at 1582, AAAAGAAA at 226.
  3. positive strand, positive direction, looking for AANNGAAA, 2, AAAAGAAA at 2278, AACGGAAA at 134.
  4. negative strand, positive direction, looking for AANNGAAA, 2, AAAGGAAA at 2831, AATAGAAA at 2629.
  5. complement, negative strand, negative direction, looking for TTNNCTTT, 13, TTTTCTTT at 4394, TTTTCTTT at 4389, TTTTCTTT at 4382, TTATCTTT at 4081, TTTTCTTT at 2838, TTTTCTTT at 2821, TTTTCTTT at 2800, TTTTCTTT at 2055, TTCCCTTT at 1660, TTTCCTTT at 1642, TTTTCTTT at 1630, TTTACTTT at 1582, TTTTCTTT at 226.
  6. complement, positive strand, negative direction, looking for TTNNCTTT, 1, TTATCTTT at 1733.
  7. complement, positive strand, positive direction, looking for TTTTTTTT, 2, TTTCCTTT at 2831, TTATCTTT at 2629.
  8. complement, negative strand, positive direction, looking for TTNNCTTT, 2, TTTTCTTT at 2278, TTGCCTTT at 134.
  9. inverse complement, negative strand, negative direction, looking for TTTCNNTT, 13, TTTCTTTT at 4395, TTTCTTTT at 4390, TTTCTTTT at 4383, TTTCTTTT at 4086, TTTCTTTT at 2839, TTTCTCTT at 2827, TTTCTTTT at 2822, TTTCTCTT at 2810, TTTCTTTT at 2805, TTTCGTTT at 2481, TTTCGTTT at 2475, TTTCTTTT at 2056, TTTCCTTT at 1642.
  10. inverse complement, positive strand, negative direction, looking for TTTCNNTT, 1, TTTCTTTT at 26.
  11. inverse complement, positive strand, positive direction, looking for TTTCNNTT, 1, TTTCCTTT at 2831.
  12. inverse complement, negative strand, positive direction, looking for TTTCNNTT, 2, TTTCTCTT at 4387, TTTCTTTT at 2279.
  13. inverse negative strand, negative direction, looking for AAAGNNAA, 1, AAAGAAAA at 26.
  14. inverse positive strand, negative direction, looking for AAAGNNAA, 13, AAAGAAAA at 4395, AAAGAAAA at 4390, AAAGAAAA at 4383, AAAGAAAA at 4086, AAAGAAAA at 2839, AAAGAGAA at 2827, AAAGAAAA at 2822, AAAGAGAA at 2810, AAAGAAAA at 2805, AAAGCAAA at 2481, AAAGCAAA at 2475, AAAGAAAA at 2056, AAAGGAAA at 1642.
  15. inverse positive strand, positive direction, looking for AAAGNNAA, 2, AAAGAGAA at 4387, AAAGAAAA at 2279.
  16. inverse negative strand, positive direction, looking for AAAGNNAA, 1, AAAGGAAA at 2831.

IRS UTRs

Main article: UTR promoter gene transcriptions

Negative strand, negative direction: TTTCTTTT at 4395, TTTCTTTT at 4390, TTTCTTTT at 4383, TTTCTTTT at 4086.

Positive strand, negative direction: AAAAGAAA at 4394, AAAAGAAA at 4389, AAAAGAAA at 4382, AATAGAAA at 4081.

IRS core promoters

Main article: Core promoter gene transcriptions

Negative strand, negative direction: TTTCTTTT at 2839, TTTCTCTT at 2827, TTTCTTTT at 2822.

Positive strand, negative direction: AAAAGAAA at 2838, AAAAGAAA at 2821.

Negative strand, positive direction: TTTCTCTT at 4387.

IRS proximal promoters

Main article: Proximal promoter gene transcriptions

Negative strand, negative direction: TTTCTCTT at 2810, TTTCTTTT at 2805.

Positive strand, negative direction: AAAAGAAA at 2800.

IRS distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: TTTCGTTT at 2481, TTTCGTTT at 2475, TTTCTTTT at 2056, AATAGAAA at 1733, TTTCCTTT at 1642.

Positive strand, negative direction: AAAAGAAA at 2055, AAGGGAAA at 1660, AAAGGAAA at 1642, AAAAGAAA at 1630, AAATGAAA at 1582, AAAAGAAA at 226, TTTCTTTT at 26.

Negative strand, positive direction: AAAGGAAA at 2831, AATAGAAA at 2629, TTTCTTTT at 2279.

Positive strand, positive direction: TTTCCTTT at 2831, AAAAGAAA at 2278, AACGGAAA at 134.

IRS random dataset samplings

  1. IRSr0: 2, AACAGAAA at 3656, AACTGAAA at 901.
  2. IRSr1: 3, AACAGAAA at 4353, AAGTGAAA at 3070, AAACGAAA at 1407.
  3. IRSr2: 3, AAAAGAAA at 1848, AATAGAAA at 1843, AACAGAAA at 945.
  4. IRSr3: 1, AAAAGAAA at 2083.
  5. IRSr4: 0.
  6. IRSr5: 3, AAGGGAAA at 4225, AAACGAAA at 4210, AAATGAAA at 2770.
  7. IRSr6: 2, AACAGAAA at 1103, AATGGAAA at 745.
  8. IRSr7: 4, AAAAGAAA at 4397, AACTGAAA at 3530, AAGGGAAA at 2954, AACGGAAA at 2008.
  9. IRSr8: 4, AATCGAAA at 3076, AAAAGAAA at 1687, AACTGAAA at 889, AAAAGAAA at 313.
  10. IRSr9: 2, AACTGAAA at 3844, AAAGGAAA at 591.
  11. IRSr0ci: 1, TTTCTATT at 4224.
  12. IRSr1ci: 5, TTTCCGTT at 3842, TTTCCATT at 2293, TTTCACTT at 2201, TTTCGGTT at 1498, TTTCGATT at 109.
  13. IRSr2ci: 2, TTTCTGTT at 1514, TTTCCCTT at 228.
  14. IRSr3ci: 3, TTTCGCTT at 4045, TTTCTTTT at 3693, TTTCATTT at 924.
  15. IRSr4ci: 1, TTTCACTT at 3947.
  16. IRSr5ci: 1, TTTCCATT at 3624.
  17. IRSr6ci: 1, TTTCCTTT at 3294.
  18. IRSr7ci: 2, TTTCGGTT at 2522, TTTCATTT at 1893.
  19. IRSr8ci: 1, TTTCATTT at 3334.
  20. IRSr9ci: 1, TTTCTTTT at 2313.

IRSr arbitrary UTRs

  1. IRSr0: AACAGAAA at 3656.
  2. IRSr0ci: TTTCTATT at 4224.
  3. IRSr8: AATCGAAA at 3076.
  4. IRSr4ci: TTTCACTT at 3947.
  5. IRSr6ci: TTTCCTTT at 3294.
  6. IRSr8ci: TTTCATTT at 3334.

IRSr alternate UTRs

  1. IRSr1: AACAGAAA at 4353, AAGTGAAA at 3070.
  2. IRSr5: AAGGGAAA at 4225, AAACGAAA at 4210.
  3. IRSr7: AAAAGAAA at 4397, AACTGAAA at 3530, AAGGGAAA at 2954.
  4. IRSr9: AACTGAAA at 3844.
  5. IRSr1ci: TTTCCGTT at 3842.
  6. IRSr3ci: TTTCGCTT at 4045, TTTCTTTT at 3693.
  7. IRSr5ci: TTTCCATT at 3624.

IRSr alternate negative direction proximal promoters

  1. IRSr5: AAATGAAA at 2770.

IRSDr arbitrary positive direction proximal promoters

  1. IRSr5: AAGGGAAA at 4225, AAACGAAA at 4210.

IRSr alternate positive direction proximal promoters

  1. IRSr0ci: TTTCTATT at 4224.

IRSr arbitrary negative direction distal promoters

  1. IRSr0: AACTGAAA at 901.
  2. IRSr2: AAAAGAAA at 1848, AATAGAAA at 1843, AACAGAAA at 945.
  3. IRSr6: AACAGAAA at 1103, AATGGAAA at 745.
  4. IRSr8: AAAAGAAA at 1687, AACTGAAA at 889, AAAAGAAA at 313.
  5. IRSr2ci: TTTCTGTT at 1514, TTTCCCTT at 228.

IRSr alternate negative direction distal promoters

  1. IRSr1: AAACGAAA at 1407.
  2. IRSr3: AAAAGAAA at 2083.
  3. IRSr7: AACGGAAA at 2008.
  4. IRSr9: AAAGGAAA at 591.
  5. IRSr1ci: TTTCCATT at 2293, TTTCACTT at 2201, TTTCGGTT at 1498, TTTCGATT at 109.
  6. IRSr3ci: TTTCATTT at 924.
  7. IRSr7ci: TTTCGGTT at 2522, TTTCATTT at 1893.
  8. IRSr9ci: TTTCTTTT at 2313.

IRSr arbitrary positive direction distal promoters

  1. IRSr1: AAGTGAAA at 3070, AAACGAAA at 1407.
  2. IRSr3: AAAAGAAA at 2083.
  3. IRSr5: AAATGAAA at 2770.
  4. IRSr7: AACTGAAA at 3530, AAGGGAAA at 2954, AACGGAAA at 2008.
  5. IRSr9: AACTGAAA at 3844, AAAGGAAA at 591.
  6. IRSr1ci: TTTCCGTT at 3842, TTTCCATT at 2293, TTTCACTT at 2201, TTTCGGTT at 1498, TTTCGATT at 109.
  7. IRSr3ci: TTTCGCTT at 4045, TTTCTTTT at 3693, TTTCATTT at 924.
  8. IRSr5ci: TTTCCATT at 3624.
  9. IRSr7ci: TTTCGGTT at 2522, TTTCATTT at 1893.
  10. IRSr9ci: TTTCTTTT at 2313.

IRSr alternate positive direction distal promoters

  1. IRSr0: AACAGAAA at 3656, AACTGAAA at 901.
  2. IRSr2: AAAAGAAA at 1848, AATAGAAA at 1843, AACAGAAA at 945.
  3. IRSr6: AACAGAAA at 1103, AATGGAAA at 745.
  4. IRSr8: AAAAGAAA at 1687, AACTGAAA at 889, AAAAGAAA at 313.
  5. IRSr2ci: TTTCTGTT at 1514, TTTCCCTT at 228.
  6. IRSr4ci: TTTCACTT at 3947.
  7. IRSr6ci: TTTCCTTT at 3294.
  8. IRSr8ci: TTTCATTT at 3334.

IRS analysis and results

Main article: Complex locus A1BG and ZNF497 § IRSs

The "IRS consensus (-78/-66, AANNGAAA), which existed in the promoter region of IFN-β, could be bound by the IRF family members [13]."[9]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 8 2 4 4 ± 0 (--4,+-4)
Randoms UTR arbitrary negative 6 10 0.6 0.9
Randoms UTR alternate negative 12 10 1.2 0.9
Reals Core negative 5 2 2.5 2.5 ± 0.5 (--3,+-2)
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 1 2 0.5 0.5 ± 0.5 (-+1,++0)
Randoms Core arbitrary positive 0 10 0 0
Randoms Core alternate positive 0 10 0 0
Reals Proximal negative 3 2 1.5 1.5 ± 0.5 (--2,+-1)
Randoms Proximal arbitrary negative 1 10 0.1 0.05
Randoms Proximal alternate negative 0 10 0 0.05
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 2 10 0.2 0.15
Randoms Proximal alternate positive 1 10 0.1 0.15
Reals Distal negative 12 2 6 6 ± 1 (--5,+-7)
Randoms Distal arbitrary negative 11 10 1.1 1.15
Randoms Distal alternate negative 12 10 1.2 1.15
Reals Distal positive 6 2 3 3 ± 0 (-+3,++3)
Randoms Distal arbitrary positive 21 10 2.1 1.8
Randoms Distal alternate positive 15 10 1.5 1.8

Comparison:

The occurrences of real IRSs are greater than the randoms. This suggests that the real IRSs are likely active or activable.

Tryptophan residue samplings

Main article: Model samplings

Copying a responsive elements consensus sequence GAAA and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence GAAA (starting with SuccessablesGAAA.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand, negative direction, looking for GAAA, 18, GAAA at 4461, GAAA at 3984, GAAA at 3075, GAAA at 3018, GAAA at 2552, GAAA at 2216, GAAA at 2099, GAAA at 1790, GAAA at 1733, GAAA at 1687, GAAA at 1418, GAAA at 1145, GAAA at 681, GAAA at 545, GAAA at 408, GAAA at 347, GAAA at 47, GAAA at 25.
  2. positive strand, negative direction, looking for AAAAAAAA, 46, GAAA at 4394, GAAA at 4389, GAAA at 4382, GAAA at 4085, GAAA at 4081, GAAA at 3922, GAAA at 3663, GAAA at 3591, GAAA at 3507, GAAA at 3376, GAAA at 3342, GAAA at 3146, GAAA at 2967, GAAA at 2957, GAAA at 2926, GAAA at 2838, GAAA at 2831, GAAA at 2821, GAAA at 2814, GAAA at 2804, GAAA at 2800, GAAA at 2746, GAAA at 2619, GAAA at 2505, GAAA at 2458, GAAA at 2282, GAAA at 2157, GAAA at 2055, GAAA at 1855, GAAA at 1676, GAAA at 1660, GAAA at 1642, GAAA at 1630, GAAA at 1625, GAAA at 1582, GAAA at 1212, GAAA at 494, GAAA at 473, GAAA at 357, GAAA at 312, GAAA at 303, GAAA at 226, GAAA at 135, GAAA at 126, GAAA at 102, GAAA at 52.
  3. positive strand, positive direction, looking for GAAA, 16, GAAA at 4382, GAAA at 4207, GAAA at 3945, GAAA at 3397, GAAA at 2585, GAAA at 2278, GAAA at 2273, GAAA at 2163, GAAA at 1981, GAAA at 1830, GAAA at 1746, GAAA at 1599, GAAA at 1179, GAAA at 1095, GAAA at 134, GAAA at 110.
  4. negative strand, positive direction, looking for GAAA, 13, GAAA at 4091, GAAA at 3926, GAAA at 3918, GAAA at 3794, GAAA at 3596, GAAA at 3165, GAAA at 2917, GAAA at 2831, GAAA at 2629, GAAA at 2623, GAAA at 2146, GAAA at 1089, GAAA at 290.
  5. complement, negative strand, negative direction, looking for CTTT, 46, CTTT at 4394, CTTT at 4389, CTTT at 4382, CTTT at 4085, CTTT at 4081, CTTT at 3922, CTTT at 3663, CTTT at 3591, CTTT at 3507, CTTT at 3376, CTTT at 3342, CTTT at 3146, CTTT at 2967, CTTT at 2957, CTTT at 2926, CTTT at 2838, CTTT at 2831, CTTT at 2821, CTTT at 2814, CTTT at 2804, CTTT at 2800, CTTT at 2746, CTTT at 2619, CTTT at 2505, CTTT at 2458, CTTT at 2282, CTTT at 2157, CTTT at 2055, CTTT at 1855, CTTT at 1676, CTTT at 1660, CTTT at 1642, CTTT at 1630, CTTT at 1625, CTTT at 1582, CTTT at 1212, CTTT at 494, CTTT at 473, CTTT at 357, CTTT at 312, CTTT at 303, CTTT at 226, CTTT at 135, CTTT at 126, CTTT at 102, CTTT at 52.
  6. complement, positive strand, negative direction, looking for CTTT, 18, CTTT at 4461, CTTT at 3984, CTTT at 3075, CTTT at 3018, CTTT at 2552, CTTT at 2216, CTTT at 2099, CTTT at 1790, CTTT at 1733, CTTT at 1687, CTTT at 1418, CTTT at 1145, CTTT at 681, CTTT at 545, CTTT at 408, CTTT at 347, CTTT at 47, CTTT at 25.
  7. complement, positive strand, positive direction, looking for CTTT, 13, CTTT at 4091, CTTT at 3926, CTTT at 3918, CTTT at 3794, CTTT at 3596, CTTT at 3165, CTTT at 2917, CTTT at 2831, CTTT at 2629, CTTT at 2623, CTTT at 2146, CTTT at 1089, CTTT at 290.
  8. complement, negative strand, positive direction, looking for CTTT, 16, CTTT at 4382, CTTT at 4207, CTTT at 3945, CTTT at 3397, CTTT at 2585, CTTT at 2278, CTTT at 2273, CTTT at 2163, CTTT at 1981, CTTT at 1830, CTTT at 1746, CTTT at 1599, CTTT at 1179, CTTT at 1095, CTTT at 134, CTTT at 110.
  9. inverse complement, negative strand, negative direction, looking for TTTC, 35, TTTC at 4504, TTTC at 4391, TTTC at 4386, TTTC at 4379, TTTC at 4082, TTTC at 3923, TTTC at 3664, TTTC at 3440, TTTC at 3377, TTTC at 3344, TTTC at 2891, TTTC at 2857, TTTC at 2835, TTTC at 2823, TTTC at 2818, TTTC at 2806, TTTC at 2801, TTTC at 2797, TTTC at 2477, TTTC at 2471, TTTC at 2174, TTTC at 2052, TTTC at 1677, TTTC at 1638, TTTC at 1627, TTTC at 1548, TTTC at 1399, TTTC at 1106, TTTC at 943, TTTC at 223, TTTC at 184, TTTC at 136, TTTC at 104, TTTC at 93, TTTC at 54.
  10. inverse complement, positive strand, negative direction, looking for TTTC, 5, TTTC at 3688, TTTC at 2884, TTTC at 1603, TTTC at 1380, TTTC at 22.
  11. inverse complement, positive strand, positive direction, looking for TTTC, 10, TTTC at 3928, TTTC at 3919, TTTC at 3597, TTTC at 3064, TTTC at 2918, TTTC at 2827, TTTC at 2708, TTTC at 2535, TTTC at 2004, TTTC at 1090.
  12. inverse complement, negative strand, positive direction, looking for TTTC, 12, TTTC at 4383, TTTC at 2645, TTTC at 2301, TTTC at 2275, TTTC at 2263, TTTC at 2164, TTTC at 1978, TTTC at 1749, TTTC at 1600, TTTC at 1180, TTTC at 1096, TTTC at 136.
  13. inverse negative strand, negative direction, looking for AAAG, 5, AAAG at 3688, AAAG at 2884, AAAG at 1603, AAAG at 1380, AAAG at 22.
  14. inverse positive strand, negative direction, looking for AAAG, 35, AAAG at 4504, AAAG at 4391, AAAG at 4386, AAAG at 4379, AAAG at 4082, AAAG at 3923, AAAG at 3664, AAAG at 3440, AAAG at 3377, AAAG at 3344, AAAG at 2891, AAAG at 2857, AAAG at 2835, AAAG at 2823, AAAG at 2818, AAAG at 2806, AAAG at 2801, AAAG at 2797, AAAG at 2477, AAAG at 2471, AAAG at 2174, AAAG at 2052, AAAG at 1677, AAAG at 1638, AAAG at 1627, AAAG at 1548, AAAG at 1399, AAAG at 1106, AAAG at 943, AAAG at 223, AAAG at 184, AAAG at 136, AAAG at 104, AAAG at 93, AAAG at 54.
  15. inverse positive strand, positive direction, looking for AAAG, 12, AAAG at 4383, AAAG at 2645, AAAG at 2301, AAAG at 2275, AAAG at 2263, AAAG at 2164, AAAG at 1978, AAAG at 1749, AAAG at 1600, AAAG at 1180, AAAG at 1096, AAAG at 136.
  16. inverse negative strand, positive direction, looking for AAAG, 10, AAAG at 3928, AAAG at 3919, AAAG at 3597, AAAG at 3064, AAAG at 2918, AAAG at 2827, AAAG at 2708, AAAG at 2535, AAAG at 2004, AAAG at 1090.

GAAA UTRs

Main article: UTR promoter gene transcriptions

Negative strand, negative direction: TTTC at 4504, GAAA at 4461, TTTC at 4391, TTTC at 4386, TTTC at 4379, TTTC at 4082, GAAA at 3984, TTTC at 3923, TTTC at 3664, TTTC at 3440, TTTC at 3377, TTTC at 3344, GAAA at 3075, GAAA at 3018, TTTC at 2891, TTTC at 2857.

Positive strand, negative direction: GAAA at 4394, GAAA at 4389, GAAA at 4382, GAAA at 4085, GAAA at 4081, GAAA at 3922, TTTC at 3688, GAAA at 3663, GAAA at 3591, GAAA at 3507, GAAA at 3376, GAAA at 3342, GAAA at 3146, GAAA at 2967, GAAA at 2957, GAAA at 2926, TTTC at 2884.

GAAA core promoters

Main article: Core promoter gene transcriptions

Negative strand, negative direction: TTTC at 2835, TTTC at 2823, TTTC at 2818.

Positive strand, negative direction: GAAA at 2838, GAAA at 2831, GAAA at 2821, GAAA at 2814.

Negative strand, positive direction: TTTC at 4383.

Positive strand, positive direction: GAAA at 4382.

GAAA proximal promoters

Main article: Proximal promoter gene transcriptions

Negative strand, negative direction: TTTC at 2806, TTTC at 2801, TTTC at 2797.

Positive strand, negative direction: GAAA at 2804, GAAA at 2800, GAAA at 2746, GAAA at 2619.

Negative strand, positive direction: GAAA at 4091.

Positive strand, positive direction: GAAA at 4207.

GAAA distal promoters

Negative direction

Negative strand, negative direction: GAAA at 2552, TTTC at 2477, TTTC at 2471, GAAA at 2216, TTTC at 2174, GAAA at 2099, TTTC at 2052, GAAA at 1790, GAAA at 1733, GAAA at 1687, TTTC at 1677, TTTC at 1638, TTTC at 1627, TTTC at 1548, GAAA at 1418, TTTC at 1399, GAAA at 1145, TTTC at 1106, TTTC at 943, GAAA at 681, GAAA at 545, GAAA at 408, GAAA at 347, TTTC at 223, TTTC at 184, TTTC at 136, TTTC at 104, TTTC at 93, TTTC at 54, GAAA at 47, GAAA at 25.

Positive strand, negative direction: GAAA at 2505, GAAA at 2458, GAAA at 2282, GAAA at 2157, GAAA at 2055, GAAA at 1855, GAAA at 1676, GAAA at 1660, GAAA at 1642, GAAA at 1630, GAAA at 1625, GAAA at 1582, GAAA at 1212, GAAA at 494, GAAA at 473, GAAA at 357, GAAA at 312, GAAA at 303, GAAA at 226, GAAA at 135, GAAA at 126, GAAA at 102, GAAA at 52.

Positive direction

Negative strand, positive direction: AAAG at 3928, GAAA at 3926, AAAG at 3919, GAAA at 3918, GAAA at 3794, AAAG at 3597, GAAA at 3596, GAAA at 3165, AAAG at 3064, AAAG at 2918, GAAA at 2917, GAAA at 2831, AAAG at 2827, AAAG at 2708, TTTC at 2645, GAAA at 2629, GAAA at 2623, AAAG at 2535, TTTC at 2301, TTTC at 2275, TTTC at 2263, TTTC at 2164, GAAA at 2146, AAAG at 2004, TTTC at 1978, TTTC at 1749, TTTC at 1600, TTTC at 1180, TTTC at 1096, AAAG at 1090, GAAA at 1089, GAAA at 290, TTTC at 136.

Positive strand, positive direction: GAAA at 3945, TTTC at 3928, TTTC at 3919, TTTC at 3597, GAAA at 3397, TTTC at 3064, TTTC at 2918, TTTC at 2827, TTTC at 2708, GAAA at 2585, TTTC at 2535, GAAA at 2278, GAAA at 2273, GAAA at 2163, TTTC at 2004, GAAA at 1981, GAAA at 1830, GAAA at 1746, GAAA at 1599, GAAA at 1179, GAAA at 1095, TTTC at 1090, GAAA at 134, GAAA at 110.

Tryptophan residue random dataset samplings

  1. GAAAr0: 28, GAAA at 4509, GAAA at 4295, GAAA at 4193, GAAA at 4138, GAAA at 4125, GAAA at 4021, GAAA at 3913, GAAA at 3656, GAAA at 3416, GAAA at 3365, GAAA at 3344, GAAA at 3275, GAAA at 2199, GAAA at 2155, GAAA at 2007, GAAA at 1931, GAAA at 1527, GAAA at 1447, GAAA at 901, GAAA at 830, GAAA at 768, GAAA at 748, GAAA at 633, GAAA at 543, GAAA at 455, GAAA at 251, GAAA at 215, GAAA at 113.
  2. GAAAr1: 22, GAAA at 4438, GAAA at 4353, GAAA at 4007, GAAA at 3969, GAAA at 3872, GAAA at 3794, GAAA at 3533, GAAA at 3268, GAAA at 3216, GAAA at 3070, GAAA at 2797, GAAA at 2713, GAAA at 2588, GAAA at 2456, GAAA at 2422, GAAA at 2243, GAAA at 1940, GAAA at 1867, GAAA at 1706, GAAA at 1421, GAAA at 1407, GAAA at 383.
  3. GAAAr2: 22, GAAA at 3795, GAAA at 3775, GAAA at 3652, GAAA at 3440, GAAA at 3120, GAAA at 3077, GAAA at 2951, GAAA at 2338, GAAA at 2228, GAAA at 2127, GAAA at 2080, GAAA at 1990, GAAA at 1848, GAAA at 1843, GAAA at 1628, GAAA at 1437, GAAA at 1331, GAAA at 1174, GAAA at 945, GAAA at 578, GAAA at 471, GAAA at 367.
  4. GAAAr3: 22, GAAA at 4420, GAAA at 4340, GAAA at 4225, GAAA at 4172, GAAA at 3966, GAAA at 3939, GAAA at 3481, GAAA at 3243, GAAA at 2934, GAAA at 2917, GAAA at 2899, GAAA at 2845, GAAA at 2461, GAAA at 2273, GAAA at 2083, GAAA at 1979, GAAA at 1833, GAAA at 1781, GAAA at 874, GAAA at 761, GAAA at 568, GAAA at 96.
  5. GAAAr4: 29, GAAA at 4482, GAAA at 4469, GAAA at 4384, GAAA at 4323, GAAA at 4021, GAAA at 3903, GAAA at 3876, GAAA at 3768, GAAA at 3626, GAAA at 3485, GAAA at 3414, GAAA at 3253, GAAA at 2873, GAAA at 2609, GAAA at 2511, GAAA at 2491, GAAA at 2336, GAAA at 2263, GAAA at 2178, GAAA at 1658, GAAA at 1611, GAAA at 1386, GAAA at 859, GAAA at 818, GAAA at 721, GAAA at 598, GAAA at 528, GAAA at 222, GAAA at 36.
  6. GAAAr5: 23, GAAA at 4523, GAAA at 4334, GAAA at 4320, GAAA at 4283, GAAA at 4225, GAAA at 4210, GAAA at 4163, GAAA at 3927, GAAA at 3917, GAAA at 3874, GAAA at 2770, GAAA at 2765, GAAA at 2281, GAAA at 2258, GAAA at 2103, GAAA at 1843, GAAA at 1398, GAAA at 1032, GAAA at 992, GAAA at 634, GAAA at 486, GAAA at 223, GAAA at 27.
  7. GAAAr6: 15, GAAA at 4248, GAAA at 4016, GAAA at 3861, GAAA at 3300, GAAA at 3187, GAAA at 1979, GAAA at 1713, GAAA at 1438, GAAA at 1236, GAAA at 1103, GAAA at 1097, GAAA at 745, GAAA at 301, GAAA at 68, GAAA at 7.
  8. GAAAr7: 25, GAAA at 4545, GAAA at 4397, GAAA at 4331, GAAA at 4201, GAAA at 3960, GAAA at 3932, GAAA at 3882, GAAA at 3827, GAAA at 3572, GAAA at 3530, GAAA at 3524, GAAA at 3484, GAAA at 3320, GAAA at 2997, GAAA at 2954, GAAA at 2855, GAAA at 2281, GAAA at 2216, GAAA at 2092, GAAA at 2062, GAAA at 2008, GAAA at 1503, GAAA at 1129, GAAA at 864, GAAA at 140.
  9. GAAAr8: 28, GAAA at 4269, GAAA at 4247, GAAA at 4108, GAAA at 3991, GAAA at 3875, GAAA at 3871, GAAA at 3424, GAAA at 3406, GAAA at 3084, GAAA at 3076, GAAA at 2977, GAAA at 2522, GAAA at 2406, GAAA at 2304, GAAA at 2163, GAAA at 2127, GAAA at 2099, GAAA at 2080, GAAA at 1955, GAAA at 1687, GAAA at 1473, GAAA at 1298, GAAA at 889, GAAA at 501, GAAA at 418, GAAA at 313, GAAA at 307, GAAA at 281.
  10. GAAAr9: 36, GAAA at 4498, GAAA at 4324, GAAA at 4315, GAAA at 4187, GAAA at 3852, GAAA at 3844, GAAA at 3464, GAAA at 3306, GAAA at 3233, GAAA at 3216, GAAA at 3203, GAAA at 3191, GAAA at 3181, GAAA at 3018, GAAA at 2908, GAAA at 2490, GAAA at 2457, GAAA at 2351, GAAA at 2183, GAAA at 2087, GAAA at 2049, GAAA at 1930, GAAA at 1864, GAAA at 1793, GAAA at 1745, GAAA at 1680, GAAA at 1376, GAAA at 1278, GAAA at 936, GAAA at 882, GAAA at 591, GAAA at 585, GAAA at 401, GAAA at 295, GAAA at 270, GAAA at 179.
  11. GAAAr0ci: 28, TTTC at 4220, TTTC at 4203, TTTC at 3709, TTTC at 3686, TTTC at 3665, TTTC at 3514, TTTC at 3031, TTTC at 2917, TTTC at 2826, TTTC at 2568, TTTC at 2344, TTTC at 2275, TTTC at 2146, TTTC at 1971, TTTC at 1921, TTTC at 1911, TTTC at 1769, TTTC at 1672, TTTC at 1570, TTTC at 1364, TTTC at 1276, TTTC at 1194, TTTC at 1167, TTTC at 1038, TTTC at 1005, TTTC at 657, TTTC at 476, TTTC at 130.
  12. GAAAr1ci: 34, TTTC at 4230, TTTC at 4035, TTTC at 3952, TTTC at 3838, TTTC at 3689, TTTC at 3647, TTTC at 3585, TTTC at 3409, TTTC at 3033, TTTC at 2812, TTTC at 2675, TTTC at 2568, TTTC at 2394, TTTC at 2289, TTTC at 2203, TTTC at 2197, TTTC at 2180, TTTC at 2163, TTTC at 2142, TTTC at 1656, TTTC at 1494, TTTC at 1292, TTTC at 1275, TTTC at 1101, TTTC at 979, TTTC at 943, TTTC at 830, TTTC at 769, TTTC at 655, TTTC at 549, TTTC at 474, TTTC at 330, TTTC at 200, TTTC at 105.
  13. GAAAr2ci: 42, TTTC at 4421, TTTC at 4203, TTTC at 4168, TTTC at 4114, TTTC at 3954, TTTC at 3812, TTTC at 3711, TTTC at 3665, TTTC at 3559, TTTC at 3493, TTTC at 3417, TTTC at 3405, TTTC at 3382, TTTC at 3342, TTTC at 3272, TTTC at 3221, TTTC at 2922, TTTC at 2826, TTTC at 2463, TTTC at 2418, TTTC at 2349, TTTC at 2287, TTTC at 2270, TTTC at 1654, TTTC at 1510, TTTC at 1408, TTTC at 1246, TTTC at 1145, TTTC at 1099, TTTC at 1057, TTTC at 1010, TTTC at 889, TTTC at 809, TTTC at 739, TTTC at 718, TTTC at 586, TTTC at 534, TTTC at 448, TTTC at 409, TTTC at 293, TTTC at 224, TTTC at 66.
  14. GAAAr3ci: 29, TTTC at 4399, TTTC at 4296, TTTC at 4094, TTTC at 4073, TTTC at 4051, TTTC at 4041, TTTC at 4005, TTTC at 3694, TTTC at 3689, TTTC at 3655, TTTC at 3589, TTTC at 3539, TTTC at 3249, TTTC at 3068, TTTC at 3001, TTTC at 2784, TTTC at 2505, TTTC at 2471, TTTC at 2359, TTTC at 2225, TTTC at 2092, TTTC at 2019, TTTC at 1542, TTTC at 1030, TTTC at 920, TTTC at 409, TTTC at 172, TTTC at 150, TTTC at 113.
  15. GAAAr4ci: 24, TTTC at 4214, TTTC at 3943, TTTC at 3869, TTTC at 3673, TTTC at 3018, TTTC at 2791, TTTC at 2732, TTTC at 2677, TTTC at 2547, TTTC at 2121, TTTC at 2075, TTTC at 1598, TTTC at 1187, TTTC at 1081, TTTC at 783, TTTC at 540, TTTC at 473, TTTC at 411, TTTC at 366, TTTC at 362, TTTC at 280, TTTC at 249, TTTC at 242, TTTC at 43.
  16. GAAAr5ci: 32, TTTC at 4469, TTTC at 4196, TTTC at 4109, TTTC at 3828, TTTC at 3695, TTTC at 3656, TTTC at 3620, TTTC at 3494, TTTC at 3460, TTTC at 3438, TTTC at 3328, TTTC at 3223, TTTC at 3191, TTTC at 2544, TTTC at 2498, TTTC at 2458, TTTC at 2356, TTTC at 1977, TTTC at 1881, TTTC at 1660, TTTC at 1609, TTTC at 1449, TTTC at 1417, TTTC at 1266, TTTC at 1175, TTTC at 1095, TTTC at 996, TTTC at 933, TTTC at 861, TTTC at 833, TTTC at 294, TTTC at 145.
  17. GAAAr6ci: 24, TTTC at 4480, TTTC at 4293, TTTC at 4266, TTTC at 4183, TTTC at 3673, TTTC at 3354, TTTC at 3295, TTTC at 3290, TTTC at 3265, TTTC at 3015, TTTC at 2965, TTTC at 2742, TTTC at 2345, TTTC at 1879, TTTC at 1472, TTTC at 1352, TTTC at 1318, TTTC at 1260, TTTC at 1119, TTTC at 1000, TTTC at 816, TTTC at 762, TTTC at 577, TTTC at 4030.
  18. GAAAr7ci: 31, TTTC at 4269, TTTC at 4234, TTTC at 3581, TTTC at 3460, TTTC at 3276, TTTC at 3258, TTTC at 3242, TTTC at 3201, TTTC at 3175, TTTC at 3094, TTTC at 2839, TTTC at 2663, TTTC at 2518, TTTC at 2491, TTTC at 2387, TTTC at 2245, TTTC at 2182, TTTC at 2119, TTTC at 1991, TTTC at 1889, TTTC at 1623, TTTC at 1344, TTTC at 1089, TTTC at 927, TTTC at 767, TTTC at 711, TTTC at 684, TTTC at 609, TTTC at 589, TTTC at 350, TTTC at 24.
  19. GAAAr8ci: 25, TTTC at 4542, TTTC at 4355, TTTC at 3776, TTTC at 3416, TTTC at 3330, TTTC at 3002, TTTC at 2544, TTTC at 2383, TTTC at 2222, TTTC at 2121, TTTC at 1889, TTTC at 1802, TTTC at 1786, TTTC at 1652, TTTC at 1551, TTTC at 1531, TTTC at 1480, TTTC at 1351, TTTC at 1314, TTTC at 1158, TTTC at 982, TTTC at 931, TTTC at 872, TTTC at 612, TTTC at 368.
  20. GAAAr9ci: 24, TTTC at 4160, TTTC at 3258, TTTC at 3028, TTTC at 2927, TTTC at 2899, TTTC at 2869, TTTC at 2783, TTTC at 2694, TTTC at 2686, TTTC at 2344, TTTC at 2314, TTTC at 2309, TTTC at 2126, TTTC at 1735, TTTC at 1691, TTTC at 1653, TTTC at 1352, TTTC at 1327, TTTC at 1238, TTTC at 1125, TTTC at 719, TTTC at 350, TTTC at 135, TTTC at 97.

GAAAr arbitrary UTRs

  1. GAAAr0: GAAA at 4509, GAAA at 4295, GAAA at 4193, GAAA at 4138, GAAA at 4125, GAAA at 4021, GAAA at 3913, GAAA at 3656, GAAA at 3416, GAAA at 3365, GAAA at 3344, GAAA at 3275.
  2. GAAAr2: GAAA at 3795, GAAA at 3775, GAAA at 3652, GAAA at 3440, GAAA at 3120, GAAA at 3077, GAAA at 2951.
  3. GAAAr4: GAAA at 4482, GAAA at 4469, GAAA at 4384, GAAA at 4323, GAAA at 4021, GAAA at 3903, GAAA at 3876, GAAA at 3768, GAAA at 3626, GAAA at 3485, GAAA at 3414, GAAA at 3253, GAAA at 2873.
  4. GAAAr6: GAAA at 4248, GAAA at 4016, GAAA at 3861, GAAA at 3300, GAAA at 3187.
  5. GAAAr8: GAAA at 4269, GAAA at 4247, GAAA at 4108, GAAA at 3991, GAAA at 3875, GAAA at 3871, GAAA at 3424, GAAA at 3406, GAAA at 3084, GAAA at 3076, GAAA at 2977.
  6. GAAAr0ci: TTTC at 4220, TTTC at 4203, TTTC at 3709, TTTC at 3686, TTTC at 3665, TTTC at 3514, TTTC at 3031, TTTC at 2917.
  7. GAAAr2ci: TTTC at 4421, TTTC at 4203, TTTC at 4168, TTTC at 4114, TTTC at 3954, TTTC at 3812, TTTC at 3711, TTTC at 3665, TTTC at 3559, TTTC at 3493, TTTC at 3417, TTTC at 3405, TTTC at 3382, TTTC at 3342, TTTC at 3272, TTTC at 3221, TTTC at 2922.
  8. GAAAr4ci: TTTC at 4214, TTTC at 3943, TTTC at 3869, TTTC at 3673, TTTC at 3018.
  9. GAAAr6ci: TTTC at 4480, TTTC at 4293, TTTC at 4266, TTTC at 4183, TTTC at 3673, TTTC at 3354, TTTC at 3295, TTTC at 3290, TTTC at 3265, TTTC at 3015, TTTC at 2965.
  10. GAAAr8ci: TTTC at 4542, TTTC at 4355, TTTC at 3776, TTTC at 3416, TTTC at 3330, TTTC at 3002.

GAAAr alternate UTRs

  1. GAAAr1: GAAA at 4438, GAAA at 4353, GAAA at 4007, GAAA at 3969, GAAA at 3872, GAAA at 3794, GAAA at 3533, GAAA at 3268, GAAA at 3216, GAAA at 3070.
  2. GAAAr3: GAAA at 4420, GAAA at 4340, GAAA at 4225, GAAA at 4172, GAAA at 3966, GAAA at 3939, GAAA at 3481, GAAA at 3243, GAAA at 2934, GAAA at 2917, GAAA at 2899.
  3. GAAAr5: GAAA at 4523, GAAA at 4334, GAAA at 4320, GAAA at 4283, GAAA at 4225, GAAA at 4210, GAAA at 4163, GAAA at 3927, GAAA at 3917, GAAA at 3874.
  4. GAAAr7: GAAA at 4545, GAAA at 4397, GAAA at 4331, GAAA at 4201, GAAA at 3960, GAAA at 3932, GAAA at 3882, GAAA at 3827, GAAA at 3572, GAAA at 3530, GAAA at 3524, GAAA at 3484, GAAA at 3320, GAAA at 2997, GAAA at 2954, GAAA at 2855.
  5. GAAAr9: GAAA at 4498, GAAA at 4324, GAAA at 4315, GAAA at 4187, GAAA at 3852, GAAA at 3844, GAAA at 3464, GAAA at 3306, GAAA at 3233, GAAA at 3216, GAAA at 3203, GAAA at 3191, GAAA at 3181, GAAA at 3018, GAAA at 2908.
  6. GAAAr1ci: TTTC at 4230, TTTC at 4035, TTTC at 3952, TTTC at 3838, TTTC at 3689, TTTC at 3647, TTTC at 3585, TTTC at 3409, TTTC at 3033.
  7. GAAAr3ci: TTTC at 4399, TTTC at 4296, TTTC at 4094, TTTC at 4073, TTTC at 4051, TTTC at 4041, TTTC at 4005, TTTC at 3694, TTTC at 3689, TTTC at 3655, TTTC at 3589, TTTC at 3539, TTTC at 3249, TTTC at 3068, TTTC at 3001.
  8. GAAAr5ci: TTTC at 4469, TTTC at 4196, TTTC at 4109, TTTC at 3828, TTTC at 3695, TTTC at 3656, TTTC at 3620, TTTC at 3494, TTTC at 3460, TTTC at 3438, TTTC at 3328, TTTC at 3223, TTTC at 3191.
  9. GAAAr7ci: TTTC at 4269, TTTC at 4234, TTTC at 3581, TTTC at 3460, TTTC at 3276, TTTC at 3258, TTTC at 3242, TTTC at 3201, TTTC at 3175, TTTC at 3094.
  10. GAAAr9ci: TTTC at 4160, TTTC at 3258, TTTC at 3028, TTTC at 2927, TTTC at 2899, TTTC at 2869.

GAAAr arbitrary negative direction core promoters

  1. GAAAr0ci: TTTC at 2826.
  2. GAAAr2ci: TTTC at 2826.

GAAAr alternate negative direction core promoters

  1. GAAAr3: GAAA at 2845.
  2. GAAAr1ci: TTTC at 2812.
  3. GAAAr7ci: TTTC at 2839.

GAAAr arbitrary positive direction core promoters

  1. GAAAr1: GAAA at 4438, GAAA at 4353.
  2. GAAAr5: GAAA at 4334, GAAA at 4320, GAAA at 4283.
  3. GAAAr7: GAAA at 4397, GAAA at 4331.
  4. GAAAr9: GAAA at 4324, GAAA at 4315.
  5. GAAAr3ci: TTTC at 4399, TTTC at 4296.
  6. GAAAr7ci: TTTC at 4269.

GAAAr alternate positive direction core promoters

  1. GAAAr0: GAAA at 4295.
  2. GAAAr4: GAAA at 4384, GAAA at 4323.
  3. GAAAr8: GAAA at 4269.
  4. GAAAr2ci: TTTC at 4421.
  5. GAAAr6ci: TTTC at 4293, TTTC at 4266.
  6. GAAAr8ci: TTTC at 4355.

GAAAr arbitrary negative direction proximal promoters

  1. GAAAr4: GAAA at 2609.
  2. GAAAr4ci: TTTC at 2791, TTTC at 2732, TTTC at 2677.
  3. GAAAr6ci: TTTC at 2742.

GAAAr alternate negative direction proximal promoters

  1. GAAAr1: GAAA at 2797, GAAA at 2713.
  2. GAAAr5: GAAA at 2770, GAAA at 2765.
  3. GAAAr1ci: TTTC at 2675.
  4. GAAAr3ci: TTTC at 2784.
  5. GAAAr7ci: TTTC at 2663.
  6. GAAAr9ci: TTTC at 2783, TTTC at 2694, TTTC at 2686.

GAAAr arbitrary positive direction proximal promoters

  1. GAAAr3: GAAA at 4225, GAAA at 4172.
  2. GAAAr5: GAAA at 4225, GAAA at 4210, GAAA at 4163.
  3. GAAAr7: GAAA at 4201.
  4. GAAAr9: GAAA at 4187.
  5. GAAAr1ci: TTTC at 4230.
  6. GAAAr3ci: TTTC at 4094, TTTC at 4073, TTTC at 4051.
  7. GAAAr5ci: TTTC at 4196, TTTC at 4109.
  8. GAAAr7ci: TTTC at 4234.
  9. GAAAr9ci: TTTC at 4160.

GAAAr alternate positive direction proximal promoters

  1. GAAAr0: GAAA at 4193, GAAA at 4138, GAAA at 4125.
  2. GAAAr8: GAAA at 4247, GAAA at 4108.
  3. GAAAr2ci: TTTC at 4203, TTTC at 4168, TTTC at 4114.
  4. GAAAr4ci: TTTC at 4214.
  5. GAAAr6ci: TTTC at 4183.

GAAAr arbitrary negative direction distal promoters

  1. GAAAr0: GAAA at 2199, GAAA at 2155, GAAA at 2007, GAAA at 1931, GAAA at 1527, GAAA at 1447, GAAA at 901, GAAA at 830, GAAA at 768, GAAA at 748, GAAA at 633, GAAA at 543, GAAA at 455, GAAA at 251, GAAA at 215, GAAA at 113.
  2. GAAAr4: GAAA at 2511, GAAA at 2491, GAAA at 2336, GAAA at 2263, GAAA at 2178, GAAA at 1658, GAAA at 1611, GAAA at 1386, GAAA at 859, GAAA at 818, GAAA at 721, GAAA at 598, GAAA at 528, GAAA at 222, GAAA at 36.
  3. GAAAr6: GAAA at 1979, GAAA at 1713, GAAA at 1438, GAAA at 1236, GAAA at 1103, GAAA at 1097, GAAA at 745, GAAA at 301, GAAA at 68, GAAA at 7.
  4. GAAAr8: GAAA at 2522, GAAA at 2406, GAAA at 2304, GAAA at 2163, GAAA at 2127, GAAA at 2099, GAAA at 2080, GAAA at 1955, GAAA at 1687, GAAA at 1473, GAAA at 1298, GAAA at 889, GAAA at 501, GAAA at 418, GAAA at 313, GAAA at 307, GAAA at 281.
  5. GAAAr0ci: TTTC at 2568, TTTC at 2344, TTTC at 2275, TTTC at 2146, TTTC at 1971, TTTC at 1921, TTTC at 1911, TTTC at 1769, TTTC at 1672, TTTC at 1570, TTTC at 1364, TTTC at 1276, TTTC at 1194, TTTC at 1167, TTTC at 1038, TTTC at 1005, TTTC at 657, TTTC at 476, TTTC at 130.
  6. GAAAr2ci: TTTC at 2463, TTTC at 2418, TTTC at 2349, TTTC at 2287, TTTC at 2270, TTTC at 1654, TTTC at 1510, TTTC at 1408, TTTC at 1246, TTTC at 1145, TTTC at 1099, TTTC at 1057, TTTC at 1010, TTTC at 889, TTTC at 809, TTTC at 739, TTTC at 718, TTTC at 586, TTTC at 534, TTTC at 448, TTTC at 409, TTTC at 293, TTTC at 224, TTTC at 66.
  7. GAAAr4ci: TTTC at 2547, TTTC at 2121, TTTC at 2075, TTTC at 1598, TTTC at 1187, TTTC at 1081, TTTC at 783, TTTC at 540, TTTC at 473, TTTC at 411, TTTC at 366, TTTC at 362, TTTC at 280, TTTC at 249, TTTC at 242, TTTC at 43.
  8. GAAAr6ci: TTTC at 2345, TTTC at 1879, TTTC at 1472, TTTC at 1352, TTTC at 1318, TTTC at 1260, TTTC at 1119, TTTC at 1000, TTTC at 816, TTTC at 762, TTTC at 577, TTTC at 403.
  9. GAAAr8ci: TTTC at 2544, TTTC at 2383, TTTC at 2222, TTTC at 2121, TTTC at 1889, TTTC at 1802, TTTC at 1786, TTTC at 1652, TTTC at 1551, TTTC at 1531, TTTC at 1480, TTTC at 1351, TTTC at 1314, TTTC at 1158, TTTC at 982, TTTC at 931, TTTC at 872, TTTC at 612, TTTC at 368.

GAAAr alternate negative direction distal promoters

  1. GAAAr1: GAAA at 2588, GAAA at 2456, GAAA at 2422, GAAA at 2243, GAAA at 1940, GAAA at 1867, GAAA at 1706, GAAA at 1421, GAAA at 1407, GAAA at 383.
  2. GAAAr3: GAAA at 2461, GAAA at 2273, GAAA at 2083, GAAA at 1979, GAAA at 1833, GAAA at 1781, GAAA at 874, GAAA at 761, GAAA at 568, GAAA at 96.
  3. GAAAr5: GAAA at 2281, GAAA at 2258, GAAA at 2103, GAAA at 1843, GAAA at 1398, GAAA at 1032, GAAA at 992, GAAA at 634, GAAA at 486, GAAA at 223, GAAA at 27.
  4. GAAAr7: GAAA at 2281, GAAA at 2216, GAAA at 2092, GAAA at 2062, GAAA at 2008, GAAA at 1503, GAAA at 1129, GAAA at 864, GAAA at 140.
  5. GAAAr9: GAAA at 2490, GAAA at 2457, GAAA at 2351, GAAA at 2183, GAAA at 2087, GAAA at 2049, GAAA at 1930, GAAA at 1864, GAAA at 1793, GAAA at 1745, GAAA at 1680, GAAA at 1376, GAAA at 1278, GAAA at 936, GAAA at 882, GAAA at 591, GAAA at 585, GAAA at 401, GAAA at 295, GAAA at 270, GAAA at 179.
  6. GAAAr1ci: TTTC at 2568, TTTC at 2394, TTTC at 2289, TTTC at 2203, TTTC at 2197, TTTC at 2180, TTTC at 2163, TTTC at 2142, TTTC at 1656, TTTC at 1494, TTTC at 1292, TTTC at 1275, TTTC at 1101, TTTC at 979, TTTC at 943, TTTC at 830, TTTC at 769, TTTC at 655, TTTC at 549, TTTC at 474, TTTC at 330, TTTC at 200, TTTC at 105.
  7. GAAAr3ci: TTTC at 2505, TTTC at 2471, TTTC at 2359, TTTC at 2225, TTTC at 2092, TTTC at 2019, TTTC at 1542, TTTC at 1030, TTTC at 920, TTTC at 409, TTTC at 172, TTTC at 150, TTTC at 113.
  8. GAAAr5ci: TTTC at 2544, TTTC at 2498, TTTC at 2458, TTTC at 2356, TTTC at 1977, TTTC at 1881, TTTC at 1660, TTTC at 1609, TTTC at 1449, TTTC at 1417, TTTC at 1266, TTTC at 1175, TTTC at 1095, TTTC at 996, TTTC at 933, TTTC at 861, TTTC at 833, TTTC at 294, TTTC at 145.
  9. GAAAr7ci: TTTC at 2518, TTTC at 2491, TTTC at 2387, TTTC at 2245, TTTC at 2182, TTTC at 2119, TTTC at 1991, TTTC at 1889, TTTC at 1623, TTTC at 1344, TTTC at 1089, TTTC at 927, TTTC at 767, TTTC at 711, TTTC at 684, TTTC at 609, TTTC at 589, TTTC at 350, TTTC at 24.
  10. GAAAr9ci: TTTC at 2344, TTTC at 2314, TTTC at 2309, TTTC at 2126, TTTC at 1735, TTTC at 1691, TTTC at 1653, TTTC at 1352, TTTC at 1327, TTTC at 1238, TTTC at 1125, TTTC at 719, TTTC at 350, TTTC at 135, TTTC at 97.

GAAAr arbitrary positive direction distal promoters

  1. GAAAr1: GAAA at 4007, GAAA at 3969, GAAA at 3872, GAAA at 3794, GAAA at 3533, GAAA at 3268, GAAA at 3216, GAAA at 3070, GAAA at 2797, GAAA at 2713, GAAA at 2588, GAAA at 2456, GAAA at 2422, GAAA at 2243, GAAA at 1940, GAAA at 1867, GAAA at 1706, GAAA at 1421, GAAA at 1407, GAAA at 383.
  2. GAAAr3: GAAA at 3966, GAAA at 3939, GAAA at 3481, GAAA at 3243, GAAA at 2934, GAAA at 2917, GAAA at 2899, GAAA at 2845, GAAA at 2461, GAAA at 2273, GAAA at 2083, GAAA at 1979, GAAA at 1833, GAAA at 1781, GAAA at 874, GAAA at 761, GAAA at 568, GAAA at 96.
  3. GAAAr5: GAAA at 3927, GAAA at 3917, GAAA at 3874, GAAA at 2770, GAAA at 2765, GAAA at 2281, GAAA at 2258, GAAA at 2103, GAAA at 1843, GAAA at 1398, GAAA at 1032, GAAA at 992, GAAA at 634, GAAA at 486, GAAA at 223, GAAA at 27.
  4. GAAAr7: GAAA at 3960, GAAA at 3932, GAAA at 3882, GAAA at 3827, GAAA at 3572, GAAA at 3530, GAAA at 3524, GAAA at 3484, GAAA at 3320, GAAA at 2997, GAAA at 2954, GAAA at 2855, GAAA at 2281, GAAA at 2216, GAAA at 2092, GAAA at 2062, GAAA at 2008, GAAA at 1503, GAAA at 1129, GAAA at 864, GAAA at 140.
  5. GAAAr9: GAAA at 3852, GAAA at 3844, GAAA at 3464, GAAA at 3306, GAAA at 3233, GAAA at 3216, GAAA at 3203, GAAA at 3191, GAAA at 3181, GAAA at 3018, GAAA at 2908, GAAA at 2490, GAAA at 2457, GAAA at 2351, GAAA at 2183, GAAA at 2087, GAAA at 2049, GAAA at 1930, GAAA at 1864, GAAA at 1793, GAAA at 1745, GAAA at 1680, GAAA at 1376, GAAA at 1278, GAAA at 936, GAAA at 882, GAAA at 591, GAAA at 585, GAAA at 401, GAAA at 295, GAAA at 270, GAAA at 179.
  6. GAAAr1ci: TTTC at 4035, TTTC at 3952, TTTC at 3838, TTTC at 3689, TTTC at 3647, TTTC at 3585, TTTC at 3409, TTTC at 3033, TTTC at 2812, TTTC at 2675, TTTC at 2568, TTTC at 2394, TTTC at 2289, TTTC at 2203, TTTC at 2197, TTTC at 2180, TTTC at 2163, TTTC at 2142, TTTC at 1656, TTTC at 1494, TTTC at 1292, TTTC at 1275, TTTC at 1101, TTTC at 979, TTTC at 943, TTTC at 830, TTTC at 769, TTTC at 655, TTTC at 549, TTTC at 474, TTTC at 330, TTTC at 200, TTTC at 105.
  7. GAAAr3ci: TTTC at 4041, TTTC at 4005, TTTC at 3694, TTTC at 3689, TTTC at 3655, TTTC at 3589, TTTC at 3539, TTTC at 3249, TTTC at 3068, TTTC at 3001, TTTC at 2784, TTTC at 2505, TTTC at 2471, TTTC at 2359, TTTC at 2225, TTTC at 2092, TTTC at 2019, TTTC at 1542, TTTC at 1030, TTTC at 920, TTTC at 409, TTTC at 172, TTTC at 150, TTTC at 113.
  8. GAAAr5ci: TTTC at 3828, TTTC at 3695, TTTC at 3656, TTTC at 3620, TTTC at 3494, TTTC at 3460, TTTC at 3438, TTTC at 3328, TTTC at 3223, TTTC at 3191, TTTC at 2544, TTTC at 2498, TTTC at 2458, TTTC at 2356, TTTC at 1977, TTTC at 1881, TTTC at 1660, TTTC at 1609, TTTC at 1449, TTTC at 1417, TTTC at 1266, TTTC at 1175, TTTC at 1095, TTTC at 996, TTTC at 933, TTTC at 861, TTTC at 833, TTTC at 294, TTTC at 145.
  9. GAAAr7ci: TTTC at 3581, TTTC at 3460, TTTC at 3276, TTTC at 3258, TTTC at 3242, TTTC at 3201, TTTC at 3175, TTTC at 3094, TTTC at 2839, TTTC at 2663, TTTC at 2518, TTTC at 2491, TTTC at 2387, TTTC at 2245, TTTC at 2182, TTTC at 2119, TTTC at 1991, TTTC at 1889, TTTC at 1623, TTTC at 1344, TTTC at 1089, TTTC at 927, TTTC at 767, TTTC at 711, TTTC at 684, TTTC at 609, TTTC at 589, TTTC at 350, TTTC at 24.
  10. GAAAr9ci: TTTC at 3258, TTTC at 3028, TTTC at 2927, TTTC at 2899, TTTC at 2869, TTTC at 2783, TTTC at 2694, TTTC at 2686, TTTC at 2344, TTTC at 2314, TTTC at 2309, TTTC at 2126, TTTC at 1735, TTTC at 1691, TTTC at 1653, TTTC at 1352, TTTC at 1327, TTTC at 1238, TTTC at 1125, TTTC at 719, TTTC at 350, TTTC at 135, TTTC at 97.

GAAAr alternate positive direction distal promoters

  1. GAAAr0: GAAA at 4021, GAAA at 3913, GAAA at 3656, GAAA at 3416, GAAA at 3365, GAAA at 3344, GAAA at 3275, GAAA at 2199, GAAA at 2155, GAAA at 2007, GAAA at 1931, GAAA at 1527, GAAA at 1447, GAAA at 901, GAAA at 830, GAAA at 768, GAAA at 748, GAAA at 633, GAAA at 543, GAAA at 455, GAAA at 251, GAAA at 215, GAAA at 113.
  2. GAAAr4: GAAA at 4021, GAAA at 3903, GAAA at 3876, GAAA at 3768, GAAA at 3626, GAAA at 3485, GAAA at 3414, GAAA at 3253, GAAA at 2873, GAAA at 2609, GAAA at 2511, GAAA at 2491, GAAA at 2336, GAAA at 2263, GAAA at 2178, GAAA at 1658, GAAA at 1611, GAAA at 1386, GAAA at 859, GAAA at 818, GAAA at 721, GAAA at 598, GAAA at 528, GAAA at 222, GAAA at 36.
  3. GAAAr6: GAAA at 4016, GAAA at 3861, GAAA at 3300, GAAA at 3187, GAAA at 1979, GAAA at 1713, GAAA at 1438, GAAA at 1236, GAAA at 1103, GAAA at 1097, GAAA at 745, GAAA at 301, GAAA at 68, GAAA at 7.
  4. GAAAr8: GAAA at 3991, GAAA at 3875, GAAA at 3871, GAAA at 3424, GAAA at 3406, GAAA at 3084, GAAA at 3076, GAAA at 2977, GAAA at 2522, GAAA at 2406, GAAA at 2304, GAAA at 2163, GAAA at 2127, GAAA at 2099, GAAA at 2080, GAAA at 1955, GAAA at 1687, GAAA at 1473, GAAA at 1298, GAAA at 889, GAAA at 501, GAAA at 418, GAAA at 313, GAAA at 307, GAAA at 281.
  5. GAAAr0ci: TTTC at 3709, TTTC at 3686, TTTC at 3665, TTTC at 3514, TTTC at 3031, TTTC at 2917, TTTC at 2826, TTTC at 2568, TTTC at 2344, TTTC at 2275, TTTC at 2146, TTTC at 1971, TTTC at 1921, TTTC at 1911, TTTC at 1769, TTTC at 1672, TTTC at 1570, TTTC at 1364, TTTC at 1276, TTTC at 1194, TTTC at 1167, TTTC at 1038, TTTC at 1005, TTTC at 657, TTTC at 476, TTTC at 130.
  6. GAAAr2ci: TTTC at 3954, TTTC at 3812, TTTC at 3711, TTTC at 3665, TTTC at 3559, TTTC at 3493, TTTC at 3417, TTTC at 3405, TTTC at 3382, TTTC at 3342, TTTC at 3272, TTTC at 3221, TTTC at 2922, TTTC at 2826, TTTC at 2463, TTTC at 2418, TTTC at 2349, TTTC at 2287, TTTC at 2270, TTTC at 1654, TTTC at 1510, TTTC at 1408, TTTC at 1246, TTTC at 1145, TTTC at 1099, TTTC at 1057, TTTC at 1010, TTTC at 889, TTTC at 809, TTTC at 739, TTTC at 718, TTTC at 586, TTTC at 534, TTTC at 448, TTTC at 409, TTTC at 293, TTTC at 224, TTTC at 66.
  7. GAAAr4ci: TTTC at 3943, TTTC at 3869, TTTC at 3673, TTTC at 3018, TTTC at 2791, TTTC at 2732, TTTC at 2677, TTTC at 2547, TTTC at 2121, TTTC at 2075, TTTC at 1598, TTTC at 1187, TTTC at 1081, TTTC at 783, TTTC at 540, TTTC at 473, TTTC at 411, TTTC at 366, TTTC at 362, TTTC at 280, TTTC at 249, TTTC at 242, TTTC at 43.
  8. GAAAr6ci: TTTC at 3673, TTTC at 3354, TTTC at 3295, TTTC at 3290, TTTC at 3265, TTTC at 3015, TTTC at 2965, TTTC at 2742, TTTC at 2345, TTTC at 1879, TTTC at 1472, TTTC at 1352, TTTC at 1318, TTTC at 1260, TTTC at 1119, TTTC at 1000, TTTC at 816, TTTC at 762, TTTC at 577, TTTC at 403.
  9. GAAAr8ci: TTTC at 2544, TTTC at 2383, TTTC at 2222, TTTC at 2121, TTTC at 1889, TTTC at 1802, TTTC at 1786, TTTC at 1652, TTTC at 1551, TTTC at 1531, TTTC at 1480, TTTC at 1351, TTTC at 1314, TTTC at 1158, TTTC at 982, TTTC at 931, TTTC at 872, TTTC at 612, TTTC at 368.

Tryptophan residue analysis and results

Main article: Complex locus A1BG and ZNF497 § Tryptophan residues

Conserved tryptophan (Trp) residues can recognize DNA sequences containing GAAA tetranucleotide.[9]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 33 2 16.5 16.5 ± 0.5 (--16,+-17)
Randoms UTR arbitrary negative 95 10 9.5 10.5 ± 1
Randoms UTR alternate negative 115 10 11.5 10.5 ± 1
Reals Core negative 7 2 3.5 3.5 ± 0.5 (--3,+-4)
Randoms Core arbitrary negative 2 10 0.2 0.25
Randoms Core alternate negative 3 10 0.3 0.25
Reals Core positive 2 2 1 1 ± 0 (-+1,++1)
Randoms Core arbitrary positive 12 10 1.2 1.0 ± 0.2
Randoms Core alternate positive 8 10 0.8 1.0 ± 0.2
Reals Proximal negative 7 2 3.5 3.5 ± 0.5 (--3,+-4)
Randoms Proximal arbitrary negative 5 10 0.5 0.75
Randoms Proximal alternate negative 10 10 1 0.75
Reals Proximal positive 2 2 1 1 ± 0 (-+1,++1)
Randoms Proximal arbitrary positive 15 10 1.5 1.25
Randoms Proximal alternate positive 10 10 1 1.25
Reals Distal negative 54 2 27 27 ± 4 (--31,+-23)
Randoms Distal arbitrary negative 148 10 14.8 14.9
Randoms Distal alternate negative 150 10 15.0 14.9
Reals Distal positive 57 2 28.5 28.5 ± 4.5 (-+33,++24)
Randoms Distal arbitrary positive 245 10 24.5 22.9
Randoms Distal alternate positive 213 10 21.3 22.9

Comparison:

The occurrences of real tryptophan residues are greater than the randoms, except for the positive cores and proximals. This suggests that the real tryptophan residues are likely active or activable.

Acknowledgements

The content on this page was first contributed by: Henry A. Hoff.

Initial content for this page in some instances came from Wikipedia.

See also

References

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