[{"@context":"http:\/\/schema.org\/","@type":"BlogPosting","@id":"https:\/\/wiki.edu.vn\/en\/wiki24\/soga2-wikipedia\/#BlogPosting","mainEntityOfPage":"https:\/\/wiki.edu.vn\/en\/wiki24\/soga2-wikipedia\/","headline":"SOGA2 – Wikipedia","name":"SOGA2 – Wikipedia","description":"Protein-coding gene in the species Homo sapiens SOGA2, also known as Suppressor of glucose autophagy associated 2 or CCDC165, is","datePublished":"2019-11-21","dateModified":"2019-11-21","author":{"@type":"Person","@id":"https:\/\/wiki.edu.vn\/en\/wiki24\/author\/lordneo\/#Person","name":"lordneo","url":"https:\/\/wiki.edu.vn\/en\/wiki24\/author\/lordneo\/","image":{"@type":"ImageObject","@id":"https:\/\/secure.gravatar.com\/avatar\/c9645c498c9701c88b89b8537773dd7c?s=96&d=mm&r=g","url":"https:\/\/secure.gravatar.com\/avatar\/c9645c498c9701c88b89b8537773dd7c?s=96&d=mm&r=g","height":96,"width":96}},"publisher":{"@type":"Organization","name":"Enzyklop\u00e4die","logo":{"@type":"ImageObject","@id":"https:\/\/wiki.edu.vn\/wiki4\/wp-content\/uploads\/2023\/08\/download.jpg","url":"https:\/\/wiki.edu.vn\/wiki4\/wp-content\/uploads\/2023\/08\/download.jpg","width":600,"height":60}},"image":{"@type":"ImageObject","@id":"https:\/\/upload.wikimedia.org\/wikipedia\/commons\/thumb\/7\/76\/Divergence3.png\/500px-Divergence3.png","url":"https:\/\/upload.wikimedia.org\/wikipedia\/commons\/thumb\/7\/76\/Divergence3.png\/500px-Divergence3.png","height":"355","width":"500"},"url":"https:\/\/wiki.edu.vn\/en\/wiki24\/soga2-wikipedia\/","about":["Wiki"],"wordCount":9595,"articleBody":"Protein-coding gene in the species Homo sapiensSOGA2, also known as Suppressor of glucose autophagy associated 2 or CCDC165, is a protein that in humans is encoded by the SOGA2 gene.[5][6]SOGA2 has two human paralogs, SOGA1 and SOGA3.[7][8]In humans, the gene coding sequence is 151,349 base pairs long, with an mRNA of 6092 base pairs, and a protein sequence of 1586 amino acids. The SOGA2 gene is conserved in gorilla, baboon, galago, rat, mouse, cat, and more. There is distant conservation seen in organisms such as zebra finches and anoles.[9]SOGA2 is ubiquitously expressed in humans, with especially high expression in brain (especially the cerebellum and hippocampus), colon, pituitary gland, small intestine, spinal cord, testis and fetal brain.[10]Table of ContentsLocus[edit]Homology and Evolution[edit]Paralogs[edit]Orthologs[edit]Distant Homologs[edit]Homologous Domains[edit]Protein[edit]Protein internal composition[edit]Primary structure and isoforms[edit]Domains and motifs[edit]Post-translational modifications[edit]Secondary structure[edit]Tertiary structure[edit]Gene expression[edit]Promoter[edit]Gene expression data[edit]Transcript variants[edit]Function[edit]Possible transcription factors[edit]Interactions[edit]Clinical significance[edit]References[edit]Further reading[edit]Locus[edit]The SOGA2 gene is located from 8717369 – 8832775 on the short arm of chromosome 18 (18p11.22).[11]Homology and Evolution[edit]Paralogs[edit]There are two main paralogs to SOGA2: human protein SOGA1 and human protein SOGA3.[9]SOGA1 has been shown to be involved in suppression of glucose by autophagy.[12] The rate at which orthologs diverge from SOGA2 human(measured by\u00a0% identity) places the approximate duplication event of SOGA1 from SOGA2 at ~254.1 MYA and the duplication event of SOGA3 from SOGA2 ~329.1 MYA.protein nameaccession numbersequence length (aa)sequence identity to human proteinnotesSOGA3NP_001012279.194758%conserved in ~500 N-terminal aaSOGA1 isoform 2NP_954650.21016 aa65%conserved in first ~900 aaSOGA1 isoform 1NP_542194.2166141%conserved across the length of sequence except ~950-1150Orthologs[edit]Many orthologs have been identified in Eukaryotes.[9]common nameprotein namedivergence from human lineage (MYA)accession numbersequence length (aa)sequence identity to human proteinprotein domain differencesgorillaprotein SOGA28.8XP_004059220.1158699%baboonprotein SOGA229XP_003914218158798%galagoprotein SOGA374XP_003801047.1158388%DUF4201 not presentratCCDC16592.3XP_237548.6206081%DUF4201 not presentmouseSOGA292.3NP_001107570.1189380%house catprotein SOGA294.2XP_003995077.1170084%DUF4201 not presentcowCCDC16694.2XP_581047.5152574%DUF4201 not presentAfrican ElephantCCDC167-like98.7XP_003406836.1154473%zebra Finchprotein SOGA2296XP_002193121.1159869%DUF4201 not presentRed JungleFowlCCDC165296XP_423729.3160070%DUF4201 not presentCarolina anoleuncharacterized protein KIAA0802-like296XP_003225723.1183967%DUF4201 not present  A graph of sequence identity to human SOGA2 as a function of time of divergence of human SOGA2 orthologs.Distant Homologs[edit]common nameprotein namedivergence from human lineage (MYA)accession numbersequence length (aa)sequence identity to human proteinprotein domain differencesTropical Clawed Froguncharacterized protein C20orf117-like371.2XP_002942331.1158439%purple sea urchinuncharacterized protein LOC578090742.9XP_783370.2158747%DUF4201 not presentbody louseCentromeric protein E, putative782.7XP_002429877.1208630%no shared domainssouthern house mosquitoconserved hypothetical protein782.7XP_001843754.1187832%no shared domainsporkwormsurface antigen repeat family protein937.5XP_003380263.1203036%no shared domainsHomologous Domains[edit]SOGA2 is conserved farthest back in its N-terminal region, where it contains its three domains of unknown function.[13]  A comparison of multiple sequence alignment of the N-terminal regions vs. C-terminal regions of distantly related SOGA2 orthologs. Here it is demonstrated that the N-terminal region is well conserved in organisms like the clawed frog (FROG_SOGA2) but the C-terminal region is not. Location 19 is an example of one of the 7 Leucine residue that is conserved across all orthologs.Protein[edit]Protein internal composition[edit]SOGA2 is rich in glycine (ratio r of SOGA2 composition to average human protein is 1.723), glutamate (r = 1.647), and arginine(r = 1.357). It also has a lower than usual composition of tyrosine (r = 0.3406), isoleucine (r = 0.4430),phenylalanine (r = 0.5808), and valine (r = 0.6161).[14][15]Primary structure and isoforms[edit]SOGA2 has 4 isoforms: Q9Y4B5-1, Q9Y4B5-2, Q9Y4B5-3, Q9Y4B5-4.[16]  A graphic depicting the 4 different isoforms of SOGA2. Isoform 1 is canonical.  Modification Key: * E \u2192 ELRGPPVLPEQSVSIEELQGQLVQAARLHQEETETFTNKIHK **Q \u2192 QNCCGYPRINIEEETLGFTRLPAGSTVKTLKSLGLQRLE *** NQTVLLTAPWGL \u2192 ELPCSALAPS…LHGLSQYNSLDomains and motifs[edit]SOGA2 contains Domain of Unknown Function 4201 (DUF4201) from aa 16-235. This domain is specific to the Coiled Coil Domain Containing family of proteins in eukaryotes.[17] It also contains two copies of Domain of Unknown Function 3166 (DUF3166): one from aa 140-235 and one from aa 269-364.[11]Post-translational modifications[edit]SOGA2 is expected to undergo a number of post-translational modifications. Modifications of human SOGA2 that are shared by orthologs include:Sumoylation at amino acids 87, 152, 235, 392, and 1379.[18]Sulfination at tyrosines 14 and 1249.[19]Phosphorylation at a number of sites, highlighted in the following graphic:  Phosphorylation sites in SOGA2 predicted by netPhos.[20] Highlighted sites are conserved as far back as African clawed frogs.Secondary structure[edit]The consensus of the prediction software PELE,[21] GOR4,[22] and SOSUICoil  is that the secondary structure of SOGA2 is dominated by alpha helices with interspersed regions of random coil. GOR4 indicated that SOGA2 is dominated by alpha-helices; it predicted a mere 5.61% ofresidues in an extended strand (parallel or antiparallel Beta-sheet) conformation, as opposed to47.79% alpha helix and 46.6% random coils.  Secondary structure of human SOGA2 predicted by the GOR4 tool. h corresponds to alpha helices, c corresponds to random coils, and e corresponds to extended strand[23]Tertiary structure[edit]SOGA2 shares sequence features in its highly conserved N-terminal region. This homology allows prediction of its tertiary structure on the basis of homology to published 3d structures via Phyre2[24] and NCBI structure.[25]  SOGA2’s 3d structure predicted by Phyre2.[24] Structure is based on the crystal structure of tropomyosin at 7 angstrom resolution, with 12% identity. 283 residues match, in the CCDC containing N-terminal region.  1I84 S, Heavy Meromyosin Subfragment Of Chicken Gizzard Smooth Muscle Myosin With Regulatory Light Chain In The Dephosphorylated State 3d structure. Highlighted region is conserved in SOGA2.[25]Gene expression[edit]Promoter[edit]The promoter for human SOGA2 is below.  The promoter of the human SOGA2 gene.Gene expression data[edit]The EST profile shows that, in humans, SOGA2 is highly expressed in many sites throughout the body, including bone, brain, ear, eye, and many others.[26] There are a large number of transcripts in liver cancer samples. Human microarray data show that SOGA2 is moderately expressed, with especially high expression in brain (especially the cerebellum and hippocampus), colon, pituitary gland, small intestine, spinal cord, testis and fetal brain.[10] Brain-tissue-specific microarray data show that SOGA2 has high expression throughout the posterior lobe of the cerebellar hemispheres and posterial lobe of the vermis in the mouse brain. There is low expression in most other areas of the brain.[27]Transcript variants[edit]In humans, the SOGA2 gene produces 17 different transcripts, 8 of which form a protein product (one undergoes nonsense mediated decay). The main transcript in humans is transcript ID ENST00000359865, or SOGA2-001.[28]Function[edit]Possible transcription factors[edit]Possible transcription factors for human SOGA2 include:[29]Modulator recognition factor 2cAMP-responsive element binding protein 1alternative splicing variant of FOXP1MDS1\/EVI1-like gene 1Ikaros 2, possible regulator of lymphocyte differentiationInteractions[edit]Protein complex co-immunoprecipitation (Co-IP) experiments revealed interacting proteins such as cell death regulators, ATP-binding cassette (ABC) transporters and protein kinase A binding proteins.[30]The 540 interacting proteins include ABCF1, ACTB, ACTL6A, BCLAF1, BCLAF1, CHEK1, and MAGEE2.[30]K-nearest neighbor analysis by wolf pSort indicates that in humans, SOGA2 is focused mainly in the nucleus, cytoplasm, and the cytonuclearspace. There is a small chance that it is localizes to the golgi.[31]A number of protein interactants were also identified via the STRING database, including MARK2, MARK4, and PPP2R2B.Clinical significance[edit]SOGA2 has no currently known disease associations or mutations.References[edit]^ a b c GRCh38: Ensembl release 89: ENSG00000168502 – Ensembl, May 2017^ a b c GRCm38: Ensembl release 89: ENSMUSG00000052105 – Ensembl, May 2017^ “Human PubMed Reference:”. National Center for Biotechnology Information, U.S. National Library of Medicine.^ “Mouse PubMed Reference:”. National Center for Biotechnology Information, U.S. National Library of Medicine.^ Nagase T; Ishikawa K; Suyama M; Kikuno R; Miyajima N; Tanaka A; Kotani H; Nomura N; Ohara O (April 1999). “Prediction of the coding sequences of unidentified human genes. XI. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro”. DNA Res. 5 (5): 277\u201386. doi:10.1093\/dnares\/5.5.277. PMID\u00a09872452.^ “Entrez Gene: SOGA2”.^ “SOGA1”. NCBI. Retrieved April 27, 2013.^ “SOGA3”. NCBI. Retrieved April 27, 2013.^ a b c “BLAST”. NCBI BLAST. Retrieved April 27, 2013.^ a b “GEO Profile 10132039”. NCBI GEO. Retrieved April 27, 2013.^ a b “NCBI”. National Center for Biotechnology Information. Retrieved 12 May 2013.^ Cowherd RB, Cowerd RB, Asmar MM,  et\u00a0al. (October 2010). “Adiponectin lowers glucose production by increasing SOGA”. Am. J. Pathol. 177 (4): 1936\u201345. doi:10.2353\/ajpath.2010.100363. PMC\u00a02947288. PMID\u00a020813965.^ “CLUSTALW”. SDSC Biology Workbench. Retrieved April 27, 2013.[permanent dead link]^ “CLC Sequence Viewer”. Retrieved 12 May 2011.[permanent dead link]^ Nagase T; Ishikawa K; Suyama M; Kikuno R; Miyajima N; Tanaka A; Kotani H; Nomura N; Ohara O (Jan 2011). “Computational analysis of amino acid composition in human proteins”. Bioinformatics Trends. 6 (1&2): 39\u201343.^ “GeneCards”. Retrieved 9 May 2011.^ “NCBI Conserved Domains”. National Center for Biotechnology Information. Retrieved 12 May 2013.^ “SumoPlot”. ABGENT. Retrieved April 27, 2013.^ “Sulfinator”. expasy. Retrieved April 27, 2013.^ Blom N; Gammeltoft S; Brunak S (December 1999). “Sequence and structure-based prediction of eukaryotic protein phosphorylation sites”. J. Mol. Biol. 294 (5): 1351\u201362. doi:10.1006\/jmbi.1999.3310. PMID\u00a010600390.^ “PELE”. SDSC Biology Workbench. Retrieved 27 April 2013.[permanent dead link]^ “GOR4”. npsa-pbil. Retrieved 27 April 2013.[permanent dead link]^ “SOSUICoil”. bp.nuap.nagoya-u.ac.jp. Archived from the original on 2011-07-22. Retrieved 27 April 2013.^ a b Kelley LA; Sternberg MJ (2009). “Protein structure prediction on the Web: a case study using the Phyre server” (PDF). Nat Protoc. 4 (3): 363\u201371. doi:10.1038\/nprot.2009.2. hdl:10044\/1\/18157. PMID\u00a019247286. S2CID\u00a012497300.^ a b “NCBI Structure”. NCBI. Retrieved May 13, 2013.^ “Unigene”. National Center for Biotechnology Information. Retrieved April 27, 2013.^ “Allen Brain Atlas, SOGA2 microarray experiments”. Allen Brain Atlas. Retrieved April 27, 2013.^ “Ensemble: gene SOGA2”. Ensembl. Retrieved April 27, 2013.^ “El Dorado”. Genomatix. Retrieved May 8, 2013.[permanent dead link]^ a b “Molecular Interaction Database – MINT”. Archived from the original on 6 May 2006. Retrieved 9 May 2011.^ Horton P, Park KJ, Obayashi T,  et\u00a0al. (July 2007). “WoLF PSORT: protein localization predictor”. Nucleic Acids Res. 35 (Web Server issue): W585\u20137. doi:10.1093\/nar\/gkm259. PMC\u00a01933216. PMID\u00a017517783.Further reading[edit]Strausberg RL, Feingold EA, Grouse LH,  et\u00a0al. (2003). “Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences”. Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16899\u2013903. Bibcode:2002PNAS…9916899M. doi:10.1073\/pnas.242603899. PMC\u00a0139241. PMID\u00a012477932.Brajenovic M, Joberty G, K\u00fcster B,  et\u00a0al. (2004). “Comprehensive proteomic analysis of human Par protein complexes reveals an interconnected protein network”. J. Biol. Chem. 279 (13): 12804\u201311. doi:10.1074\/jbc.M312171200. PMID\u00a014676191.Ota T, Suzuki Y, Nishikawa T,  et\u00a0al. (2004). “Complete sequencing and characterization of 21,243 full-length human cDNAs”. Nat. Genet. 36 (1): 40\u20135. doi:10.1038\/ng1285. PMID\u00a014702039.Gerhard DS, Wagner L, Feingold EA,  et\u00a0al. (2004). “The Status, Quality, and Expansion of the NIH Full-Length cDNA Project: The Mammalian Gene Collection (MGC)”. Genome Res. 14 (10B): 2121\u20137. doi:10.1101\/gr.2596504. PMC\u00a0528928. PMID\u00a015489334.Nusbaum C, Zody MC, Borowsky ML,  et\u00a0al. (2005). “DNA sequence and analysis of human chromosome 18”. Nature. 437 (7058): 551\u20135. Bibcode:2005Natur.437..551N. doi:10.1038\/nature03983. PMID\u00a016177791.Nousiainen M, Sillj\u00e9 HH, Sauer G,  et\u00a0al. (2006). “Phosphoproteome analysis of the human mitotic spindle”. Proc. Natl. Acad. Sci. U.S.A. 103 (14): 5391\u20136. Bibcode:2006PNAS..103.5391N. doi:10.1073\/pnas.0507066103. PMC\u00a01459365. PMID\u00a016565220.Beausoleil SA, Vill\u00e9n J, Gerber SA,  et\u00a0al. (2006). “A probability-based approach for high-throughput protein phosphorylation analysis and site localization”. Nat. Biotechnol. 24 (10): 1285\u201392. doi:10.1038\/nbt1240. PMID\u00a016964243. S2CID\u00a014294292.Olsen JV, Blagoev B, Gnad F,  et\u00a0al. (2006). “Global, in vivo, and site-specific phosphorylation dynamics in signaling networks”. Cell. 127 (3): 635\u201348. doi:10.1016\/j.cell.2006.09.026. PMID\u00a017081983. 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