C3orf62

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C3orf62
Identifiers
SymbolC3orf62
Alt. namesCC062, FLJ43654
Entrez375341
HUGO24771
RefSeqNM_198562.21
UniProtQ6ZUJ4
Other data
LocusChr. 3 p21.31{{{LocusSupplementaryData}}}

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.[1] C3orf62 has a KKXX-like motif and is predicted to be localized in the nucleus.[2] Expression of C3orf62 remains highest in whole blood.[3]

Gene

Locus

C3orf62 is mapped to the reverse strand of chromosome 3 at 3p21.31 and spans 9.313 bases.[4] 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.[5][3][6][7][8]

Gene neighborhood

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

File:Gene Neighborhood C3orf62.gif
C3orf62 and its gene neighbors on chromosome 3 from NCBI

Aliases

C3orf62 possesses the following alternate names and synonyms: CC062; FLJ43654.[6][9]

Protein

Primary sequence

C3orf62 human protein (Q6ZUJ4) is 267 amino acids long, and has a molecular mass of 30,194 Daltons.[5] 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.[1] 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.[10]

Name Ensembl Transcript ID[7][3] 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

There are no known transmembrane domains for C3orf62.[9] 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.[11]

Secondary structure

Roughly 7 alpha helices are predicted for C3orf62 through Pele Protein Structure Protein Prediction and strengthened through orthologous secondary structure predictions by Ali2D.[9][12]

Subcellular localization

C3orf62 is predicted to be localized in the nucleus.[2] 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.[2]

Expression

C3orf62 is expressed in more than 30 different tissues; highest expression is in whole blood.[6][3][5] 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.[13] C3orf62 has low expression in brain tissues.

File:C3orf62 Tissue Expression.png
Diagram depicting the expression of C3orf62 in tissues throughout the body

Post-transcriptional modifications

C3orf62 possess two post-translational modifications, both are phosphorylation sites with locations at amino acid 210 and 224.[5] A natural variant is found at amino acid 110 (Glutamic acid (E)--> Lysine K).[8][7]

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.[14]

Regulation of expression

Thirteen promoters have been predicted for C3orf62.[15]

Transcript variants

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.[6] QIAGEN denotes the following as transcription factor binding sites in the C3orf62 promoter: TFCP2, Pax-6, p53, MyoD, YY1, Ik-2, AREB6, IRF-7A3.[3]

Function

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

Interactions

Upwards of 12 interacting proteins have been predicted for C3orf62.[16][17][18] 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.[6]

Clinical significance

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).[19][20][21]

In the gene region, NCBI SNP identified 1,326 SNPS on the reverse minus strand of C3orf62.[22] In the coding region, NCBI SNP identified 147 common SNPs.

Homology

Paralogs

There are no known paralogs of C3orf62.[23]

Orthologs

The ortholog space of C3orf62 is fairly narrow, with the majority of orthologs found in mammals.[23] 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.[23]

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%.[23] 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

The most distant ortholog of C3orf62 are species of fish and amphibians. Orthologs of C3orf62 are not seen in birds, invertebrates, or bacteria.[23]

References

  1. ↑ 1.0 1.1 "SAPS". SDSC Biology Workbench. Retrieved 23 April 2017.
  2. ↑ 2.0 2.1 2.2 "C3orf62 Homo sapiens". PSORT WWW Server.[permanent dead link]
  3. ↑ 3.0 3.1 3.2 3.3 3.4 "Homo sapiens C3orf62". GeneCards. Retrieved 5 February 2017.
  4. ↑ "Homo sapiens C3orf62". NCBI Nucleotide. Retrieved 5 February 2017.
  5. ↑ 5.0 5.1 5.2 5.3 "Homo sapiens C3orf62". NCBI Gene. Retrieved 5 February 2017.
  6. ↑ 6.0 6.1 6.2 6.3 6.4 "Humans 2010-C3orf62". Aceview. Retrieved 5 February 2017.
  7. ↑ 7.0 7.1 7.2 "C3orf62". UniProtKB.
  8. ↑ 8.0 8.1 "C3orf62". Ensembl. Retrieved 5 February 2017.
  9. ↑ 9.0 9.1 9.2 "Human Gene C3orf62". UCSC. Retrieved 5 February 2017.
  10. ↑ "PI". SDSC Biology Workbench.
  11. ↑ "C3orf62". PSORT WWW Server. Retrieved 7 May 2017.[permanent dead link]
  12. ↑ "C3orf62". Ali2D. Retrieved 7 May 2017.
  13. ↑ "C3orf62 GEO Profiles". NCBI GEO. Retrieved 24 April 2017.
  14. ↑ "C3orf62". YingOYang. Retrieved 7 May 2017.
  15. ↑ "C3orf62". Genomatix. Retrieved 7 May 2017.
  16. ↑ "C3orf62". STRING Interaction Network. Retrieved 7 May 2017.
  17. ↑ "C3orf62". BioGRID. Retrieved 7 May 2017.
  18. ↑ "C3orf62". InAct. Retrieved 7 May 2017.
  19. ↑ 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.
  20. ↑ 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.
  21. ↑ 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.
  22. ↑ "C3orf62". NCBI SNP.
  23. ↑ 23.0 23.1 23.2 23.3 23.4 "C3orf62". NCBI BLAST. Retrieved 7 May 2017.
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