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FAM237A

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FAM237A is a protein coding gene which encodes a protein of the same name.[1] Within Homo sapiens, FAM237A is believed to be primarily expressed within the brain, with moderate heart and lesser testes expression[1],.[2] FAM237A is hypothesized to act as a specific activator of receptor GPR83.[3]

Gene

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FAM237A is alternatively known as HCG1657980 and LOC200726.[2][4] Homo sapiens FAM237A's sequence resides on chromosome 2’s + strand, and extends from bases 207486904 to 207514174.[2] Homo sapiens FAM237A sequence contains 13 exons unspliced.[2]

Transcripts

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Homo sapiens FAM237A is predicted to produce six unique transcripts, of which four are spliced.[2]

Alternate Transcripts of Homo sapiens FAM237A[2]
Name Size (Base Pairs) Exon Usage
aAug10 1797 2,3,8,10
bAug10 1376 4,6,13
cAug10 1121 5,12
dAug10 (Unspliced) 798 7
eAug10 (Unspliced) 873 9
fAug10 706 1,11

Proteins

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Homo sapiens FAM237A is associated with three unnamed protein isoforms.[2] FAM237A's most-researched isoform is 181 amino acids long, and is predicted to contain a transmembrane domain.[2] FAM237A's second protein isoform is predicted to be 417 amino acids long; it contains a transmembrane domain and an upstream open reading frame.[2] The last protein isoform of FAM237A is made up of 158 amino acids and contains a transmembrane domain; this isoform is predicted to localize within the membrane.[2] Several databases, including NCBI, only recognize FAM237A's 181 amino acid isoform.[1] Given the relative abundance of literature surrounding it, the remainder of this page's findings only discuss FAM237A's 181 amino acid isoform.

The theoretical molecular weight of this isoform is 20.56 kDA.[5][6][7] Its theoretical isoelectric point is 8.96.[5][6][7] Homo sapiens FAM237A amino acid composition is predicted to be relatively standard.[8] It notably contains a repeat LFWD motif at amino acids 90 and 97.[8]

FAM237A's transmembrane domain is generally predicted to reside on amino acids 14-32 within the protein.[8][9] However, structure prediction tool Phyre2 predicts that the protein's transmembrane domain resides on amino acids 91–106.[10]

Regulation

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Three promoters of Homo sapiens FAM237A are predicted: GXP_8991091, GXP_7539237, and GXP_8991092.[11] Of these, GXP_8991091 has the greatest predicted tissue expression levels.[11]

AceView predicts that Homo sapiens FAM237A is localized to membranes.[2] However, this is disputed, with protein localization prediction resource Hum-mPLoc predicting that Homo sapiens FAM237A is expressed within the nucleus and resource PSORT II predicting ER localization, with lesser chances of expression within the mitochondria and Golgi apparatus.[12][13][14][15][16][17]

An abundance of predicted phosphorylation sites reside on Homo sapiens FAM237A's sequence.[18][19][20][21] Homo sapiens FAM237A contains two predicted fatty acid addition sites at amino acids 18 and 26; these sites overlap with one of the FAM237A's predicted transmembrane sequences.[22][23] Homo sapiens FAM237A is additionally predicted to contain two sites of ubiquitination at amino acids 179 and 181 on its sequence.[24][25] These ubiquitination sites are predicted to perfectly overlap two acetylation sites.[26][27]

Homology

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Homo sapiens FAM237A has one predicted paralog: FAM237B.[4] FAM237B has 21.6% predicted identity with FAM237A[28]

FAM237A has orthologs in a broad range of vertebrate organisms, including other Mammals, Reptilia, Actinopterygii, and Aves.[29] The gene is not found in invertebrates. Based upon BLAST analysis, FAM237A is not found in invertebrates.[29] The only reptiles which FAM237A is found in are predicted to be of the suborder Cryptodira, based upon BLAST searches.[29]

Function

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Information regarding FAM237A's function is limited; however, FAM237A is predicted to be a specific activator of GPR83, which is implicated in energy metabolism, dietary patterns, and reward signaling.[3][30] GPR83 is additionally suspected to be correlated to immune system function[30]

References

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  1. ^ a b c "FAM237A family with sequence similarity 237 member A [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2020-12-15.
  2. ^ a b c d e f g h i j k "AceView: Gene:LOC200726, a comprehensive annotation of human, mouse and worm genes with mRNAs or ESTsAceView". www.ncbi.nlm.nih.gov. Retrieved 2020-12-15.
  3. ^ a b Sallee, Nathan A.; Lee, Ernestine; Leffert, Atossa; Ramirez, Silvia; Brace, Arthur D.; Halenbeck, Robert; Kavanaugh, W. Michael; Sullivan, Kathleen M. C. (2020-07-25). "A Pilot Screen of a Novel Peptide Hormone Library Identified Candidate GPR83 Ligands". SLAS Discovery. 25 (9): 1047–1063. doi:10.1177/2472555220934807. ISSN 2472-5552. PMID 32713278. S2CID 220798057.
  4. ^ a b "FAM237A Gene - GeneCards | F237A Protein | F237A Antibody". www.genecards.org. Retrieved 2020-12-19.
  5. ^ a b Bjellqvist, Bengt; Hughes, Graham J.; Pasquali, Christian; Paquet, Nicole; Ravier, Florence; Sanchez, Jean-Charles; Frutiger, Séverine; Hochstrasser, Denis (1993). "The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences". Electrophoresis. 14 (1): 1023–1031. doi:10.1002/elps.11501401163. ISSN 0173-0835. PMID 8125050. S2CID 38041111.
  6. ^ a b Bjellqvist, Bengt; Basse, Bodil; Olsen, Eydfinnur; Celis, Julio E. (1994). "Reference points for comparisons of two-dimensional maps of proteins from different human cell types defined in a pH scale where isoelectric points correlate with polypeptide compositions". Electrophoresis. 15 (1): 529–539. doi:10.1002/elps.1150150171. ISSN 0173-0835. PMID 8055880. S2CID 25560231.
  7. ^ a b Wilkins, Marc R.; Gasteiger, Elisabeth; Bairoch, Amos; Sanchez, Jean-Charles; Williams, Keith L.; Appel, Ron D.; Hochstrasser, Denis F. (1998), "Protein Identification and Analysis Tools in the ExPASy Server", 2-D Proteome Analysis Protocols, vol. 112, New Jersey: Humana Press, pp. 531–552, doi:10.1385/1-59259-584-7:531, ISBN 1-59259-584-7, PMID 10027275, retrieved 2020-12-19
  8. ^ a b c Madeira, Fábio; Park, Young Mi; Lee, Joon; Buso, Nicola; Gur, Tamer; Madhusoodanan, Nandana; Basutkar, Prasad; Tivey, Adrian R N; Potter, Simon C; Finn, Robert D; Lopez, Rodrigo (30 June 2019). "The EMBL-EBI search and sequence analysis tools APIs in 2019". Nucleic Acids Research. 47 (W1): 636–641. doi:10.1093/nar/gkz268. PMC 6602479. PMID 30976793.
  9. ^ "protein FAM237A [Homo sapiens] - Protein - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2020-12-19.
  10. ^ Kelley, Lawrence A; Mezulis, Stefans; Yates, Christopher M; Wass, Mark N; Sternberg, Michael J E (2015-05-07). "The Phyre2 web portal for protein modeling, prediction and analysis". Nature Protocols. 10 (6): 845–858. doi:10.1038/nprot.2015.053. ISSN 1754-2189. PMC 5298202. PMID 25950237.
  11. ^ a b "Genomatix - NGS Data Analysis & Personalized Medicine". www.genomatix.de. Archived from the original on 2021-08-19. Retrieved 2020-12-19.
  12. ^ Chou, Kuo-Chen; Shen, Hong-Bin (2008). "Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms". Nature Protocols. 3 (2): 153–162. doi:10.1038/nprot.2007.494. ISSN 1750-2799. PMID 18274516. S2CID 226104.
  13. ^ Shen, Hong-Bin; Chou, Kuo-Chen (2007-04-20). "Hum-mPLoc: An ensemble classifier for large-scale human protein subcellular location prediction by incorporating samples with multiple sites". Biochemical and Biophysical Research Communications. 355 (4): 1006–1011. doi:10.1016/j.bbrc.2007.02.071. ISSN 0006-291X. PMID 17346678.
  14. ^ Chou, K.-C. (2004-08-12). "Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes". Bioinformatics. 21 (1): 10–19. doi:10.1093/bioinformatics/bth466. ISSN 1367-4803. PMID 15308540.
  15. ^ Shen, Hong-Bin; Chou, Kuo-Chen (2006-07-15). "Ensemble classifier for protein fold pattern recognition". Bioinformatics. 22 (14): 1717–1722. doi:10.1093/bioinformatics/btl170. ISSN 1367-4811. PMID 16672258.
  16. ^ Nakai, K; Horton, P (January 1999). "PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization". Trends Biochem. Sci. 24 (1): 34–36. doi:10.1016/s0968-0004(98)01336-x. PMID 10087920.
  17. ^ Nakai, Kenta; Kanehisa, Minoru (December 1992). "A knowledge base for predicting protein localization sites in eukaryotic cells". Genomics. 14 (4): 897–911. doi:10.1016/s0888-7543(05)80111-9. ISSN 0888-7543. PMC 7134799. PMID 1478671.
  18. ^ Xue, Yu; Ren, Jian; Gao, Xinjiao; Jin, Changjiang; Wen, Longping; Yao, Xuebiao (September 2008). "GPS 2.0, a Tool to Predict Kinase-specific Phosphorylation Sites in Hierarchy". Molecular & Cellular Proteomics. 7 (9): 1598–1608. doi:10.1074/mcp.M700574-MCP200. ISSN 1535-9476. PMC 2528073. PMID 18463090.
  19. ^ Xue, Yu; Liu, Zexian; Cao, Jun; Ma, Qian; Gao, Xinjiao; Wang, Qingqi; Jin, Changjiang; Zhou, Yanhong; Wen, Longping; Ren, Jian (March 2011). "GPS 2.1: enhanced prediction of kinase-specific phosphorylation sites with an algorithm of motif length selection". Protein Engineering, Design & Selection. 24 (3): 255–260. doi:10.1093/protein/gzq094. ISSN 1741-0134. PMID 21062758.
  20. ^ Wang, Chenwei; Xu, Haodong; Lin, Shaofeng; Deng, Wankun; Zhou, Jiaqi; Zhang, Ying; Shi, Ying; Peng, Di; Xue, Yu (2020-02-01). "GPS 5.0: An Update on the Prediction of Kinase-specific Phosphorylation Sites in Proteins". Genomics, Proteomics & Bioinformatics. 18 (1): 72–80. doi:10.1016/j.gpb.2020.01.001. ISSN 1672-0229. PMC 7393560. PMID 32200042.
  21. ^ Xue, Yu; Zhou, Fengfeng; Zhu, Minjie; Ahmed, Kashif; Chen, Guoliang; Yao, Xuebiao (2005-07-01). "GPS: a comprehensive www server for phosphorylation sites prediction". Nucleic Acids Research. 33 (Web Server issue): W184–W187. doi:10.1093/nar/gki393. ISSN 0305-1048. PMC 1160154. PMID 15980451.
  22. ^ Xie, Yubin; Zheng, Yueyuan; Li, Hongyu; Luo, Xiaotong; He, Zhihao; Cao, Shuo; Shi, Yi; Zhao, Qi; Xue, Yu; Zuo, Zhixiang; Ren, Jian (2016-06-16). "GPS-Lipid: a robust tool for the prediction of multiple lipid modification sites". Scientific Reports. 6: 28249. Bibcode:2016NatSR...628249X. doi:10.1038/srep28249. ISSN 2045-2322. PMC 4910163. PMID 27306108.
  23. ^ Ren, Jian; Wen, Longping; Gao, Xinjiao; Jin, Changjiang; Xue, Yu; Yao, Xuebiao (November 2008). "CSS-Palm 2.0: an updated software for palmitoylation sites prediction". Protein Engineering, Design & Selection. 21 (11): 639–644. doi:10.1093/protein/gzn039. ISSN 1741-0134. PMC 2569006. PMID 18753194.
  24. ^ Ren, Jian; Gao, Xinjiao; Jin, Changjiang; Zhu, Mei; Wang, Xiwei; Shaw, Andrew; Wen, Longping; Yao, Xuebiao; Xue, Yu (2009). "Systematic study of protein sumoylation: Development of a site-specific predictor of SUMOsp 2.0". Proteomics. 9 (12): 3409–3412. doi:10.1002/pmic.200800646. ISSN 1615-9861. PMID 29658196. S2CID 4900031.
  25. ^ Zhao, Qi; Xie, Yubin; Zheng, Yueyuan; Jiang, Shuai; Liu, Wenzhong; Mu, Weiping; Liu, Zexian; Zhao, Yong; Xue, Yu; Ren, Jian (2014-07-01). "GPS-SUMO: a tool for the prediction of sumoylation sites and SUMO-interaction motifs". Nucleic Acids Research. 42 (Web Server issue): W325–W330. doi:10.1093/nar/gku383. ISSN 0305-1048. PMC 4086084. PMID 24880689.
  26. ^ Deng, Wankun; Wang, Chenwei; Zhang, Ying; Xu, Yang; Zhang, Shuang; Liu, Zexian; Xue, Yu (22 December 2016). "GPS-PAIL: prediction of lysine acetyltransferase-specific modification sites from protein sequences". Scientific Reports. 6 (1): 39787. Bibcode:2016NatSR...639787D. doi:10.1038/srep39787. ISSN 2045-2322. PMC 5177928. PMID 28004786.
  27. ^ Li, Ao; Xue, Yu; Jin, Changjiang; Wang, Minghui; Yao, Xuebiao (1 December 2006). "Prediction of Nε-acetylation on internal lysines implemented in Bayesian Discriminant Method". Biochemical and Biophysical Research Communications. 350 (4): 818–824. doi:10.1016/j.bbrc.2006.08.199. ISSN 0006-291X. PMC 2093955. PMID 17045240.
  28. ^ "Using sequence similarity searching tools at EMBL-EBI: webinar". doi:10.6019/tol.seqsim-w.2015.00001.1. {{cite journal}}: Cite journal requires |journal= (help)
  29. ^ a b c Boratyn, Grzegorz M; Thierry-Mieg, Jean; Thierry-Mieg, Danielle; Busby, Ben; Madden, Thomas L (2018-08-13). "Magic-BLAST, an accurate DNA and RNA-seq aligner for long and short reads". doi:10.1101/390013. S2CID 92268893. {{cite journal}}: Cite journal requires |journal= (help)
  30. ^ a b Müller, Timo D.; Müller, Anne; Yi, Chun-Xia; M Habegger, Kirk; Meyer, Carola W.; Gaylinn, Bruce D.; Finan, Brian; Heppner, Kristy; Trivedi, Chitrang; Bielohuby, Maximilian; Abplanalp, William (2013-06-07). "The orphan receptor Gpr83 regulates systemic energy metabolism via ghrelin-dependent and ghrelin-independent mechanisms". Nature Communications. 4 (1): 1968. Bibcode:2013NatCo...4.1968M. doi:10.1038/ncomms2968. ISSN 2041-1723. PMC 3709495. PMID 23744028.
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