C4orf29

Chromosome 4 open reading frame 29
Identifiers
Symbol C4orf29
Entrez 80167
HUGO 26111
RefSeq NP_001034806.1
UniProt Q0P651
Other data
Locus Chr. 4 q28.2

Chromosome 4 open reading frame 29 (C4orf29) is a protein that in Homo sapiens is encoded by the C4orf29 gene.[1]

Gene

C4orf29 is found on the positive strand of the human genome at 4q28.2. It is 74.4 kbp. The gene contains 17 exons.[2] The longest mRNA transcript is composed of 13 exons and is 2200 base pairs.[1]

Homology

Orthologs

Many orthologs to human C4orf29 have been discovered, with the most distant ortholog with high (over 90%) coverage is found in rice Oryza sativa.[4] The protein is not found in fungi. Bacteria of the order Myxobacteria and genus Chitinimonas contain orthologous regions to the C4orf29 protein. The few bacterial homologs indicate a horizontal gene transfer event. The domain of unknown function, DUF2048, is conserved throughout orthologs.

Organism NCBI Accession Number Divergence from Humans (Million Years) Protein Length (Amino Acids) Sequence Identity to Human Sequence Similarity to Human
Human NP_001034806.1 0 414 100% 100%
Dog XP_005631879.1 94.2 484 87% 89%
Canary XP_009094557.1 296 414 75% 87%
Painted Turtle XP_005282815.1 296 464 73% 83%
Ant XP_011141314.1 782 468 46% 64%
Flat Worm NP_492206.1 937 378 33% 50%
Rice NP_001046183.1 1369 366 31% 47%
Cystobacter violaceus WP_043404439.1 2535 321 31% 52%
Tertiary structure of C4orf29 [5]

Protein

C4orf29 codes a 414 amino acid sequence of 46.9 kDa in humans. The predicted isoelectric point is 9.37.[6] The domain of unknown function, DUF2048, is found from amino acid residues 25 to 414 in the precursor C4orf29 protein.[7] This domain is part of the alpha/beta hydrolase superfamily, which comprises enzymes that catalyze fat metabolism. Predicted post-translational modifications include glycosylation at residues Ser287 and Ser319 [8] and sumoylation[9] at the motifs Phe240 to Gly243, Ala377 to Asp340, and Phe408 to Gly411.

Expression

The protein product of C4orf29 in humans is predicted to be a secreted product. It is ubiquitously expressed at low to moderate levels.[10] In humans, the protein is found at high levels the digestive tract and parathyroid gland.[11] The homologous mouse protein 3110057O12Rik is expressed at high levels in the granule layer of the cerebellum.[12]

Alpha actin expression in mouse brain, shown as control.

Clinical significance

C4orf29 contains highly variable numbers of Alu repeats.[13] A low number of Alu repeats in the human C4orf29 protein is associated with increase prevalence of hepatocellular carcinoma (HCC) in Asian populations. This information is used as a genetic marker to determine genetic risk of HCC.[14] Swine muscle transcriptome analysis indicates high expression of C4orf29 in swine with extreme low levels of fatty acid composition.[15]

References

  1. 1 2 "C4orf29". NCBI Gene. NCBI. Retrieved 5 May 2015.
  2. ↑ "C4orf29". NCBI AceView. Retrieved 2015-05-05.
  3. ↑ "C4orf29". GeneCards Human Gene Database.
  4. ↑ "NP_001034806". NCBI Protein BLAST.
  5. ↑ Kelley, LA; Sternberg, MJE. "Protein structure prediction on the web: a case study using the Phyre server". Phyre2. Retrieved 16 Apr 2015.
  6. ↑ "C4orf29 (human)". Phosphosite.org. Retrieved 2015-05-05.
  7. ↑ "uncharacterized protein C4orf29 precursor [Homo sapiens]". NCBI Protein.
  8. ↑ "NetOGlyc4.0 C4orf29". CBS Prediction Servers.
  9. ↑ "C4orf29 Sumoylation". ABGENT.
  10. ↑ "Large-scale analysis of the human transcriptome GDS596". NCBI GeoProfile. Retrieved 2015-05-05.
  11. ↑ "C4orf29". The Human Protein Atlas. Retrieved 2015-05-05.
  12. ↑ "3110057O12Rik". Allen Brain Atlas. Retrieved 2015-05-05.
  13. ↑ Osenberg, Sivan (21 Jun 2010). "Alu Sequences in Undifferentiated Human Embryonic Stem Cells Display High Levels of A-to-I RNA Editing". PLOS ONE 5: e11173. doi:10.1371/journal.pone.0011173.
  14. ↑ Clifford, Robert (23 Nov 2010). "Genetic variations at loci involved in the immune response are risk factors for hepatocellular carcinoma". Hepatology 52 (6): 2034–2043. doi:10.1002/hep.23943.
  15. ↑ Puig-Oliveras, A (June 2014). "Differences in muscle transcriptome among pigs phenotypically extreme for fatty acid composition". PLOS ONE 13 (9): 6. doi:10.1371/journal.pone.0099720. PMC 4057286. PMID 24926690.
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