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C3orf62

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C3orf62
Identifiers
AliasesC3orf62, chromosome 3 open reading frame 62, MAPS
External IDsMGI: 2148248; HomoloGene: 14230; GeneCards: C3orf62; OMA:C3orf62 - orthologs
Orthologs
SpeciesHumanMouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_198562

NM_053216

RefSeq (protein)

NP_940964

NP_444446

Location (UCSC)Chr 3: 49.27 – 49.28 MbChr 9: 108.27 – 108.29 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse
C3orf62
Identifiers
SymbolC3orf62
Alt. namesCC062, FLJ43654
NCBI gene375341
HGNC24771
RefSeqNM_198562.21
UniProtQ6ZUJ4
Other data
LocusChr. 3 p21.31{{{LocusSupplementaryData}}}
Search for
StructuresSwiss-model
DomainsInterPro

Chromosome 3 open reading frame 62 (C3orf62) is a protein that in humans is encoded by the C3orf62 gene. C3orf62 is a glycine-depleted protein relative to the amount of glycine in proteins in the rest of the genome.[5] C3orf62 has a KKXX-like motif and is predicted to be localized in the nucleus.[6] Expression of C3orf62 remains highest in whole blood.[7]

Gene

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Locus

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C3orf62 is mapped to the reverse strand of chromosome 3 at 3p21.31 and spans 9,313 bases.[8] C3orf62 starts at 49,268,597 base pairs from the terminus of the short arm (pter) and ending at 49,277,909 base pairs pter. This gene is known to have 3 exons, 4 transcripts, and 37 orthologues.[9][7][10][11][12]

Gene neighborhood

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C3orf62 is flanked by Ubiquitin Specific Protease 4 (USP4) and Coil-Coiled Domain Containing 36 (CCDC36).

C3orf62 and its gene neighbors on chromosome 3 from NCBI

Aliases

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C3orf62 possesses the following alternate names and synonyms: CC062; FLJ43654.[10][13]

Protein

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Primary sequence

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C3orf62 human protein (Q6ZUJ4) is 267 amino acids long, and has a molecular mass of 30,194 daltons.[9] The isoelectric point of C3orf62 is roughly 5.2. The unmodified C3orf62 protein is a “glycine depleted protein” relative to amounts of glycine in proteins in the rest of the genome.[5] It appears that glycine is evenly distributed throughout the C3orf62 sequence with no preference of areas to cluster in. Before post-translational modifications, C3orf62 is an acidic protein. No charge clusters are present in C3orf62, and no specific spacing of cysteine is found. The isoelectric point of C3orf62 is 5.211000.[14]

Name Ensembl Transcript ID[11][7] Base Pairs Protein Biotype CCDS Uniprot Refseq
C3orf62-001 ENST00000343010.7 4235 267aa Protein encoding CCDS2792 Q6ZUJ4 NM_198562, NP_940964
C3orf62-004 ENST00000436325.1 581 190aa Protein encoding - C9JW57 -
C3orf62-003 ENST00000424960.1 602 98aa Nonsense mediated decay - H7BZX3 -
C3orf62-002 ENST00000479673.1 3330 No protein Retained intron - - -

Domains and motifs

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There are no known transmembrane domains for C3orf62.[13] C3orf62 has a KKXX-like motif in the C-terminus meaning C3orf62 may be responsible for retrieval of endoplasmic reticulum (ER) membrane proteins from the Golgi apparatus.[15]

Secondary structure

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Roughly 7 alpha helices are predicted for C3orf62 through Pele Protein Structure Protein Prediction and strengthened through orthologous secondary structure predictions by Ali2D.[13][16]

Subcellular localization

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C3orf62 is predicted to be localized in the nucleus.[6] The k-nearest neighbors algorithm predicts C3orf62 to be classified as follows: k=9/23; 69.6% nuclear, 13.0% mitochondrial, 13.0% cytoskeletal, 4.3% cytoplasmic.[6]

Expression

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C3orf62 is expressed in more than 30 different tissues; highest expression is in whole blood.[10][7][9] Specifically, highest expression of C3orf62 is in the following tissues: lung, tonsil, trachea, small intestine, mammary gland, and salivary gland. Through analysis of various microarray studies, C3orf62 is found to have consistently high expression compared to other genes tested in the datasets.[17] C3orf62 has low expression in brain tissues.

Diagram depicting the expression of C3orf62 in tissues throughout the body

Post-transcriptional modifications

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C3orf62 possess two post-translational modifications, both are phosphorylation sites with locations at amino acid 210 and 224.[9] A natural variant is found at amino acid 110 (Glutamic acid (E)--> Lysine K).[12][11]

It appears as though C3orf62 may have a YinOYang site at residue 115, meaning that this Threonine residue is predicted to be O-GlycNAcylated as well as phosphorylated. This site may be reversibly and dynamically modified by O-GlcNAc or Phosphate groups at different times in the cell.[18]

Regulation of expression

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Thirteen promoters have been predicted for C3orf62.[19]

Transcript variants

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Transcription of C3orf62 produces 5 alternatively spliced variants and 1 unspliced form. Of the four splice variants, two of them are protein coding, one is nonsense meditated decay, and one is a retained intron.[10] QIAGEN denotes the following as transcription factor binding sites in the C3orf62 promoter: TFCP2, Pax-6, p53, MyoD, YY1, Ik-2, AREB6, IRF-7A3.[7]

Function

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Function of C3orf62 is not currently understood by the scientific community.

Interactions

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Upwards of 12 interacting proteins have been predicted for C3orf62.[20][21][22] Interacting proteins with the strongest confidence to interact with C3orf62 include: HAUS augmin-like complex subunit 1 (HAUS-1), Inhibitor of growth protein 5 (ING5), Thioredoxin domain-containing protein 9 (TXNDC9), and MORF4-family associated proteins (MORF4L1, MFRAP1).

Chemicals known to interact with C3orf62 include the following: Aflatoxin B1, Hydralazine, Valproic acid, and Decitabine.[10]

Clinical significance

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Interstitial deletions of chromosome 3 are rare, and only a few patients with a microdeletion of 3p21.31 have been reported to date. Characteristic clinical features found in patients with a microdeletion of 3p21.31 include developmental delay and distinctive facial features (including arched eyebrows, hypertelorism, epicanthus, and micrognathia).[23][24][25]

In the gene region, NCBI SNP identified 1,326 SNPS on the reverse minus strand of C3orf62.[26] In the coding region, NCBI SNP identified 147 common SNPs.

Homology

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Paralogs

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There are no known paralogs of C3orf62.[27]

Orthologs

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The ortholog space of C3orf62 is fairly narrow, with the majority of orthologs found in mammals.[27] A small fraction of orthologs have also been found in the following classes: Reptila, Sarcopterygii, and Actinoptergii.

The groupings of nearly all Mammalia ortholog sequences of C3orf62 are as follows: E-value: 2e-94 to 1e-169; similarity 56-84%. Mammals in this group consist largely of primates but also include the following orders: Perissodactyla, Rodentia, Carnivora, Proboscidea, Cetartiodactyla, Cingulata, Artiodactyla, Eulipotyphla, Diselphimorphia, and Afrosoricida.[27]

More distantly related ortholog sequences of C3orf62 include organisms from classes Reptilia, Sarcopterygii, and Actinopterygii ranging from an E-value of 8e-10 to 3e-59 with similarity of 24-39%.[27] Organisms in this grouping consist of Testudines, Coelacanthiformes, Squamata, and Osteoglossiformes orders. No ortholog sequences of C3orf62 were found for the following life forms: Bacteria, archaea, protist, plant, fungus, trichoplax, invertebrate, amphibian, or bird.

Genus and Species Common Name Class Accession Percent Identity
Homo sapiens Human Mammalia NP_940964 100
Microcebus murinus Grey Mouse Lemur Mammalia XP_012626718 88
Propithecus coquereli Coquerel's sifaka (lemur) Mammalia XP_012510880 86.9
Equus caballus Horse Mammalia NP_001295877 84.3
Loxodonta Africana African elephant Mammalia XP_003409711 83.2
Castor Canadensis North American Beaver Mammalia XP_020037316 81.6
Otolemur garnettii Garnett's Greater Galago Mammalia XP_003800633 81.6
Camelus bactrianus Bactrian camel Mammalia XP_010967491.1 78.3
Ailuropoda melanoleuca Giant Panda Mammalia XP_019656626 77.7
Canis lupus familiaris Dog Mammalia XP_003432924 77.2
Vicugna pacos Alpaca Mammalia XP_006196356 77.2
Condylura cristata Star-nosed mole Mammalia XP_012575760 76.8
Felis catus Cat Mammalia XP_003982269 75.1
Pteropus vampyrus Large flying fox Mammalia XP_011373720 73.3
Pantholops hodgsonii Tibetan antelope Mammalia XP_005969318 72.6
Ictidomys tridecemlineatus Thirteen lines ground squirrel Mammalia XP_005326967 71
Sorex araneus Common Shrew Mammalia XP_012789682 69.5
Monodelphis domestica Gray short-tailed opossum Mammalia XP_001367907 65.4
Echinops telfairi Lesser Hedgehog Tenrec Mammalia XP_004715283 63.7
Orcinus orca Killer whale Mammalia XP_004283985 61.2
Dasypus novemcinctus Nine banded armadillo Mammalia XP_004451950 58.2
Dipodomys ordii Ord's Kangaroo Rat Mammalia XP_012883511 56.3
Myotis lucifugus Little Brown Myotis Mammalia XP_006107033 39.3
Pelodiscus sinensis Chinese softshell turtle Reptillia XP_014426235 38.5
Chelonia mydas Green Sea Turtle Reptillia XP_007061837 37.1
Latimeria chalumnae West Indian Ocean coelacanth (fish) Sarcopterygii XP_005992740 35.3
Anolis carolinensis Green anole (lizard) Reptillia XP_008103227 33.1
Gekko japonicus Japanese Gecko Reptillia XP_015262861 30.1

Phylogeny

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The most distant ortholog of C3orf62 are species of fish and amphibians. Orthologs of C3orf62 are not seen in birds, invertebrates, or bacteria.[27]

References

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  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000188315Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000032611Ensembl, 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. ^ a b "SAPS". SDSC Biology Workbench. Retrieved 23 April 2017.
  6. ^ a b c "C3orf62 Homo sapiens". PSORT WWW Server.[permanent dead link]
  7. ^ a b c d e "Homo sapiens C3orf62". GeneCards. Retrieved 5 February 2017.
  8. ^ "Homo sapiens C3orf62". NCBI Nucleotide. Retrieved 5 February 2017.
  9. ^ a b c d "Homo sapiens C3orf62". NCBI Gene. Retrieved 5 February 2017.
  10. ^ a b c d e "Humans 2010-C3orf62". Aceview. Retrieved 5 February 2017.
  11. ^ a b c "C3orf62". UniProtKB.
  12. ^ a b "C3orf62". Ensembl. Retrieved 5 February 2017.
  13. ^ a b c "Human Gene C3orf62". UCSC. Retrieved 5 February 2017.
  14. ^ "PI". SDSC Biology Workbench.
  15. ^ "C3orf62". PSORT WWW Server. Retrieved 7 May 2017.[permanent dead link]
  16. ^ "C3orf62". Ali2D. Archived from the original on 22 December 2016. Retrieved 7 May 2017.
  17. ^ "C3orf62 GEO Profiles". NCBI GEO. Retrieved 24 April 2017.
  18. ^ "C3orf62". YingOYang. Retrieved 7 May 2017.
  19. ^ "C3orf62". Genomatix. Archived from the original on 2 December 2021. Retrieved 7 May 2017.
  20. ^ "C3orf62". STRING Interaction Network. Retrieved 7 May 2017.
  21. ^ "C3orf62". BioGRID. Retrieved 7 May 2017.
  22. ^ "C3orf62". InAct. Retrieved 7 May 2017.
  23. ^ Haldeman-Englert CR, Gai X, Perin JC, Ciano M, Halbach SS, Geiger EA, McDonald-McGinn DM, Hakonarson H, Zackai EH, Shaikh TH (13 Dec 2008). "A 3.1-Mb microdeletion of 3p21.31 associated with cortical blindness, cleft lip, CNS abnormalities, and developmental delay". European Journal of Medical Genetics. 52 (4): 265–8. doi:10.1016/j.ejmg.2008.11.005. PMC 4391973. PMID 19100872.
  24. ^ Eto K, Sakai N, Shimada S, Shioda M, Ishigaki K, Hamada Y, Shinpo M, Azuma J, Tominaga K, Shimojima K, Ozono K, Osawa M, Yamamoto T (December 2013). "Microdeletions of 3p21.31 characterized by developmental delay, distinctive features, elevated serum creatine kinase levels, and white matter involvement". American Journal of Medical Genetics. Part A. 161A (12): 3049–56. doi:10.1002/ajmg.a.36156. PMID 24039031. S2CID 272908.
  25. ^ Lovrecic L, Bertok S, Žerjav Tanšek M (May 2016). "A New Case of an Extremely Rare 3p21.31 Interstitial Deletion". Molecular Syndromology. 7 (2): 93–8. doi:10.1159/000445227. PMC 4906427. PMID 27385966.
  26. ^ "C3orf62". NCBI SNP.
  27. ^ a b c d e "C3orf62". NCBI BLAST. Retrieved 7 May 2017.