Y box gene transcriptions: Difference between revisions
m (→Human genes) |
mNo edit summary |
||
| Line 39: | Line 39: | ||
# XR_001748906.2 RNA Sequence, transcript variant X3, misc RNA. | # XR_001748906.2 RNA Sequence, transcript variant X3, misc RNA. | ||
Gene ID: 51087 is YBX2 Y-box binding protein 2. "This gene encodes a nucleic acid binding protein which is highly expressed in germ cells. The encoded protein binds to a Y-box element in the promoters of certain genes but also binds to mRNA transcribed from these genes. Pseudogenes for this gene are located on chromosome 10 and 15."<ref name=RefSeq51087>{{ cite | Gene ID: 51087 is YBX2 Y-box binding protein 2. "This gene encodes a nucleic acid binding protein which is highly expressed in germ cells. The encoded protein binds to a Y-box element in the promoters of certain genes but also binds to mRNA transcribed from these genes. Pseudogenes for this gene are located on chromosome 10 and 15."<ref name=RefSeq51087>{{ cite web | ||
|author=RefSeq | |author=RefSeq | ||
|title=YBX2 Y-box binding protein 2 [ Homo sapiens (human) ] | |title=YBX2 Y-box binding protein 2 [ Homo sapiens (human) ] | ||
| Line 47: | Line 47: | ||
|url=https://www.ncbi.nlm.nih.gov/gene/51087 | |url=https://www.ncbi.nlm.nih.gov/gene/51087 | ||
|accessdate=19 November 2018 }}</ref> | |accessdate=19 November 2018 }}</ref> | ||
# NP_057066.2 Y-box-binding protein 2. | # NP_057066.2 Y-box-binding protein 2. | ||
# XP_016880202.1 Y-box-binding protein 2 isoform X1. | # XP_016880202.1 Y-box-binding protein 2 isoform X1. | ||
| Line 56: | Line 55: | ||
==Sampling of A1BG promoters== | ==Sampling of A1BG promoters== | ||
{{main|Model samplings}} | |||
For the Basic programs (starting with SuccessablesYbox.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: | For the Basic programs (starting with SuccessablesYbox.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: | ||
# negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesYbox--.bas, looking for 3'-(A/G)CTAACC(A/G)(A/G)(C/T)-5', 0, | # negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesYbox--.bas, looking for 3'-(A/G)CTAACC(A/G)(A/G)(C/T)-5', 0, | ||
| Line 74: | Line 73: | ||
# inverse, positive strand, negative direction, is SuccessablesYboxi+-.bas, looking for 3'-(C/T)(A/G)(A/G)CCAATC(A/G)-5', 0, | # inverse, positive strand, negative direction, is SuccessablesYboxi+-.bas, looking for 3'-(C/T)(A/G)(A/G)CCAATC(A/G)-5', 0, | ||
# inverse, positive strand, positive direction, is SuccessablesYboxi++.bas, looking for 3'-(C/T)(A/G)(A/G)CCAATC(A/G)-5', 0. | # inverse, positive strand, positive direction, is SuccessablesYboxi++.bas, looking for 3'-(C/T)(A/G)(A/G)CCAATC(A/G)-5', 0. | ||
==Acknowledgements== | |||
The content on this page was first contributed by: Henry A. Hoff. | |||
==See also== | ==See also== | ||
{{div col|colwidth=20em}} | {{div col|colwidth=20em}} | ||
* [[A1BG gene transcription core promoters]] | |||
* [[A1BG gene transcriptions]] | |||
* [[A1BG regulatory elements and regions]] | |||
* [[A1BG response element negative results]] | |||
* [[A1BG response element positive results]] | |||
* [[Box gene transcriptions]] | * [[Box gene transcriptions]] | ||
* [[Complex locus A1BG and ZNF497]] | |||
* [[W box gene transcriptions]] | * [[W box gene transcriptions]] | ||
* [[X box gene transcriptions]] | * [[X box gene transcriptions]] | ||
| Line 87: | Line 96: | ||
==External links== | ==External links== | ||
* [http://www.genome.jp/ GenomeNet KEGG database] | |||
* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene Home - Gene - NCBI] | |||
* [http://www.ncbi.nlm.nih.gov/sites/gquery NCBI All Databases Search] | |||
* [http://www.ncbi.nlm.nih.gov/ncbisearch/ NCBI Site Search] | |||
* [http://www.ncbi.nlm.nih.gov/pccompound PubChem Public Chemical Database] | |||
<!-- footer templates --> | <!-- footer templates --> | ||
{{Gene project | {{Gene project}} | ||
<!-- footer categories --> | <!-- footer categories --> | ||
[[Category:Resources last modified in January 2021]] | |||
[[Category:Resources last modified in | |||
Latest revision as of 21:24, 9 January 2021
Editor-In-Chief: Henry A. Hoff
The "Y-box [is] an inverted CCAAT box, in the promoter region of many genes; this domain is highly conserved in evolution [1, 3, 4]."[1]
Human genes
Gene ID: 4904 is YBX1 Y-box binding protein 1 aka CCAAT-binding transcription factor I subunit A, DNA-binding protein B, Y-box transcription factor, enhancer factor I subunit A, major histocompatibility complex, class II, Y box-binding protein I, nuclease-sensitive element-binding protein 1: "This gene encodes a highly conserved cold shock domain protein that has broad nucleic acid binding properties. The encoded protein functions as both a DNA and RNA binding protein and has been implicated in numerous cellular processes including regulation of transcription and translation, pre-mRNA splicing, DNA reparation and mRNA packaging. This protein is also a component of messenger ribonucleoprotein (mRNP) complexes and may have a role in microRNA processing. This protein can be secreted through non-classical pathways and functions as an extracellular mitogen. Aberrant expression of the gene is associated with cancer proliferation in numerous tissues. This gene may be a prognostic marker for poor outcome and drug resistance in certain cancers. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene are found on multiple chromosomes."[2]
- NP_004550.2 nuclease-sensitive element-binding protein 1.[2]
- NR_132737.1 RNA Sequence (variant 2), non-coding RNA.[2]
Gene ID: 8531 is YBX3 Y-box binding protein 3.
- NP_003642.3 Y-box-binding protein 3 isoform a.
- NP_001138898.1 Y-box-binding protein 3 isoform b.
- XP_016875611.1 Y-box-binding protein 3 isoform X1.
- XP_016875612.1 Y-box-binding protein 3 isoform X2.
- XP_011519173.1 Y-box-binding protein 3 isoform X3.
- XR_001748906.2 RNA Sequence, transcript variant X3, misc RNA.
Gene ID: 51087 is YBX2 Y-box binding protein 2. "This gene encodes a nucleic acid binding protein which is highly expressed in germ cells. The encoded protein binds to a Y-box element in the promoters of certain genes but also binds to mRNA transcribed from these genes. Pseudogenes for this gene are located on chromosome 10 and 15."[3]
- NP_057066.2 Y-box-binding protein 2.
- XP_016880202.1 Y-box-binding protein 2 isoform X1.
Consensus sequences
On the template strand, the CAAT box consensus sequence is 3'-(C/T)(A/G)(A/G)CCAATC(A/G)-5'. An inverted CAAT box has the consensus sequence 3'-(A/G)CTAACC(A/G)(A/G)(C/T)-5'.
Sampling of A1BG promoters
For the Basic programs (starting with SuccessablesYbox.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:
- negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesYbox--.bas, looking for 3'-(A/G)CTAACC(A/G)(A/G)(C/T)-5', 0,
- negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesYbox-+.bas, looking for 3'-(A/G)CTAACC(A/G)(A/G)(C/T)-5', 0,
- positive strand in the negative direction is SuccessablesYbox+-.bas, looking for 3'-(A/G)CTAACC(A/G)(A/G)(C/T)-5', 0,
- positive strand in the positive direction is SuccessablesYbox++.bas, looking for 3'-(A/G)CTAACC(A/G)(A/G)(C/T)-5', 0,
- complement, negative strand, negative direction is SuccessablesYboxc--.bas, looking for 3'-(C/T)GATTGG(C/T)(C/T)(A/G)-5', 0,
- complement, negative strand, positive direction is SuccessablesYboxc-+.bas, looking for 3'-(C/T)GATTGG(C/T)(C/T)(A/G)-5', 0,
- complement, positive strand, negative direction is SuccessablesYboxc+-.bas, looking for 3'-(C/T)GATTGG(C/T)(C/T)(A/G)-5', 0,
- complement, positive strand, positive direction is SuccessablesYboxc++.bas, looking for 3'-(C/T)GATTGG(C/T)(C/T)(A/G)-5', 0,
- inverse complement, negative strand, negative direction is SuccessablesYboxci--.bas, looking for 3'-(A/G)(C/T)(C/T)GGTTAG(C/T)-5', 0,
- inverse complement, negative strand, positive direction is SuccessablesYboxci-+.bas, looking for 3'-(A/G)(C/T)(C/T)GGTTAG(C/T)-5', 0,
- inverse complement, positive strand, negative direction is SuccessablesYboxci+-.bas, looking for 3'-(A/G)(C/T)(C/T)GGTTAG(C/T)-5', 0,
- inverse complement, positive strand, positive direction is SuccessablesYboxci++.bas, looking for 3'-(A/G)(C/T)(C/T)GGTTAG(C/T)-5', 0,
- inverse, negative strand, negative direction, is SuccessablesYboxi--.bas, looking for 3'-(C/T)(A/G)(A/G)CCAATC(A/G)-5', 0,
- inverse, negative strand, positive direction, is SuccessablesYboxi-+.bas, looking for 3'-(C/T)(A/G)(A/G)CCAATC(A/G)-5', 0,
- inverse, positive strand, negative direction, is SuccessablesYboxi+-.bas, looking for 3'-(C/T)(A/G)(A/G)CCAATC(A/G)-5', 0,
- inverse, positive strand, positive direction, is SuccessablesYboxi++.bas, looking for 3'-(C/T)(A/G)(A/G)CCAATC(A/G)-5', 0.
Acknowledgements
The content on this page was first contributed by: Henry A. Hoff.
See also
- A1BG gene transcription core promoters
- A1BG gene transcriptions
- A1BG regulatory elements and regions
- A1BG response element negative results
- A1BG response element positive results
- Box gene transcriptions
- Complex locus A1BG and ZNF497
- W box gene transcriptions
- X box gene transcriptions
- Z box gene transcriptions
References
- ↑ Koji Koike, Takeshi Uchiumi, Takefumi Ohga, Satoshi Toh, Morimasa Wada, Kimitoshi Kohno, and Michihiko Kuwano (1997). "Nuclear translocation of the Y-box binding protein by ultraviolet irradiation". FEBS Letters. 417 (3): 390–4. doi:10.1016/S0014-5793(97)01296-9. Retrieved 2017-04-05. Unknown parameter
|month=ignored (help) - ↑ 2.0 2.1 2.2 RefSeq (September 2015). "YBX1 Y-box binding protein 1 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 19 November 2018.
- ↑ RefSeq (February 2012). "YBX2 Y-box binding protein 2 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 19 November 2018.