C10orf53

Last updated
C10orf53
Identifiers
Aliases C10orf53 , chromosome 10 open reading frame 53
External IDs MGI: 1914335 HomoloGene: 28053 GeneCards: C10orf53
Orthologs
SpeciesHumanMouse
Entrez

282966

67085

Ensembl

ENSG00000178645

ENSMUSG00000072473

UniProt

Q8N6V4

Q3KNL4

RefSeq (mRNA)

NM_182554
NM_001042427

NM_001034037

RefSeq (protein)

NP_001035892
NP_872360

NP_001029209

Location (UCSC) Chr 10: 49.68 – 49.71 Mb Chr 14: 32.1 – 32.11 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse
Conceptual translation of C10orf53. The full nucleotide and amino acid sequence are shown and aligned to show the relationship between the sequences. Information regarding post translation modifications, exon boundaries, untranslated regions, and disordered regions are emphasized in the translation. Conceptual translation of C10orf53.jpg
Conceptual translation of C10orf53. The full nucleotide and amino acid sequence are shown and aligned to show the relationship between the sequences. Information regarding post translation modifications, exon boundaries, untranslated regions, and disordered regions are emphasized in the translation.

C10orf53 is a protein that in humans is encoded by the C10orf53 gene. [6] The gene is located on the positive strand of the DNA and is 30,611 nucleotides in length. [8] The protein is 157 amino acids and the gene has 3 exons. [6] C10orf53 orthologs are found in mammals, birds, reptiles, amphibians, fish, and invertebrates. [9] It is primarily expressed in the testes and at very low levels in the cerebellum, liver, placenta, and trachea. [6]

Contents

Gene

Chromosome 10 open reading frame 53 (10orf53), also known as uncharacterized protein family 0728 (UPF0728), in humans, is encoded by Chromosome 10 (10q11.23), [6] spanning 30,611 nucleotides. [8] The gene is located on the positive strand [8] with 3 identified exons. [6]

Transcript

IsoformAccession # [6] Length

(amino acids) [6]

Length (nucleotides) [6] Exons translated [6] Additional comments [6]
a NM_182554.4

NP_872360.2

15730,6113Less common isoform
b NM_001042427.3

NP_001035892.1

9317,8823More common isoform – alternative 3’ exon and distinct C-terminus

The table outlines the two identified isoforms of C10orf53. The most common isoform has 93 amino acids which is a shorter amino acid sequence due to an alternative 3’ terminal exon and distinct C-terminus. [6] Isoform A has a higher frequency of analysis due to it being the longer isoform. [8] The analysis in this article is focused on isoform A.

Structure

The molecular weight predicted was 17.6 kDa. [10] The isoelectric point for C10orf53 is estimated to be 6.36 pl [10]

Secondary

Predicted tertiary structure through I-TASSER. This is a predicted visual representation of the secondary structure including alpha-helices and beta-pleated sheets. Tertiary structure C10orf53.jpg
Predicted tertiary structure through I-TASSER. This is a predicted visual representation of the secondary structure including alpha-helices and beta-pleated sheets. 
MPKNAVVILRYGPYSAAGLPVEHHTFRLQGLQAVLAIDGHEVILEKIEDWNVVELMVNEEVIFHCNI         67
CCCCCSSSSSSCCCHHCCSSSSSCHHHHHHHHHHHHHCCCSSSSSSSCCCCSSSSSSCCCSSSSSCC         67
KDLEFGKLTPSSDKRTTSSSRLTFHQLSSPCRMKVSPLQQFPQKTQDLTCTVLAQIGSCIHFQTNLC         134
CCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHCCCHHHHCCCCCCCSSSSSHHHHCCSSSSSCCCC         134
DLGWPGLDHMLISGLEKRGTQPY                                                     157
CCCCCCCHHHHHHHHHHCCCCCC                                                     157

The secondary structure above illustrates the estimated secondary structure for Isoform A of C10orf53. [11] The C that are italicized indicate that the amino acid is located within a coil, the bolded S is referring to the amino acid being in a strand, and the underlined H shows the amino acid is in a helix. [11] The strand and helix structures can then be translated into the predicted tertiary structure done through I-TASSER.

Tertiary

The predicted tertiary structure of C10orf53 is shown. The tertiary structure contains the seven helix and 8 strand structures predicted through I-TASSER. [11]

Regulation

This figure illustrates the evolution trend for the genes above. The amino acid sequences of C10orf53, Fibrinogen Alpha, and Cytochrome C in Homo sapiens were compared to the same sequences of Homo sapiens, Macaca fascicularis, Mus musculus, Monodelphis domestica, Ornithorhynchus anatinus, Gallus gallus, Xenopus tropicalis, and Danio rerio. C10orf53 is shown to have a quicker evolution compared to cytochrome C, but is slower than the fibrinogen alpha's evolution. C10orf53 Evolution Rate.png
This figure illustrates the evolution trend for the genes above. The amino acid sequences of C10orf53, Fibrinogen Alpha, and Cytochrome C in Homo sapiens were compared to the same sequences of Homo sapiens, Macaca fascicularis, Mus musculus, Monodelphis domestica, Ornithorhynchus anatinus, Gallus gallus, Xenopus tropicalis, and Danio rerio . C10orf53 is shown to have a quicker evolution compared to cytochrome C, but is slower than the fibrinogen alpha's evolution.

Gene

C10orf53 is primarily expressed in the testes, but also has very low levels of expression in the cerebellum, liver, placenta, and trachea. [6] It is tissue-specific to the testes due to the low expression in other tissues compared to the testes. C10orf53 majorly is secreted in the cytoplasm of cells and has moderate levels in the nucleus and mitochondria. [12]

Protein

C10orf53 was found to have two phosphorylation sites, two SUMOylation sites, and one lysine acetylation site. [5] All of these regions are shown in the conceptual translation of C10orf53.

Evolution

This figure illustrates the orthologs of C10orf53 with the species, common name, taxonomic group, date of divergence, accession number, sequence length, sequence identity percentage, and sequence similarity percentage using NCBI, Integrated Taxonomic Information System, and Time Tree. C10orf53 Orthologs by taxa.png
This figure illustrates the orthologs of C10orf53 with the species, common name, taxonomic group, date of divergence, accession number, sequence length, sequence identity percentage, and sequence similarity percentage using NCBI, Integrated Taxonomic Information System, and Time Tree.

C10orf53 is predicted to have a slower evolution compared to the gene, fibrinogen alpha, but it also has a quicker evolution compared to cytochrome c. Fibrinogen alpha is considered as a gene that had evolved rather quickly when examining the gene in different organisms. When two organisms diverged into different taxa, the gene went through alterations that made it significantly different from other organisms, causing it to have a quick rate of evolution. In contrast, Cytochrome C is relatively conserved throughout different organisms, which shows that it has a slow rate of evolution. C10orf53 has a rate of evolution that is smaller than fibrinogen alpha, but larger than cytochrome c.

Homology

A group of distantly and closely related orthologs were chosen and categorized by their date of divergence from humans. [13] The percent similarity and percent identity in relation to humans showed the predicted conservation between C10orf53 in humans compared to their orthologs.

Interacting Proteins

Protein [14] Protein Name [14] Identification [14] Function [15]
PIGR Polymeric Immunoglobulin Receptor Affinity chromatography Aids in the movement of polymeric IgA and IgM across mucosal epithelial cells
DSCC1 DNA Replication And Sister Chromatid Cohesion 1 Affinity chromatography Loads PCNA onto primed templates to manipulate replication forks
UXT Ubiquitously Expressed Prefoldin Like Chaperone Affinity chromatography Regulates androgen receptor transcription
ZG16B Zymogen Granule Protein 16B Affinity chromatography Located in the extracellular exosome and enables carbohydrate binding activity
SPECC1L Sperm Antigen With Calponin Homology And Coiled-Coil Domains 1 Like Affinity chromatography Helps with spindle organization and cytokinesis
MNAT1 CDK Activating Kinase Affinity chromatography Creates the CDK-activating kinase enzyme complex
SPTB Spectrin Beta, Erythrocytic Affinity chromatography Composes the cytoskeletal network in erythrocyte membranes

The table contains all predicted proteins that were found to interact with C10orf53. [14] It includes the protein acronym and name, the means that identification occurred, and the function of each protein. Due to the related function of some of the proteins, this provides evidence that these interactions coincide with the predicted location.

Clinical Significance

A study was conducted that compared the relative spermatogenesis in humans to the relative expression of RNAs correlated to teratozoospermia. In non-afflicted humans, there is a relatively high expression of C10orf53 across the RNAs tested. However, when a human had teratozoospermia, those levels dropped to almost zero. [16] Another study examined the expression of C10orf53 in spermatogenesis and testis development in mice during development. C10orf53 is only highly expressed from day 30-56 of mice development, with the expression decreasing slightly on each five-day period until 56 days were reached. [17] The final study looked at research done within the past five years has correlated African American prostate cancer patients with the presence of C10orf535. When examining the exosome found in Caucasian populations associated with prostate cancer (PCC) against the African American exosome (PAA), C10orf53 was unique only to PAA. [18]

Related Research Articles

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<span class="mw-page-title-main">C12orf24</span> Protein-coding gene in humans

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<span class="mw-page-title-main">C9orf85</span> Protein-coding gene in the species Homo sapiens

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<span class="mw-page-title-main">FAM214B</span> Protein-coding gene in the species Homo sapiens

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<span class="mw-page-title-main">C6orf136</span> Protein-coding gene in the species Homo sapiens

C6orf136 is a protein in humans encoded by the C6orf136 gene. The gene is conserved in mammals, mollusks, as well some porifera. While the function of the gene is currently unknown, C6orf136 has been shown to be hypermethylated in response to FOXM1 expression in Head Neck Squamous Cell Carcinoma (HNSCC) tissue cells. Additionally, elevated expression of C6orf136 has been associated with improved survival rates in patients with bladder cancer. C6orf136 has three known isoforms.

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<span class="mw-page-title-main">TMEM61</span> Protein and coding gene in humans

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References

  1. 1 2 3 GRCh38: Ensembl release 89: ENSG00000178645 - Ensembl, May 2017
  2. 1 2 3 GRCm38: Ensembl release 89: ENSMUSG00000072473 - 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 "Kinase-specific Phosphorylation Site Prediction". Group-based Prediction System (GPS) 5.0. Wuhan, Hubei, China: Huazhong University of Science and Technology. Retrieved 2022-12-16.
  6. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 "C10orf53 chromosome 10 open reading frame 53 [Homo sapiens (human)] - Gene". National Center for Biotechnology Information (NCBI). U.S. National Library of Medicine. Retrieved 2022-12-16.
  7. ↑ "ELM - unknown". Eukaryotic Linear Motif (ELM). Retrieved 2022-12-17.
  8. 1 2 3 4 "C10orf53 Gene". GeneCards. Retrieved 2022-12-16.
  9. 1 2 3 4 5 "BLAST: Basic Local Alignment Search Tool". National Center for Biotechnology Information (NCBI). U.S. Library of Medicine. Retrieved 2022-12-16.
  10. 1 2 "Statistical Analysis of Protein Sequences (SAPS)". European Bioinformatics Institute (EMBL-EBI). European Molecular Biology Laboratory (EMBL). Retrieved 2022-12-16.
  11. 1 2 3 4 "I-TASSER server for protein structure and function prediction". Yang Zhang's Research Group. University of Michigan. Retrieved 2022-12-16.
  12. ↑ "PSORT II Prediction". psort.hgc.jp. Retrieved 2022-12-16. Program to predict the subcellular localization sites of proteins from their amino acid sequences.
  13. 1 2 "TimeTree :: The Timescale of Life". www.timetree.org. Retrieved 2022-12-17.
  14. 1 2 3 4 "PSICQUIC View". www.ebi.ac.uk. Retrieved 2022-12-16.
  15. ↑ "GeneCards - Human Genes | Gene Database | Gene Search". www.genecards.org. Retrieved 2022-12-16.
  16. ↑ Platts AE, Dix DJ, Chemes HE, Thompson KE, Goodrich R, Rockett JC, et al. (April 2007). "Success and failure in human spermatogenesis as revealed by teratozoospermic RNAs". Human Molecular Genetics. 16 (7): 763–773. doi: 10.1093/hmg/ddm012 . PMID   17327269.
  17. ↑ Shima JE, McLean DJ, McCarrey JR, Griswold MD (July 2004). "The murine testicular transcriptome: characterizing gene expression in the testis during the progression of spermatogenesis". Biology of Reproduction. 71 (1): 319–330. doi: 10.1095/biolreprod.103.026880 . PMID   15028632. S2CID   16839090.
  18. ↑ Panigrahi GK, Praharaj PP, Kittaka H, Mridha AR, Black OM, Singh R, et al. (March 2019). "Exosome proteomic analyses identify inflammatory phenotype and novel biomarkers in African American prostate cancer patients". Cancer Medicine. 8 (3): 1110–1123. doi:10.1002/cam4.1885. PMC   6434210 . PMID   30623593.
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