Immunoglobulin like domain cd05751

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

The United States National Library of Medicine (NLM) is a biomedical library in the United States as part of the National Institutes of Health that contains "hierarchical classifications of widely distributed protein domain families [and records] conserved sites associated with molecular function, so that they can be mapped onto user queries in support of hypothesis-driven biomolecular research."[1]

"At the time of writing, the CDD version v3.17 is the live production version with 52,910 protein- and protein domain-models obtained from Pfam (1), SMART (2), the COGs collection (3), TIGRFAMS (4), the NCBI Protein Clusters collection (5), NCBIfam (6) and CDD’s in-house data curation effort (7)."[1]

Immunoglobulin supergene family

Main article: Immunoglobulin supergene family

The immunoglobulin supergene family is "the group of proteins that have immunoglobulin-like domains, including histocompatibility antigens, the T-cell antigen receptor, poly-IgR, and other proteins involved in the vertebrate immune response (17)."[2]

Alpha-1-B glycoprotein variants

Gene ID: 1 A1BG alpha-1-B glycoprotein on 19q13.43: "The protein encoded by this gene is a plasma glycoprotein of unknown function. The protein shows sequence similarity to the variable regions of some immunoglobulin supergene family member proteins."[3]

"𝛂1B-glycoprotein(𝛂1B) [...] consists of a single polypeptide chain N-linked to four glucosamine oligosaccharides. The polypeptide has five intrachain disulfide bonds and contains 474 amino acid residues. [...] 𝛂1B exhibits internal duplication and consists of five repeating structural domains, each containing about 95 amino acids and one disulfide bond. [...] several domains of 𝛂1B, especially the third, show statistically significant homology to variable regions of certain immunoglobulin light and heavy chains. 𝛂1B [...] exhibits sequence similarity to other members of the immunoglobulin supergene family such as the receptor for transepithelial transport of IgA and IgM and the secretory component of human IgA."[2]

"Some of the domains of 𝛂1B show significant homology to variable (V) and constant (C) regions of certain immunoglobulins. Likewise, there is statistically significant homology between 𝛂1B and the secretory component (SC) of human IgA (15) and also with the extracellular portion of the rabbit receptor for transepithelial transport of polymeric immunoglobulins (IgA and IgM). Mostov et al. (16) have called the later protein the poly-Ig receptor or poly-IgR and have shown that it is the precursor of SC."[2]

"𝛂1B-glycoprotein(𝛂1B) [...] consists of a single polypeptide chain N-linked to four glucosamine oligosaccharides. The polypeptide has five intrachain disulfide bonds and contains 474 amino acid residues. [...] 𝛂1B exhibits internal duplication and consists of five repeating structural domains, each containing about 95 amino acids and one disulfide bond. [...] several domains of 𝛂1B, especially the third, show statistically significant homology to variable regions of certain immunoglobulin light and heavy chains. 𝛂1B [...] exhibits sequence similarity to other members of the immunoglobulin supergene family such as the receptor for transepithelial transport of IgA and IgM and the secretory component of human IgA."[2]

A1BG contains the immunoglobulin domain: cl11960 and three immunoglobulin-like domains: pfam13895, cd05751 and smart00410 in the order and nucleotide sequence: cd05751 Location: 401 → 493, smart00410 Location: 218 → 280, pfam13895 Location: 210 → 301 and cl11960 Location: 28 → 110.

Carcinoembryonic antigen gene family

Main article: Carcinoembryonic antigen gene family

Immunoglobulin superfamily genes

Main article: Immunoglobulin superfamily

Major histocompatibility complex genes

Main article: Major histocompatibility complex

Class I

Main article: MHC class I
Main article: Major histocompatibility complex class I gene family

Class II

Main article: MHC class II
Main article: Major histocompatibility complex class II gene family

Class III

Main article: MHC class III
Main article: Major histocompatibility complex class III gene family

Immunoglobulin domain genes

Main article: Immunoglobulin domain genes

Immunoglobulin receptor superfamily

Main article: Immunoglobulin receptor superfamily genes

Genes having immunoglobulin like domain cd05751

Gene ID: 1 see Immunoglobulin domain genes.

Gene ID: 2204 is FCAR Fc fragment of IgA receptor on 19q13.42: "This gene is a member of the immunoglobulin gene superfamily and encodes a receptor for the Fc region of IgA. The receptor is a transmembrane glycoprotein present on the surface of myeloid lineage cells such as neutrophils, monocytes, macrophages, and eosinophils, where it mediates immunologic responses to pathogens. It interacts with IgA-opsonized targets and triggers several immunologic defense processes, including phagocytosis, antibody-dependent cell-mediated cytotoxicity, and stimulation of the release of inflammatory mediators. Multiple alternatively spliced transcript variants encoding different isoforms have been described for this gene."[4]

  1. NP_001991.1 immunoglobulin alpha Fc receptor isoform a precursor: "Transcript Variant: This variant (1, also known as a.1) represents the longest transcript and encodes the longest isoform (a)."[4] Conserved Domains (2) summary: cd05711 Location: 125 → 215 Ig2_LILR_KIR_like; Second immunoglobulin (Ig)-like domain found in Leukocyte Ig-like receptors, natural and similar domains and cd05751 Location: 27 → 120 Ig1_LILR_KIR_like; First immunoglobulin (Ig)-like domain found in Leukocyte Ig-like receptors (LILRs), Natural killer inhibitory receptors (KIRs) and similar domains.[4]
  2. NP_579803.1 immunoglobulin alpha Fc receptor isoform b precursor: "Transcript Variant: This variant (2, also known as a.2, delta66EC2, or U06) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (b) is shorter than isoform a."[4] Conserved Domains (1) summary: cl11960 Location: 125 → 197 Ig; Immunoglobulin domain.[4]
  3. NP_579805.1 immunoglobulin alpha Fc receptor isoform c precursor: "Transcript Variant: This variant (3, also known as a.3, Rla2, deltaE2, or U08) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. The encoded isoform (c) is shorter than isoform a."[4] Conserved Domains (1) summary: cl11960 Location: 27 → 120 Ig; Immunoglobulin domain.[4]
  4. NP_579806.1 immunoglobulin alpha Fc receptor isoform d: "Transcript Variant: This variant (4, also known as deltaS2 or U11) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. The encoded isoform (d) is shorter than isoform a."[4] Conserved Domains (2) summary: cd05711 Location: 113 → 203 Ig_FcalphaRI; Immunoglobulin (IG)-like domain of of FcalphaRI and cl11960 Location: 15 → 108 Ig; Immunoglobulin domain.[4]
  5. NP_579807.1 immunoglobulin alpha Fc receptor isoform e: "Transcript Variant: This variant (5, also known as U10) lacks alternate in-frame exons in the 5' and 3' coding region, compared to variant 1. The encoded isoform (e) is shorter than isoform a."[4] Conserved Domains (1) summary: cl11960 Location: 15 → 108 Ig; Immunoglobulin domain.[4]
  6. NP_579808.1 immunoglobulin alpha Fc receptor isoform f: "Transcript Variant: This variant (6, also known as U09) lacks an in-frame exon in the 5' coding region and uses an alternate splice site in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (f) has a distinct C-terminus and is shorter than isoform a."[4] Conserved Domains (1) summary: cl11960 Location: 113 → 180 Ig; Immunoglobulin domain.[4]
  7. NP_579811.1 immunoglobulin alpha Fc receptor isoform g: "Transcript Variant: This variant (7, also known as deltaS2ECl or L10) lacks two in-frame exons in the 5' coding region, compared to variant 1. The encoded isoform (g) is shorter than isoform a."[4] Conserved Domains (1) summary: cd05711 Location: 16 → 106 Ig_FcalphaRI; Immunoglobulin (IG)-like domain of of FcalphaRI.[4]
  8. NP_579812.1 immunoglobulin alpha Fc receptor isoform h: "Transcript Variant: This variant (8, also known as deltaS266Ec2 or U13) lacks an in-frame exon in the 5' coding region and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (h) is shorter than isoform a."[4] Conserved Domains (1) summary: cl11960 Location: 113 → 185 Ig; Immunoglobulin domain.[4]
  9. XP_011524927.1 immunoglobulin alpha Fc receptor isoform X1, Conserved Domains (2) summary: cd05711 Location: 98 → 188 Ig_FcalphaRI; Immunoglobulin (IG)-like domain of of FcalphaRI and cl11960 Location: 2 → 93 Ig; Immunoglobulin domain.[4]
  10. XP_016881962.1 immunoglobulin alpha Fc receptor isoform X1, Conserved Domains (2) summary: cd05711 Location: 98 → 188 Ig_FcalphaRI; Immunoglobulin (IG)-like domain of of FcalphaRI and cl11960 Location: 2 → 93 Ig; Immunoglobulin domain.[4]
  11. XP_016881963.1 immunoglobulin alpha Fc receptor isoform X1, Conserved Domains (2) summary: cd05711 Location: 98 → 188 Ig_FcalphaRI; Immunoglobulin (IG)-like domain of of FcalphaRI and cl11960 Location: 2 → 93 Ig; Immunoglobulin domain.[4]

Gene ID: 9437 is NCR1 natural cytotoxicity triggering receptor 1 on 19q13.42.[5]

  1. NP_001138929.2 natural cytotoxicity triggering receptor 1 isoform b precursor: "Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region compared to variant 1. This results in a shorter protein (isoform b) compared to isoform a."[5] Conserved Domains (2) summary: cd05711 Location: 123 → 210 Ig_FcalphaRI; Immunoglobulin (IG)-like domain of of FcalphaRI and cd05751 Location: 27 → 118 Ig1_LILRB1_like; First immunoglobulin (Ig)-like domain found in Leukocyte Ig-like receptors (LILR)B1 (also known as LIR-1) and similar proteins.[5]
  2. NP_001138930.2 natural cytotoxicity triggering receptor 1 isoform c precursor: "Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. This results in a shorter protein (isoform c) compared to isoform a."[5] Conserved Domains (2) summary: cd05711 Location: 123 → 210 Ig_FcalphaRI; Immunoglobulin (IG)-like domain of of FcalphaRI, cd05751 Location: 27 → 118 Ig1_LILRB1_like; First immunoglobulin (Ig)-like domain found in Leukocyte Ig-like receptors (LILR)B1 (also known as LIR-1) and similar proteins.[5]
  3. NP_001229285.1 natural cytotoxicity triggering receptor 1 isoform d precursor: "Transcript Variant: This variant (4) lacks an alternate exon in the 5' coding region compared variant 1. The resulting protein (isoform d) is shorter but has the same N- and C-termini compared to isoform a." Conserved Domains (1) summary: cd05711 Location: 28 → 115 Ig_FcalphaRI; Immunoglobulin (IG)-like domain of of FcalphaRI.[5]
  4. NP_001229286.1 natural cytotoxicity triggering receptor 1 isoform e precursor: "Transcript Variant: This variant (5) lacks two alternate exons in the coding region compared to variant 1. The resulting protein (isoform e) is shorter but has the same N- and C-termini compared to isoform a."[5] Conserved Domains (1) summary: cd05711 Location: 28 → 115 Ig_FcalphaRI; Immunoglobulin (IG)-like domain of of FcalphaRI.[5]
  5. NP_004820.2 natural cytotoxicity triggering receptor 1 isoform a precursor: "Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a)."[5] Conserved Domains (2) summary: cd05711 Location: 123 → 210 Ig_FcalphaRI; Immunoglobulin (IG)-like domain of of FcalphaRI and cd05751 Location: 27 → 118 Ig1_LILRB1_like; First immunoglobulin (Ig)-like domain found in Leukocyte Ig-like receptors (LILR)B1 (also known as LIR-1) and similar proteins.[5]
  6. XP_011525830.1 natural cytotoxicity triggering receptor 1 isoform X1, Conserved Domains (2) summary: cd05711 Location: 123 → 210 Ig_FcalphaRI; Immunoglobulin (IG)-like domain of of FcalphaRI and cd05751 Location: 27 → 118 Ig1_LILRB1_like; First immunoglobulin (Ig)-like domain found in Leukocyte Ig-like receptors (LILR)B1 (also known as LIR-1) and similar proteins.[5]
  7. XP_011525831.1 natural cytotoxicity triggering receptor 1 isoform X2, Conserved Domains (2) summary: cd05711 Location:123 → 210, Ig_FcalphaRI; Immunoglobulin (IG)-like domain of of FcalphaRI and cd05751 Location: 27 → 118 Ig1_LILRB1_like; First immunoglobulin (Ig)-like domain found in Leukocyte Ig-like receptors (LILR)B1 (also known as LIR-1) and similar proteins.[5]
  8. XP_011525832.1 natural cytotoxicity triggering receptor 1 isoform X3, Conserved Domains (2) summary: cd05711 Location: 123 → 210 Ig_FcalphaRI; Immunoglobulin (IG)-like domain of of FcalphaRI and cd05751 Location: 27 → 118 Ig1_LILRB1_like; First immunoglobulin (Ig)-like domain found in Leukocyte Ig-like receptors (LILR)B1 (also known as LIR-1) and similar proteins.[5]

Gene ID: 10859 see Immunoglobulin receptor superfamily genes.

Gene ID: 11006 see Immunoglobulin receptor superfamily genes.

Gene ID: 11024 see Immunoglobulin receptor superfamily genes.

Gene ID: 11025 see Immunoglobulin receptor superfamily genes.

Gene ID: 11026 see Immunoglobulin receptor superfamily genes.

Gene ID: 51206

Gene ID: 79168 see Immunoglobulin domain genes.

Gene ID: 353514 see Immunoglobulin receptor superfamily genes.

Gene ID: 102725035

Gene ID: 107987425

Gene ID: 107987462

Hypotheses

  1. Downstream core promoters may work as transcription factors even as their complements or inverses.
  2. In addition to the DNA binding sequences listed above, the transcription factors that can open up and attach through the local epigenome need to be known and specified.
  3. The function of A1BG is the same as other immunoglobulin genes possessing the immunoglobulin domain cl11960 and/or any of three immunoglobulin-like domains: pfam13895, cd05751 and smart00410 in the order and nucleotide sequence: cd05751 Location: 401 → 493, smart00410 Location: 218 → 280, pfam13895 Location: 210 → 301 and cl11960 Location: 28 → 110.

See also

References

  1. ↑ 1.0 1.1 Shennan Lu, Jiyao Wang, Farideh Chitsaz, Myra K Derbyshire, Renata C Geer, Noreen R Gonzales, Marc Gwadz, David I Hurwitz, Gabriele H Marchler, James S Song, Narmada Thanki, Roxanne A Yamashita, Mingzhang Yang, Dachuan Zhang, Chanjuan Zheng, Christopher J Lanczycki, and Aron Marchler-Bauer (8 January 2020). "CDD/SPARCLE: The Conserved Domain Database in 2020". Nucleic Acids Research. 48 (D1): D265–D268. doi:10.1093/nar/gkz991. PMID 31777944. Retrieved 24 June 2020.
  2. ↑ 2.0 2.1 2.2 2.3 Noriaki Ishioka, Nobuhiro Takahashi, and Frank W. Putnam (April 1986). "Amino acid sequence of human plasma 𝛂1B-glycoprotein: Homology to the immunoglobulin supergene family" (PDF). Proceedings of the National Academy of Sciences USA. 83 (8): 2363–7. doi:10.1073/pnas.83.8.2363. PMID 3458201. Retrieved 9 March 2020.
  3. ↑ RefSeq (July 2008). "A1BG alpha-1-B glycoprotein [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 17 April 2020.
  4. ↑ 4.00 4.01 4.02 4.03 4.04 4.05 4.06 4.07 4.08 4.09 4.10 4.11 4.12 4.13 4.14 4.15 4.16 4.17 4.18 4.19 RefSeq (July 2008). "FCAR Fc fragment of IgA receptor [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 25 June 2020.
  5. ↑ 5.00 5.01 5.02 5.03 5.04 5.05 5.06 5.07 5.08 5.09 5.10 5.11 5.12 HGNC (7 June 2020). "NCR1 natural cytotoxicity triggering receptor 1 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 25 June 2020.

External links

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