Wikipedia

SHOC1

(Redirected from C9orf84)

Shortage In Chiasmata 1, also known as SHOC1, is a protein that in humans is encoded by the SHOC1 gene.

SHOC1
Identifiers
AliasesSHOC1, chromosome 9 open reading frame 84, ZIP2H, ZIP2, shortage in chiasmata 1, C9orf84, MZIP2
External IDsOMIM: 618038 MGI: 2140313 HomoloGene: 79783 GeneCards: SHOC1
Orthologs
SpeciesHumanMouse
Entrez

158401

100155

Ensembl

ENSG00000165181

ENSMUSG00000038598

UniProt

Q5VXU9

A2ALV5

RefSeq (mRNA)

NM_001080551
NM_173521
NM_001378211
NM_001378212

NM_001033200
NM_001370843

RefSeq (protein)

NP_001074020
NP_775792
NP_001365140
NP_001365141

NP_001357772

Location (UCSC)Chr 9: 111.69 – 111.8 MbChr 4: 59.04 – 59.14 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse

Gene edit

The chromosomal locus of SHOC1 is 9q31.3, which it shares with at least 115 other protein encoding genes, and it is located on the negative strand.[5][6] In humans it contains 34 exons, and it is 108,834 base pairs long, including introns and exons. C9orf84 is located between the protein encoding genes GNG10 and UGCG. When this gene is transcribed in humans, it most often forms a mRNA which is 4,721 base pairs long and contains 26 exons. There are at least 13 alternate splice forms of C9orf84, with more predicted.[7]

Protein edit

SHOC1 in humans has at least 6 alternate isoforms, with at least 10 more predicted.[8] The primarily used sequence in humans is C9orf84 Isoform 1. This isoform is 1444 aa long, contains 26 exons, has a predicted molecular weight of 165.190 kDa, and a predicted pI of 5.10.[9]

SHOC1 has been shown to undergo phosphorylation.[10] It is predicted that C9orf84 undergoes several other post-translational modifications, including glycosylation and o-linked glycosylation, and it contains leucine-rich nuclear export signals.[11][12][13] Compared to the generic reference set swp23s.q, the primary structure of the protein is deficient in the amino acid grouping AGP (alanine, glycine, proline), and contains more acidic amino acids (glutamate, aspartate) than basic amino acids (lysine, arginine).[14] This is true for the protein in all vertebrates. In the human Isoform 1, there have been 220 identified single nucleotide polymorphisms detected in the coding region, but none have currently been linked to human disease.[15] The secondary structure of this protein is predicted to be mainly alpha-helices in roughly the first two thirds of the protein, and coils in the last third.[16] It is predicted that this protein is localized in the nucleus.[17]

Expression edit

SHOC1 is ubiquitously expressed in most tissues with higher than average expression in the testes, the kidney, the thymus, and the adrenal gland.[18][19]

The promoter for SHOC1 Isoform 1 in humans is 639 bp long and overlaps with the 5’ untranslated region of the gene. There are four alternate promoters that promote different transcript variants.[20]

Interactions edit

SHOC1 has been experimentally determined, through a two hybrid pooling approach, to interact with methionine aminopeptidase, a protein encoded by the maP3 gene in Bacillus anthracis.[21]

Several of the most common and most conserved transcription factor binding sites families that are predicted to be found in C9orf84's promoter region are ETS1 factors, Ccaat/Enhancer Binding Proteins, and Lymphoid enhancer-binding factor 1.[22] ETS1, Ccaat-enhancer-binding proteins, and Lymphoid enhancer-binding factor 1 are all related to immunity.

Evolutionary history edit

This gene is found in all vertebrates, and some invertebrates. The most distant ortholog detectable by NCBI BLAST is in Nematostella vectensis (starlet sea anemone).[23] The closest plant ortholog to C9orf84 is the SHOC1 protein in Arabidopsis thaliana.[24] C9orf84 is not very well conserved even among mammals.

Clinical significance edit

SHOC1 is highly upregulated in psoriasis patients with lesional skin as opposed to psoriasis patients with non-lesional skin and non-psoriasis patients.[25]

References edit

  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000165181 – Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000038598 – Ensembl, May 2017
  3. ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. ^ "1) C9orf84 chromosome 9 open reading frame 84 [ Homo sapiens (human) ]". National Center for Biotechnology Information.
  6. ^ "Homo sapiens (human) Map Location: 9q31". GenScript. Archived from the original on 2015-09-24. Retrieved 2015-05-09.
  7. ^ "Homo sapiens complex locus C9orf84, encoding chromosome 9 open reading frame 84". AceView.
  8. ^ "Protein Search C9orf84". National Center for Biotechnology Information.
  9. ^ "Compute pI/MW". ExPASy.
  10. ^ Wu X, Tian L, Li J, Zhang Y, Han V, Li Y, Xu X, Li H, Chen X, Chen J, Jin W, Xie Y, Han J, Zhong CQ (December 2012). "Investigation of receptor interacting protein (RIP3)-dependent protein phosphorylation by quantitative phosphoproteomics". Molecular & Cellular Proteomics. 11 (12): 1640–51. doi:10.1074/mcp.M112.019091. PMC 3518118. PMID 22942356.
  11. ^ "NetGlycate". Center for Biological Sequence Analysis.
  12. ^ "NetOGlyc". Center for Biological Sequence Analysis.
  13. ^ "NetNES". Center for Biological Sequence Analysis.
  14. ^ "SAPS". SDSC Biology WorkBench.[permanent dead link]
  15. ^ "SNP linked to Gene (geneID:158401) Via Contig Annotation". NCBI dbSNP.
  16. ^ "PELE". SDSC Biology WorkBench.[permanent dead link]
  17. ^ "PSORTII". PSORT.
  18. ^ Dezso Z, Nikolsky Y, Sviridov E, Shi W, Serebriyskaya T, Dosymbekov D, Bugrim A, Rakhmatulin E, Brennan RJ, Guryanov A, Li K, Blake J, Samaha RR, Nikolskaya T (November 2008). "A comprehensive functional analysis of tissue specificity of human gene expression". BMC Biology. 6: 49. doi:10.1186/1741-7007-6-49. PMC 2645369. PMID 19014478.
  19. ^ Shyamsundar R, Kim YH, Higgins JP, Montgomery K, Jorden M, Sethuraman A, van de Rijn M, Botstein D, Brown PO, Pollack JR (2005). "A DNA microarray survey of gene expression in normal human tissues". Genome Biology. 6 (3): R22. doi:10.1186/gb-2005-6-3-r22. PMC 1088941. PMID 15774023.
  20. ^ "ElDorado". Genomatix.[permanent dead link]
  21. ^ Dyer MD, Neff C, Dufford M, Rivera CG, Shattuck D, Bassaganya-Riera J, Murali TM, Sobral BW (August 2010). "The human-bacterial pathogen protein interaction networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis". PLOS ONE. 5 (8): e12089. Bibcode:2010PLoSO...512089D. doi:10.1371/journal.pone.0012089. PMC 2918508. PMID 20711500.
  22. ^ "MatInspector". Genomatix.[permanent dead link]
  23. ^ "BLAST". National Center for Biotechnology Information.
  24. ^ Macaisne N, Novatchkova M, Peirera L, Vezon D, Jolivet S, Froger N, Chelysheva L, Grelon M, Mercier R (September 2008). "SHOC1, an XPF endonuclease-related protein, is essential for the formation of class I meiotic crossovers". Current Biology. 18 (18): 1432–7. Bibcode:2008CBio...18.1432M. doi:10.1016/j.cub.2008.08.041. PMID 18812090. S2CID 16418136.
  25. ^ Nair RP, Duffin KC, Helms C, Ding J, Stuart PE, Goldgar D, Gudjonsson JE, Li Y, Tejasvi T, Feng BJ, Ruether A, Schreiber S, Weichenthal M, Gladman D, Rahman P, Schrodi SJ, Prahalad S, Guthery SL, Fischer J, Liao W, Kwok PY, Menter A, Lathrop GM, Wise CA, Begovich AB, Voorhees JJ, Elder JT, Krueger GG, Bowcock AM, Abecasis GR (February 2009). "Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways". Nature Genetics. 41 (2): 199–204. doi:10.1038/ng.311. PMC 2745122. PMID 19169254.
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