Immunoglobulin domain cl11960: Difference between revisions

Revision as of 12:13, 28 June 2020

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

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.

"Immunoglobulin (Ig) domain [cl11960] found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."^[4]

Carcinoembryonic antigen gene family

Immunoglobulin superfamily genes

Major histocompatibility complex genes

Class I

Class II

Class III

Immunoglobulin domain genes

Immunoglobulin receptor superfamily

Genes having immunoglobulin domain cl11960

Gene ID: 1 see Immunoglobulin domain genes.

Gene ID: 177 see Major histocompatibility complex class III gene family.

Gene ID: 214 see Carcinoembryonic antigen gene family.

Gene ID: 634 see Carcinoembryonic antigen gene family.

Gene ID: 682 see Immunoglobulin supergene family.

Gene ID: 915 see Immunoglobulin domain genes.

Gene ID: 924 see Immunoglobulin supergene family.

Gene ID: 942 see Immunoglobulin like domain pfam13895.

Gene ID: 1048 see Carcinoembryonic antigen gene family.

Gene ID: 1630 see Immunoglobulin receptor superfamily genes.

Gene ID: 1826 see Carcinoembryonic antigen gene family.

Gene ID: 2204 see Immunoglobulin like domain cd05751.

Gene ID: 2263 see Immunoglobulin like domain smart00410.

Gene ID: 2321 see Immunoglobulin like domain smart00410.

Gene ID: 2324 see Immunoglobulin like domain pfam13895.

Gene ID: 3084 see Immunoglobulin like domain smart00410.

Gene ID: 3321 see Immunoglobulin supergene family.

Gene ID: 3339 see Immunoglobulin like domain pfam13895.

Gene ID: 3383 see Carcinoembryonic antigen gene family.

Gene ID: 3385 see Carcinoembryonic antigen gene family.

Gene ID: 3791 see Immunoglobulin like domain smart00410.

Gene ID: 3805 see Immunoglobulin receptor superfamily genes.

Gene ID: 3811 see Immunoglobulin receptor superfamily genes.

Gene ID: 3812 see Immunoglobulin receptor superfamily genes.

Gene ID: 3897 see Carcinoembryonic antigen gene family.

Gene ID: 3904 see Immunoglobulin receptor superfamily genes.

Gene ID: 4059 see Carcinoembryonic antigen gene family.

Gene ID: 4680 see Carcinoembryonic antigen gene family.

Gene ID: 4684 see Carcinoembryonic antigen gene family.

Gene ID: 4685 see Carcinoembryonic antigen gene family.

Gene ID: 4897 see Carcinoembryonic antigen gene family.

Gene ID: 4978 see Carcinoembryonic antigen gene family.

Gene ID: 5156 see Immunoglobulin like domain smart00410.

Gene ID: 5175 see Carcinoembryonic antigen gene family.

Gene ID: 5159 see Immunoglobulin like domain smart00410.

Gene ID: 7087 see Carcinoembryonic antigen gene family.

Gene ID: 7273 see Immunoglobulin like domain smart00410.

Gene ID: 7441 see Immunoglobulin supergene family.

Gene ID: 8174 see Carcinoembryonic antigen gene family.

Gene ID: 8482 see Immunoglobulin domain genes.

Gene ID: 10288 see Immunoglobulin receptor superfamily genes.

Gene ID: 10507 see Immunoglobulin domain genes.

Gene ID: 10752 see Carcinoembryonic antigen gene family.

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 like domain cd05751.

Gene ID: 11026 see Immunoglobulin receptor superfamily genes.

Gene ID: 11027 see Immunoglobulin receptor superfamily genes.

Gene ID: 11326 see Immunoglobulin domain genes.

Gene ID: 23547 see Immunoglobulin receptor superfamily genes.

Gene ID: 26103 see Immunoglobulin domain genes.

Gene ID: 29126 see Immunoglobulin like domain smart00410.

Gene ID: 50937 see Carcinoembryonic antigen gene family.

Gene ID: 51206 see Immunoglobulin like domain cd05751.

Gene ID: 57453 see Carcinoembryonic antigen gene family.

Gene ID: 59307 see Immunoglobulin domain genes.

Gene ID: 79037 see Immunoglobulin domain genes.

Gene ID: 79168 see Immunoglobulin domain genes.

Gene ID: 83417 see Immunoglobulin receptor superfamily genes.

Gene ID: 90273 see Carcinoembryonic antigen gene family.

Gene ID: 115352 see Immunoglobulin receptor superfamily genes.

Gene ID: 115653 see Immunoglobulin receptor superfamily genes.

Gene ID: 120425 see Carcinoembryonic antigen gene family.

Gene ID: 125931 see Carcinoembryonic antigen gene family.

Gene ID: 126014 see Immunoglobulin receptor superfamily genes.

Gene ID: 126259 see Immunoglobulin domain genes.

Gene ID: 150084 see Immunoglobulin supergene family.

Gene ID: 199731 see Carcinoembryonic antigen gene family.

Gene ID: 285313 see Immunoglobulin supergene family.

Gene ID: 339398 see Immunoglobulin domain genes.

Gene ID: 102725035 see Immunoglobulin like domain cd05751.

Gene ID: 107987425 see Immunoglobulin like domain cd05751.

Gene ID: 107987462 see Immunoglobulin like domain cd05751.

Hypotheses

Downstream core promoters may work as transcription factors even as their complements or inverses.
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.
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.

References

↑ ^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.
↑ ^2.0 ^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.
↑ 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.
↑ NCBI (2 February 2016). "Conserved Protein Domain Family cl11960: Ig Superfamily". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 22 May 2020.

External links

{{Phosphate biochemistry}}Template:Sisterlinks

[Lu-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.

[Ishioka-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.

[RefSeq1-3] 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.

[NCBI386229-4] NCBI (2 February 2016). "Conserved Protein Domain Family cl11960: Ig Superfamily". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 22 May 2020.

[1]

[2]

[3]

[4]

@@ Line 119: / Line 119: @@
 Gene ID: 915 see [[Immunoglobulin domain genes]].
+Gene ID: 924 see [[Immunoglobulin supergene family]].
 Gene ID: 942 see [[Immunoglobulin like domain pfam13895]].

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transcriptions MYB recognition element gene transcriptions Myelocytomatosis transcription factor gene transcriptions Myocyte enhancer factor gene transcriptions N-boxes Ndt80p gene transcriptions Nuclear factor 1 Nuclear factor 𝜿B Nuclear factor gene transcriptions Nuclear factor of activated T cell gene transcriptions (NFAT) Nuclear factor Y gene transcriptions Nutrient-sensing response element gene transcriptions Oaf1p gene transcriptions ORE1 binding site gene transcriptions p53 response element gene transcriptions P63 DNA-binding site gene transcriptions P box gene transcriptions Pdr1,3p gene transcriptions Peroxisome proliferator hormone response element gene transcriptions Phosphate starvation-response transcription factor gene transcriptions Pollen1 element gene transcriptions Polycomb response element gene transcriptions Preinitiation complex Preinitiation complex gene transcriptions Pribnow box gene transcriptions Prolamin box gene transcriptions Promoter gene transcriptions 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