C1orf141

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Chromosome 1 open reading frame 141, or C1orf141 is a protein which, in humans, is encoded by gene C1orf141. [1] It is a precursor protein that becomes active after cleavage. [2] The function is not yet well understood, but it is suggested to be active during development [3]

Contents

Gene

Locus

This gene is located on chromosome 1 at position 1p31.3. It is encoded on the antisense strand of DNA spanning from 67,092,176 to 67,141,646 and has 10 total exons. It overlaps slightly with the gene IL23R being encoded on the sense strand. [1]

Chromosome 1 spanning from 66,924,895 to 67,267,726. Chromosome 1 (66924895 to 67267726).gif
Chromosome 1 spanning from 66,924,895 to 67,267,726.

Transcription regulation

A specific promoter region has not been predicted for C1orf141 so the 1000 base pairs upstream of the start of transcription was analyzed for transcription factor binding sites. [4] The transcription factors below represent a subset of the transcription factor binding sites found within this region that give an idea of the kind of factors that could bind to the promoter [4]

mRNA

Alternative Splicing

The C1orf141 gene appears to have two common isoforms and seven less common transcript variants. [1]

C1orf141 Isoforms
NamemRNA Length (base pairs)Protein Length (amino acids)
C1orf141 Isoform 12177400
C1orf141 Isoform 22203217
C1orf141 Isoform X12348471
C1orf141 Isoform X22265458
C1orf141 Isoform X31875333
C1orf141 Isoform X4920243
C1orf141 Isoform X5612154
C1orf141 Isoform X6639146
C1orf141 Isoform X7514138

Protein

The primary encoded precursor protein (C1orf141 Isoform 1) consists of 400 amino acid residues and is 2177 base pairs long. It consists of 7 exons and a domain of unknown function DUF4545. [5] Its predicted molecular mass is 54.4 kDa and predicted isoelectric point is 9.63. [6]

Composition

Conceptual Translation of C1orf141 that shows predicted Post-translational modifications. C1orf141 Conceptual Tranlastion.png
Conceptual Translation of C1orf141 that shows predicted Post-translational modifications.

The C1orf141 precursor protein has more lysine amino acid residues and less glycine amino acid residues than expected when compared to other human proteins. The sequence has 11.7% lysine and only 2.1% glycine. [6]

Post-translational modifications

C1orf141 is modified post translation to form a mature protein product. It undergoes O-linked glycosylation, sumoylation, glycation, and phosphorylation. [7] [8] [9] [10] One N-terminal cleavage occurs followed by acetylation. Propeptide cleavage occurs at the start site of the final exon. [2]

Model of the Tertiary Structure for precursor human protein C1orf141 as predicted by I-TASSER. C1orf141 Tertiary Structure Model.jpg
Model of the Tertiary Structure for precursor human protein C1orf141 as predicted by I-TASSER.

Structure

The secondary structure for uncleaved C1orf141 consists primarily of alpha helices with a few small segments of beta sheets. These helices can be seen in the model of the tertiary structure predicted by the I-TASSER program. [11] The program Phyre2 also predicts the protein to be made up primarily of alpha helices. [12] After propeptide cleavage of C1orf141, I-TASSER predicts that only alpha helices remain.

Interactions

There are currently no experimentally confirmed interactions for C1orf141. The STRING database for protein interactions identified ten potential proteins that interact with C1orf141 through text mining. [13] These include SALT1, C8orf74, SHCBP1L, ACTL9, RBM44, CCDC116, ADO, WDR78, ZNF365, SPATA45. [14] [15] [16] [17] Through investigation of the papers where these interaction predictions were found, a solid link was not clear for any of the identified proteins.

Expression

Expression data for C1orf141 from HPA RNA-Seq normal tissues project. C1orf141 Expression.png
Expression data for C1orf141 from HPA RNA-Seq normal tissues project.

C1orf141 is expressed in 30 different tissues but primarily in the testes. [1] Other tissues where expression is above baseline levels are the brain, lungs, and ovaries. [3]

Localization

The subcellular localization for C1orf141 is predicted to be in the nucleus. There are two nuclear localization signals within the protein sequence, one of which stays present after propeptide cleavage. [18]

Function

The function of C1orf141 is not yet fully understood and has not been experimentally confirmed. However, expression data shows that the protein is active in some developmental stages. RNA-Seq data taken at different stages of development show expression at varying levels throughout. [3] Expression rates are seen at higher levels in the fetal developmental stage than the adult in the protein's ETS profile. [19] Microarray data for cumulus cells during natural and stimulated in vitro fertilization show relatively high levels of expression. [20] There is no significant change in expression in adult tissue disease states. [19]

Homology

Paralogs

There are no paralogs for C1orf141 [21]

Orthologs

Orthologous sequences are seen primarily in other mammalian species. The most distant ortholog identified through a NCBI BLAST search is a Reptilian species, but that is the only non-mammalian species. [21] This list contains a subset of the species identified as orthologs to display the diversity of the species where orthologs can be found. Each species was compared to the human C1orf141 isoform that includes each coding exon, isoform X1. [1]

C1orf141 Orthologs
Genus and SpeciesCommon NameTaxonomic GroupAccession NumberDate of Divergence (millions of years)Sequence Length (amino acids)Sequence IdentitySequence Similarity
Homo sapiens Human Primate XP_011539768.10471100%100%
Gorilla gorilla gorilla Western Lowland GorillaPrimateXP_018892062.18.6146997%98%
Otolemur garnettii Northern Greater GalagoPrimateXP_023365656.18445759%70%
Tupaia chinensis Northern Treeshrew Scandentia XP_006171456.18846862%74%
Oryctolagus

cuniculus

European Rabbit Lagomorpha XP_017201685.18847056%68%
Fukomys damarensis Damaraland Mole Rat Rodentia XP_010603404.18847954%66%
Chinchilla lanigera Long-tailed ChincillaRodentiaXP_013369940.19447650%65%
Ochotona princeps American PikaLagomorphaXP_012783463.19445050%67%
Miniopterus natalensis Natal long-fingered bat Chiroptera XP_016064273.19439063%72%
Panthera pardus Leopard Carnivora XP_019304485.19445062%74%
Enhydra lutris kenyoni Sea OtterCarnivoraXP_022351992.19445162%74%
Balaenoptera acutorostrata scammoni Minke Whale Cetacea XP_007164359.19443260%60%
Delphinapterus leucas Beluga WhaleCetaceaXP_022436606.19443259%72%
Sus scrofa Wild Boar Cetartiodactyla XP_005656203.19444256%70%
Pteropus vampyrus Large Flying FoxChiropteraXP_011367916.19447056%68%
Ovis aries SheepCetartiodactylaXP_012026840.19443155%69%
Bos taurus CattleCetartiodactylaNP_001070559.19443054%69%
Condylura cristata Star-nosed Mole Eulipotyphla XP_012577585.19443252%64%
Desmodus rotundus Common Vampire BatChiropteraXP_024421106.19439848%59%
Sarcophilus harrisii Tasmanian Devil Marsupiala XP_012405605.116035643%63%
Phascolarctos cinereus KoalaMarsupialaXP_020848724.116020429%50%
Monodelphis domestica Gray Short-tailed OpossumMarsupialaXP_007480481.116052425%48%
Pogona vitticeps Central Bearded Dragon Reptilia XP_020661721.132050128%54%

Evolutionary History

Using the Molecular Clock Hypothesis, the m value (the number of corrected amino acid changes per 100 residues) was calculated for C1orf141 and plotted against the divergence of species. When compared to the same m value plot for hemoglobin, fibrinogen alpha chain, and cytochrome c, it is clear that the C1orf141 gene is evolving at a faster rate than all three.

References

  1. 1 2 3 4 5 6 "C1orf141 chromosome 1 open reading frame 141 [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2019-05-03.
  2. 1 2 "ProP 1.0 Server". www.cbs.dtu.dk. Retrieved 2019-05-03.
  3. 1 2 3 4 "C1orf141 Gene Expression - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2019-05-03.
  4. 1 2 "Genomatix: Gene2Promoter Subtasks". www.genomatix.de. Retrieved 2019-05-03.[ permanent dead link ]
  5. ↑ "C1orf141 Gene (Protein Coding)". www.genecards.org. Retrieved 2019-05-03.
  6. 1 2 "SAPS < Sequence Statistics < EMBL-EBI". www.ebi.ac.uk. Retrieved 2019-05-03.
  7. ↑ "NetOGlyc 4.0 Server". www.cbs.dtu.dk. Retrieved 2019-05-05.
  8. ↑ "SUMOplot™ Analysis Program | Abgent". www.abgent.com. Archived from the original on 2005-01-03. Retrieved 2019-05-05.
  9. ↑ "NetGlycate 1.0 Server". www.cbs.dtu.dk. Retrieved 2019-05-05.
  10. ↑ "NetPhos 3.1 Server". www.cbs.dtu.dk. Retrieved 2019-05-05.
  11. 1 2 "I-TASSER results". zhanglab.ccmb.med.umich.edu. Archived from the original on 2019-05-03. Retrieved 2019-05-03.
  12. ↑ "PHYRE2 Protein Fold Recognition Server". www.sbg.bio.ic.ac.uk. Retrieved 2019-05-03.
  13. ↑ "C1orf141 protein (human) - STRING interaction network". string-db.org. Retrieved 2019-05-03.
  14. ↑ Sammut, Stephen J.; Feichtinger, Julia; Stuart, Nicholas; Wakeman, Jane A.; Larcombe, Lee; McFarlane, Ramsay J. (2014-05-06). "A novel cohort of cancer-testis biomarker genes revealed through meta-analysis of clinical data sets". Oncoscience. 1 (5): 349–359. doi:10.18632/oncoscience.37. ISSN   2331-4737. PMC   4278308 . PMID   25594029.
  15. ↑ Swami, Meera (2014). "Genome-wide association study identifies three new melanoma susceptibility loci". Nature Medicine. 17 (11): 1357. doi:10.1038/nm.2568. hdl: 2445/128818 . ISSN   1078-8956. S2CID   42251944.
  16. ↑ Lu, Weining; Quintero-Rivera, Fabiola; Fan, Yanli; Alkuraya, Fowzan S.; Donovan, Diana J.; Xi, Qiongchao; Turbe-Doan, Annick; Li, Qing-Gang; Campbell, Craig G. (2007). "NFIA Haploinsufficiency Is Associated with a CNS Malformation Syndrome and Urinary Tract Defects". PLOS Genetics. 3 (5) e80. doi: 10.1371/journal.pgen.0030080 . ISSN   1553-7390. PMC   1877820 . PMID   17530927.
  17. ↑ Yao, Fang; Zhang, Chi; Du, Wei; Liu, Chao; Xu, Ying (2015-09-16). "Identification of Gene-Expression Signatures and Protein Markers for Breast Cancer Grading and Staging". PLOS ONE. 10 (9) e0138213. Bibcode:2015PLoSO..1038213Y. doi: 10.1371/journal.pone.0138213 . ISSN   1932-6203. PMC   4573873 . PMID   26375396.
  18. ↑ "Welcome to psort.org!!". www.psort.org. Retrieved 2019-05-03.
  19. 1 2 "EST Profile - Hs.666621". www.ncbi.nlm.nih.gov. Retrieved 2019-05-03.[ dead link ]
  20. ↑ "Modified natural and stimulated in vitro fertilization cycles: cumulus cells - - GEO DataSets - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2019-05-03.
  21. 1 2 "BLAST: Basic Local Alignment Search Tool". blast.ncbi.nlm.nih.gov. Retrieved 2019-05-03.
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