C12orf50
| C12orf50 | |||||||||||||||||||||||||||||||||||||||||||||||||||
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| Aliases | C12orf50, chromosome 12 open reading frame 50 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| External IDs | MGI: 1913855 HomoloGene: 45135 GeneCards: C12orf50 | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Chromosome 12 Open Reading Frame 50 (C12orf50) is a protein-encoding gene which in humans encodes for the C12orf50 protein. The accession id for this gene is NM_152589. The location of C12orf50 is 12q21.32. It covers 55.42 kb, from 88429231 to 88373811 (NCBI 37, August 2010), on the reverse strand.[5] Some of the neighboring genes to C12orf50 are RPS4XP15, LOC107984542, and C12orf29.[6] RPS4XP15 is upstream C12orf50 and is on the same strand. LOC107984542 and C12orf29 are both downstream. LOC107984542 is on the opposite strand while C12orf29 is on the same strand. C12orf50 has six isoforms. This page is focusing on isoform X1. C12orf50 isoform X1 is 1711 nucleotides long and has a protein with a length of 414 aa.
Function[edit]
The ontology points to the function of C12orf50 is to enable mRNA and protein binding.[6] It also is involved in poly(A)+ mRNA export from the nucleus.
Isoforms[edit]
The C12orf50 gene has 6 isoforms.
| Isoform | NCBI Accession | mRNA length (nt) | Protein length (aa) | Features |
|---|---|---|---|---|
| X1 | NM_152589.3 | 1711 | 414 | Longest protein with a zinc finger |
| X2 | NM_001363616.2 | 1669 | 375 | |
| X3 | XM_017018887.1 | 1940 | 468 | Longest protein without a zinc finger |
| X4 | XM_017018888.2 | 1550 | 375 | |
| X5 | XM_011537985.1 | 3879 | 395 | Longest mRNA |
| X6 | XM_024448868.1 | 1577 | 374 |
Gene expression[edit]
In an analysis of human tissues with specific expression by the genome, RNA-seq was performed on tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity protein-coding genes found that the expression of C12orf50 is very low in most human tissues with the exception of the testis.[7] C12orf50’s expression was restricted towards testis.[8]
Protein[edit]
Uncharacterized protein Chromosome 12 Open Reading Frame 50 is a protein in humans, encoded by the C12orf50 gene. The protein accession id is Q8NA57. The protein has a length of 414aa. The predicted mass of the protein is 47.2 kDa.[9] The protein includes a CCCH-type Zn Finger Domain.[10] The protein has a CCCH-type Zn Finger Domain with a C-X8-C-X5-C-X3-H motif. The domain starts at the beginning of the protein and goes to the 44th amino acid. The protein also has three disordered regions from the 136th amino acid to 168th with of length of 33 aa, 297th to 333rd with a length of 37 aa, and 346th to 414th with a length of 69 aa.[11] The predicted molecular weight is 47.3 kDa and the predicted isoelectric point is 8.79.
Structure[edit]
The predicted tertiary structure for C12orf50 has two beta-sheets towards the beginning of the protein in the zinc finger domain and a helix from 106-124aa.[12] These are conserved throughout mammalian orthologs. There is also a large number of coiled regions. The promoter, 3’ UTR region, and 5’ UTR are very well conserved. There is a negative cluster (acidic domain) before and at the beginning of the helix from amino acid 87 to 111.[13]
Localization[edit]
There is a 47.8% probability of being in the nucleus and a 30.4% probability of being in the cytoplasm.[14] This was confirmed by immunohistochemistry and immunofluorescence by Sigma-Aldrich showing positivity in both the nucleus and cytoplasm.[15] There is a nuclear location signal and acidic domain. The orthologs also confirm that C12orf50 is localized in the nucleus and cytoplasm.
Protein Interactions[edit]
There are two proteins (GAPDHS and GOLGA2) that interact with C12orf50. Glyceraldehyde-3-phosphate dehydrogenase, spermatogenic (GAPDHS) enzyme may play an important role in regulating the switch between different energy-producing pathways, and it is required for sperm motility and male fertility.[16]
Post-translation Modifications[edit]
C12orf50 has been predicted to undergo various phosphorylation, c-mannosylation, and O-glycosylations. The phosphorylation sites are at amino acids 262, 349 and 370. The O-glycosylation sites are amino acids 139, 238, and 374. The c-mannosylation sites are amino acids 13, 102, 292, and 388.
Evolution[edit]
C12orf50 has an evolutionary rate that is close to Fibrinogen alpha, making it relatively quick. Orthologs for C12orf50 have been found in mammals, reptiles, birds, and amphibians caecilians. No orthologs were found for frogs, fish, invertebrates, or fungi. The mammalian orthologs shared the most similarity with humans with the exception of the platypus. The range of divergence from humans from mammals was 6.4-180 million years. The reptilian orthologs were the next similar and diverged around 318 million years ago. Then the birds diverged from humans at the same time as the reptiles. The least similar was the amphibian caecilians and they diverged around 351.7 million years ago.
Homology[edit]
Orthologs[edit]
C12orf50 has orthologs in mammals, aves, reptiles and caecilian amphibians. No orthologs were found in amphibian frogs, invertebrates, plants, fungi, or yeast. The table below shows some of the orthologs that can be found on BLAST.[17]
| Species | Organism common name | NCBI Accession | Sequence Identity | Sequence Similarity | Length(AAs) |
|---|---|---|---|---|---|
| Homo sapiens | Human | NP_689802.1 | 100% | 100% | 414 |
| Pan paniscus | Bonobo | XP_003828373.1 | 98.8% | 99.3% | 414 |
| Phoca vitulina | Harbor seal | XP_032272023.1 | 87.7% | 93.0% | 415 |
| Lipotes vexillifer | Daiji dolphin | XP_007449184.1 | 86.3% | 92.3% | 415 |
| Gavialis gangeticus | Gharial | XP_019370370.1 | 47.1% | 63.5% | 378 |
| Gopherus gangeticus | Tortoises | XP_030404453.1 | 47.1% | 61.3% | 414 |
| Alligator sinensis | Chinese alligator | XXP_006027976.1 | 44.2% | 60.1% | 363 |
| Gallus gallus | Chicken | XP_040518234.1 | 38.5% | 52.3% | 405 |
| Coturnix japonica | Japanese quail | XP_032299702.1 | 36.8% | 50.9% | 403 |
| Geotrypetes seraphini | Gaboon caecilian | XP_033807710.1 | 39.7% | 55.3% | 409 |
Paralogs[edit]
C12orf50 has two paralogs: ZC3H11A and ZC3H11B. The zinc the finger domain is considered in both of the paralogs.
| Gene | NCBI Accession | Sequence Similarity | Length(AAs) |
|---|---|---|---|
| C12orf50 | NP_689802.1 | 100% | 414 |
| ZC3H11A | NP_001306167.1 | 16.2% | 810 |
| ZC3H11B | NNP_001342386.1 | 15.9% | 805 |
References[edit]
- ^ a b c GRCh38: Ensembl release 89: ENSG00000165805 – Ensembl, May 2017
- ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000056912 – Ensembl, May 2017
- ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
- ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
- ^ "AceView: Gene:C12orf50, a comprehensive annotation of human, mouse and worm genes with mRNAs or ESTsAceView". www.ncbi.nlm.nih.gov.
- ^ a b "C12orf50 chromosome 12 open reading frame 50 [Homo sapiens (human)". www.ncbi.nlm.nih.gov. National Center for Biotechnology Information.
- ^ Fagerberg, Linn; Hallström, Björn M.; Oksvold, Per; Kampf, Caroline; Djureinovic, Dijana; Odeberg, Jacob; Habuka, Masato; Tahmasebpoor, Simin; Danielsson, Angelika; Edlund, Karolina; Asplund, Anna; Sjöstedt, Evelina; Lundberg, Emma; Szigyarto, Cristina Al-Khalili; Skogs, Marie; Takanen, Jenny Ottosson; Berling, Holger; Tegel, Hanna; Mulder, Jan; Nilsson, Peter; Schwenk, Jochen M.; Lindskog, Cecilia; Danielsson, Frida; Mardinoglu, Adil; Sivertsson, Åsa; von Feilitzen, Kalle; Forsberg, Mattias; Zwahlen, Martin; Olsson, IngMarie; Navani, Sanjay; Huss, Mikael; Nielsen, Jens; Ponten, Fredrik; Uhlén, Mathias (February 2014). "Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics". Molecular & Cellular Proteomics. 13 (2): 397–406. doi:10.1074/mcp.M113.035600. PMC 3916642. PMID 24309898.
- ^ "AceView: Gene:C12orf50, a comprehensive annotation of human, mouse and worm genes with mRNAs or ESTsAceView". www.ncbi.nlm.nih.gov.
- ^ "RecName: Full=Uncharacterized Protein C12orf50". www.ncbi.nlm.nih.gov. National Center for Biotechnology Information.
- ^ "C12orf50 chromosome 12 open reading frame 50 [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov.
- ^ "C12orf50 - Uncharacterized protein C12orf50 - Homo sapiens (Human) - C12orf50 gene & protein". www.uniprot.org.
- ^ "AlphaFold Protein Structure Database". alphafold.ebi.ac.uk.
- ^ "SAPS Results". www.ebi.ac.uk.
- ^ https://psort.hgc.jp/cgi-bin/runpsort.pl.
{{cite web}}: Missing or empty|title=(help)[permanent dead link] - ^ "C12orf50 antibody".
- ^ "GAPDHS glyceraldehyde-3-phosphate dehydrogenase, spermatogenic [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov.
- ^ "BLAST: Basic Local Alignment Search Tool". blast.ncbi.nlm.nih.gov.