C1orf216
C1orf216
UPF0500 is a 229 amino acid long protein that in humans is encoded by the C1orf216 gene. C1orf216 is located on GRCh38 minus strand.[1]. C1orf216 encodes a protein called UPF0500, which is 229 amino acids long. The longest possible mRNA transcript from C1orf216 is 2891 bp long, containing 2 of 3 exons in total. UPF0500 has a domain of unknown function DUF4653.
Gene information
Overall expression in tissues
C1orf216 shows a much higher expression in the brain than any other tissue. This not only includes adult brain, but also covers fetal brain (figure 1)[2]. Such expression is consistent with some findings that C1orf216 is likely related to neurodegenerative diseases.[3]
Expression changes under Rett Syndrome
C1orf216 is thought to be related to Rett Syndrome. As seen in figure 2[4], patients suffering from Rett Syndrome have a higher expression of C1orf216.
Subcellular localization
Combining the results from the immunofluorescence image in Hela cells and prediction[6] from Deeploc[7], C1orf216 is located in the nucleus and cytoplasm.
Structure
The gene structure predicted by Alpha Fold[9] and Phyre 2[10] are quite similar. It seems that the result of Phyre 2 was only an incomplete part of the outcome of Alpha Fold.
Homology and Evolution
The orthologs of C1orf216 have been found in all vertebrates, but not in any invertebrates. The most distant ortholog is found in cartilaginous fishes. It seems that C1orf216 is evolving rapidly, since it has a steep slope on the evolutionary graph (figure 3). No paralogs have been found in humans.
| mammals | Names | Common names | Similarity percentage | Identity to humans | Divergence Time (MYA) | |||||
| NP_001335620.1 | Homo sapiens | Humans | 100% | 100% | 0 | |||||
| XP_025221478.1 | Theropithecus gelada | Gelada | 97.4% | 95.6% | 28.8 | |||||
| XP_011356267.1 | Vespertilio vampyrus | Large flying bat | 93.0% | 89.5% | 94 | |||||
| XP_025847547.1 | Vulpes vulpes | Red fox | 89.1% | 89.1% | 94 | |||||
| XP_046940968.1 | Lynx rufus | Bobcat | 90.4% | 88.2% | 94 | |||||
| XP_026372475.2 | Ursus arctos | Brown bear | 90.4% | 86.5% | 94 | |||||
| XP_021539367.1 | Neomonachus schauinslandi | Hawaiian monk seal | 90.0% | 87.3% | 94 | |||||
| Birds/Reptiles | ||||||||||
| XP_042690006.1 | Centrocercus urophasianus | White-tailed ptarmigan | 52.1% | 43.2% | 319 | |||||
| XP_031450529.1 | Phasianus colchicus | Helmeted guineafowl | 55.0% | 45.7% | 319 | |||||
| XP_059344885.1 | Ammospiza nelsoni | Great reed warbler | 58.2% | 50.5% | 319 | |||||
| XP_024058658.1 | Terrapene carolina triunguis | Three-toed box turtle | 53.7% | 43.9% | 319 | |||||
| Amphibians | ||||||||||
| XP_053562977.1 | Bombina bombina | Fire-bellied toad | 47.6% | 39.9% | 352 | |||||
| XP_029427081.1 | Rhinatrema bivittatum | Two-lined caecilian | 48.0% | 39.4% | 352 | |||||
| XP_030075869.1 | Microcaecilia unicolor | 39.9% | 32.1% | 352 | ||||||
| Bony fishes | ||||||||||
| XP_039596207.1 | Polypterus senegalus | Senegal bichir | 42.2% | 32.9% | 429 | |||||
| XP_028675131.1 | Erpetoichthys calabaricus | Snakefish | 42.2% | 32.0% | 429 | |||||
| XP_026785321.3 | Pangasianodon hypophthalmus | Striped catfish | 35.1% | 26.1% | 429 | |||||
| cartilaginous fishes | ||||||||||
| XP_055512253.1 | Leucoraja erinacea | Little skate | 51.3% | 37.3% | 462 | |||||
| XP_048414284.1 | Stegostoma tigrinum | Zebra shark | 47.9% | 36.9% | 462 | |||||
| XP_048469126.1 | Rhincodon typus | Whale shark | 46.9% | 35.9% | 462 | |||||
| XP_032901100.1 | Amblyraja radiata | Thorny skate | 50.4% | 36.9% | 462 |
Interactions
C1orf216 interacts with multiple proteins. According to BioGRID[11], there are 72 interactors of C1orf216. A large number of these interactors are keratins. Among these interactors, two seem to be important due to their specific functions in the brain: CDR2 and CEP55. CDR2, known as cerebellar degeneration related protein 2, can be related to the nervous system and neurodegenerative diseases like Parkinson’s disease.[12] CEP55, centrosomal protein 55, is considered to play an important role in neuroblastoma.[13]
Clinical Significance
Overall, C1orf216 is a gene in the brain that is related to nervous diseases. The reason is that C1orf216 has higher expression levels in Rett Syndrome, and it has interactors related to nerve functions.
References
- ↑ "Human hg38 chr1:35,713,877-35,716,911 UCSC Genome Browser v457". genome.ucsc.edu. Retrieved 2023-12-16.
- ↑ "C1orf216 chromosome 1 open reading frame 216 [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2023-12-16.
- ↑ Haenig, Christian; Atias, Nir; Taylor, Alexander K.; Mazza, Arnon; Schaefer, Martin H.; Russ, Jenny; Riechers, Sean-Patrick; Jain, Shushant; Coughlin, Maura; Fontaine, Jean-Fred; Freibaum, Brian D.; Brusendorf, Lydia; Zenkner, Martina; Porras, Pablo; Stroedicke, Martin (August 2020). "Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains". Cell Reports. 32 (7): 108050. doi:10.1016/j.celrep.2020.108050. PMID 32814053 Check
|pmid=value (help). - ↑ "36036871 - GEO Profiles - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2023-12-16.
- ↑ "C1orf216 - Antibodies - The Human Protein Atlas". www.proteinatlas.org. Retrieved 2023-12-16.
- ↑ "C1orf216 - Antibodies - The Human Protein Atlas". www.proteinatlas.org. Retrieved 2023-12-16.
- ↑ "DeepLoc 2.0 - DTU Health Tech - Bioinformatic Services". services.healthtech.dtu.dk. Retrieved 2023-12-16.
- ↑ "PHYRE2 Protein Fold Recognition Server". www.sbg.bio.ic.ac.uk. Retrieved 2023-12-16.
- ↑ "AlphaFold Protein Structure Database". alphafold.com. Retrieved 2023-12-16.
- ↑ "PHYRE2 Protein Fold Recognition Server". www.sbg.bio.ic.ac.uk. Retrieved 2023-12-16.
- ↑ "BioGRID | Database of Protein, Chemical, and Genetic Interactions". thebiogrid.org. Retrieved 2023-12-07.
- ↑ Hwang, J-Y; Lee, J; Oh, C-K; Kang, H W; Hwang, I-Y; Um, J W; Park, H C; Kim, S; Shin, J-H; Park, W-Y; Darnell, R B; Um, H-D; Chung, K C; Kim, K; Oh, Y J (2016-06-02). "Proteolytic degradation and potential role of onconeural protein cdr2 in neurodegeneration". Cell Death & Disease. 7 (6): e2240. doi:10.1038/cddis.2016.151. ISSN 2041-4889. PMC 5143381. PMID 27253404.
- ↑ Putra, Vina; Hulme, Amy J.; Tee, Andrew E.; Sun, Jane Q.J.; Atmadibrata, Bernard; Ho, Nicholas; Chen, Jingwei; Gao, Jixuan; Norris, Murray D.; Haber, Michelle; Kavallaris, Maria; Henderson, Michelle J.; McCarroll, Joshua; Trahair, Toby; Liu, Tao (April 2021). "The RNA-helicase DDX21 upregulates CEP55 expression and promotes neuroblastoma". Molecular Oncology. 15 (4): 1162–1179. doi:10.1002/1878-0261.12906. ISSN 1574-7891. PMC 8024731 Check
|pmc=value (help). PMID 33497018 Check|pmid=value (help).
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