C3orf62

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C3orf62
Identifiers
Symbol?
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.
  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.
  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, Chad; Gai, Xiaowu; Perin, Juan Carlos; Ciano, Melissa; Halbach, Sara; Geiger, Elizabeth; McDonald-McGinn, Donna; Hakonarson, Hakon; Zackai, Elaine; Shaikh, Tamim (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. Retrieved 7 May 2017.
  20. Eto, K; Sakai, N; Shioda, M; Ishigaki, K; Hamada, Y; Shinpo, M; Azuma, J; Tominaga, K; Shimojima, K; Ozono, K; Osawa, M; Yamamoto, T (16 Aug 2013). "Microdeletions of 3p21.31 characterized by developmental delay, distinctive features, elevated serum creatine kinase levels, and white matter involvement". Wiley Online Library. American Journal of Medical Genetics. doi:10.1002/ajmg.a.36156. Retrieved 7 May 2017.
  21. Lovrecic, Luca; Bertok, Sara; Tansek, Moica Zeriav (19 Apr 2016). "A New Case of an Extremely Rare 3p21.31 Interstitial Deletion". PubMed. Molecular Syndromology. doi:10.1159/000445227. Retrieved 7 May 2017.
  22. "C3orf62". NCBI SNP.
  23. 23.0 23.1 23.2 23.3 23.4 "C3orf62". NCBI BLAST. Retrieved 7 May 2017.