C3orf38
Identifiers
AliasesC3orf38, chromosome 3 open reading frame 38
External IDsMGI: 1914859 HomoloGene: 27867 GeneCards: C3orf38
Orthologs
SpeciesHumanMouse
Entrez

285237

67609

Ensembl

ENSG00000179021

ENSMUSG00000059920

UniProt

Q5JPI3

Q3TTL0

RefSeq (mRNA)

NM_173824

NM_026273

RefSeq (protein)

NP_776185

NP_080549

Location (UCSC)Chr 3: 88.15 – 88.17 MbChr 16: 64.57 – 64.59 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse

Chromosome 3 open reading frame 38 (C3orf38) is a protein which in humans is encoded by the C3orf38 gene.

Gene

Figure depicting human chromosome 3 and the 3p11.1 location at which the C3orf38 gene is found. Image derived from GeneCards.[5]

The C3orf38 gene is located on chromosome 3 (3p11.1) on the forward strand.[5] It spans 18,771 bases from chr3:88,149,959-88,168,729.[5] It contains 3 exons.[6] Common aliases for this gene are MGC26717, LOC285237, and FLJ54270.[7] Some of the genes neighboring C3orf38 include ZNF654, CGGBP1, and LOC105377202.[8]

Transcripts

C3orf38 Transcripts
Protein Name Gene ID Transcript Accession Length (nt) Length (aa)
uncharacterized protein C3orf38 285237 NM_173824.4 2414 329
uncharacterized protein C3orf38 isoform X1 285237 XM_005264745.5 2356 328

Protein

Multiple sequence alignment of C3orf38 protein in humans and various orthologs showing DUF conservation. MSA created using BoxShade tools.

The C3orf38 protein is 329 amino acids in length.[9] A large domain of unknown function, DUF4518, encompasses majority of the C3orf38 protein.[9] This domain is a part of the protein family pfam15008, which is thought to be involved in apoptosis regulation.[10] This pfam15008 is the only member of the cl20886 superfamily.[10] While the C3orf38 protein does not have any abnormal amino acid abundance as a whole, the DUF4518 has a high abundance of histidines and a low abundance of serines, according to compositional analysis.[11] The predicted molecular weight of the entire C3orf38 protein is 37.0 kD and the isoelectric point is 6.01.[12] The DUF4518 contained inside the C3orf38 protein has a predicted molecular weight of 31 kD and an isoelectric point of 6.49.[12]

Regulation

Gene Level Regulation

There have been a number of potential promoters identified for the C3orf38 gene, which are described in the table below.[13]

Potential Promoters for the C3orf38 Gene[13]
Promoter Start End Length (bp) Transcripts
GXP_203118 88148634 88150046 1413 GXT_23216585, GXT_22791246, GXT_2803824, GXT_26239186
GXP_9795962 88148768 88149807 1040 no transcript assigned; promoter based on comparative genomics
GXP_9795963 88148794 88150027 1234 no transcript assigned; promoter based on comparative genomics
GXP_3194836 88149604 88150643 1040 GXT_24485561

The C3orf38 gene exhibits ubiquitous expression in human tissues.[14]

Normal human tissue expression profiling (HG-U95E) for the C3orf38 gene. Data pictured is captured from the NCBI GEO database.[14]

Protein Level Regulation

The C3orf38 protein is expected to be found with the highest confidence in the cytoplasm.[15] This finding is supported by examination of an array of C3orf38 orthologs.[15]

There are several well conserved post translation modification sites found amongst the human C3orf38 protein and its orthologs, which are depicted in the table below.[16] Majority of these PTMs are PKC phosphorylation sites.[16] Additionally, two confirmed active sites are located in the C3orf38 protein. The first is an aldehyde dehydrogenases glutamic acid active site located from amino acids 1-8.[16] The second site is a eukaryotic thiol (cysteine) proteases histidine active site located from amino acids 227-237.[16]

Predicted cellular localization of C3orf38 in humans and several orthologs. Localization predictions gathered from PSORT II Prediction tool.[15]
Conserved Post Translational Modification Sites
PTM Protein Location (aa)
Myristyl site 235-240
PKC phosphorylation site 34-36
PKC phosphorylation site 86-88
PKC phosphorylation site 199-201
PKC phosphorylation site 265-267

Homology/evolution

Orthologs for the C3orf38 protein can be found in mammals, reptiles, birds, amphibians, fish, and invertebrates using BLAST searches.[17] A selection of these orthologs can be found in the ortholog table below. There are no paralogs.[17] Additionally, by comparing sequences of C3orf38 protein with cytochrome C and fibrinogen alpha proteins, a moderate rate of evolution was determined for the C3orf38 protein.

C3orf38 Ortholog Table[17][18][19]
Genus, species Common Name Taxonomic Group Divergence Date (MYA) Accession Number Sequence Length (aa) Sequence Identity (%) Sequence Similarity (%)
Mammals Homo sapiens Human Primates 0 NP_776185.2 329 100 100
Pan paniscus Bonobo Primates 6.7 XP_003831564.1 329 99.4 99.7
Puma concolor Puma Carnivora 96 XP_025769652.1 348 79.8 86.6
Reptiles Mauremys reevesii Reeve's Turtle Testudines 312 XP_039379932.1 315 55.7 70.5
Chelonoidis abingdonii Abingdon Island Giant Tortoise Testudines 312 XP_032650981.1 304 55.4 69.9
Birds Strigops habroptila Kakapo Psittaciformes 312 XP_030327387.1 309 52.1 66.3
Taeniopygia guttata Zebra Finch Passeriformes 312 XP_002190058.5 306 51 63.9
Gallus gallus Chicken Galliformes 312 XP_004938363.2 312 44.2 59.9
Amphibians Rhinatrema bivittatum Two-Lined Caecilian Gymnophiona 351.8 XP_029434832.1 289 49.7 64.5
Bufo bufo Common Toad Anura 351.8 XP_040279187.1 289 43.9 62.1
Xenopus tropicalis Tropical Clawed Frog Anura 351.8 XP_017946806.1 261 38.6 54.8
Fish Chelmon rostratus Copperband Butterflyfish Perciformes 435 XP_041807133.1 302 42.7 58.2
Coregonus clupeaformis Lake Whitefish Salmoniformes 435 XP_041700482.1 308 42.4 60.6
Carcharodon carcharias Great White Shark Lamniformes 473 XP_041066710.1 308 45 59.8
Amblyraja radiata Thorny Skate Rajiformes 473 XP_032888490.1 382 32.5 46.5
Invertebrates Lytechinus variegatus Sea Urchin Temnopleuroida 684 XP_041465399.1 312 36.4 48.3
Patiria miniata Bat Star Valvatida 684 XP_038067113.1 294 34.1 46.2
Cryptotermes secundus Termite Blattodea 797 XP_023724689.1 296 30.1 48
Crassostrea virginica Eastern Oyster Ostreidae 797 XP_022335568.1 340 29.6 46.5
Diabrotica virgifera Western Corn Rootworm Coleoptera 797 XP_028133096.1 284 26.9 43.6
Acropora millepora Branching Stony Coral Scleractinia 824 XP_029194133.1 288 32.6 50.9
Figure showing an evolution rate graph comparing the C3orf38, cytochrome C, and fibrinogen alpha proteins. Noting the cytochrome C to be a relatively slow-evolving protein and the fibrinogen alpha to be a relatively fast-evolving protein, it is clear that C3orf38 protein evolves at a comparatively moderate rate.

Function

Although investigation into the function of the C3orf38 gene is ongoing, a couple studies have granted valuable insights into its role. One study has identified C3orf38 as a candidate proapoptotic gene.[20] Another study identified C3orf38 as a top candidate tumor suppressor gene (TSG).[21]

Interacting proteins

Of the various proteins C3orf38 protein interacts with, two are particularly interesting seeing as C3orf38 is a candidate proapoptotic and tumor suppressor gene. First, BAG family molecular chaperone regulator 4 (BAG4) is an anti-apoptotic protein that is known to interact with a number of apoptosis and growth-related proteins.[22] Second, DnaJ Heat Shock Protein Family Member B4 (DNAJB4) is a member of the heat shock protein-40 family (Hsp40), a molecular chaperone, and a tumor suppressor (specifically for colorectal carcinoma).[23]

References

  1. 1 2 3 GRCh38: Ensembl release 89: ENSG00000179021 - Ensembl, May 2017
  2. 1 2 3 GRCm38: Ensembl release 89: ENSMUSG00000059920 - 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 2 3 "C3orf38". www.genecards.org. Archived from the original on 2011-11-29. Retrieved 2021-09-30.
  6. ↑ "Homo sapiens chromosome 3 open reading frame 38 (C3orf38), mRNA". 2021-04-16. {{cite journal}}: Cite journal requires |journal= (help)
  7. ↑ "AceView: Gene:C3orf38, a comprehensive annotation of human, mouse and worm genes with mRNAs or ESTsAceView". www.ncbi.nlm.nih.gov. Retrieved 2021-09-30.
  8. ↑ "C3orf38 chromosome 3 open reading frame 38 [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2021-12-17.
  9. 1 2 "uncharacterized protein C3orf38 [Homo sapiens] - Protein - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2021-09-30.
  10. 1 2 "CDD Conserved Protein Domain Family: DUF4518". www.ncbi.nlm.nih.gov. Retrieved 2021-12-17.
  11. ↑ "SAPS < Sequence Statistics < EMBL-EBI". www.ebi.ac.uk. Retrieved 2021-12-17.
  12. 1 2 "ExPASy - Compute pI/Mw tool". web.expasy.org. Retrieved 2021-12-17.
  13. 1 2 "Genomatix Software Suite". Archived from the original on 2012-01-14.
  14. 1 2 "2928464 - GEO Profiles - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2021-12-18.
  15. 1 2 3 "PSORT II Prediction". psort.hgc.jp. Retrieved 2021-12-18.
  16. 1 2 3 4 "Motif Scan". myhits.sib.swiss. Retrieved 2021-12-18.
  17. 1 2 3 "Protein BLAST: search protein databases using a protein query". blast.ncbi.nlm.nih.gov. Retrieved 2021-12-17.
  18. ↑ "EMBOSS Needle < Pairwise Sequence Alignment < EMBL-EBI". www.ebi.ac.uk. Retrieved 2021-12-17.
  19. ↑ "TimeTree :: The Timescale of Life". timetree.org. Retrieved 2021-12-17.
  20. ↑ Park, Kyung Mi; Kang, Eunju; Jeon, Yeo-Jin; Kim, Nayoung; Kim, Nam-Soon; Yoo, Hyang-Sook; Yeom, Young Il; Kim, Soo Jung (2007-04-30). "Identification of novel regulators of apoptosis using a high-throughput cell-based screen". Molecules and Cells. 23 (2): 170–174. ISSN 1016-8478. PMID 17464193.
  21. ↑ Cody, Neal A. L.; Shen, Zhen; Ripeau, Jean-Sebastien; Provencher, Diane M.; Mes-Masson, Anne-Marie; Chevrette, Mario; Tonin, Patricia N. (2009). "Characterization of the 3p12.3-pcen region associated with tumor suppression in a novel ovarian cancer cell line model genetically modified by chromosome 3 fragment transfer". Molecular Carcinogenesis. 48 (12): 1077–1092. doi:10.1002/mc.20535. ISSN 1098-2744. PMID 19347865. S2CID 10259832.
  22. ↑ "BAG4". www.genecards.org. Archived from the original on 2011-11-27. Retrieved 2021-12-18.
  23. ↑ "DNAJB4". www.genecards.org. Archived from the original on 2021-12-18. Retrieved 2021-12-18.
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