C13orf42

Last updated
C13orf42
Identifiers
Aliases C13orf42 , LINC00372, LINC00371, long intergenic non-protein coding RNA 371, chromosome 13 open reading frame 42
External IDs GeneCards: C13orf42
Orthologs
SpeciesHumanMouse
Entrez

647166

n/a

Ensembl

ENSG00000226792

n/a

UniProt

n
a

n/a

RefSeq (mRNA)

NM_001351589

n/a

RefSeq (protein)

n/a

n/a

Location (UCSC) Chr 13: 51.08 – 51.2 Mb n/a
PubMed search [2] n/a
Wikidata
View/Edit Human

C13orf42 is a protein which, in humans, is encoded by the gene chromosome 13 open reading frame 42 (C13orf42). RNA sequencing data shows low expression of the C13orf42 gene in a variety of tissues. [3] The C13orf42 protein is predicted to be localized in the mitochondria, nucleus, and cytosol. [4] Tertiary structure predictions for C13orf42 indicate multiple alpha helices. [5]

Contents

Gene

Summary

C13orf42 is a protein encoding gene containing 4 exons. C13orf42 is also known by aliases LINC00371 and LINC00372. [3] RNA sequencing shows the gene's expression at low levels in various tissues. [3] [6]

Location

C13orf42 is located on the minus strand of chromosome 13 at 13q14.3 in humans. [3] [7] C13orf42 is located from 51.08 Mb to 51.20 Mb on chromosome 13 and spans 118 kilobases. [8]

Neighborhood

The genomic neighborhood of C13orf42 consists of several pseudogenes along with ribonuclease H2 subunit B (RNASEH2B), uncharacterized LOC107984554, and family with sequence similarity 124 member A (FAM124A). [3]

A depiction of exons to scale on the C13orf42 gene. Image was created using Illustrator for Biological Sciences (IBS) from biocuckoo and gene information from UCSC BLAT. C13orf42 exon diagram to scale.png
A depiction of exons to scale on the C13orf42 gene. Image was created using Illustrator for Biological Sciences (IBS) from biocuckoo and gene information from UCSC BLAT.

Exons

The C13orf42 gene contains 4 exons. [10]

Expression

RNA sequencing of C13orf42 shows expression in a variety of tissues including the spleen, kidney, heart, brain, testis, skin, esophagus, colon, small intestine, stomach, lung, placenta, salivary gland, thymus, and adipose. [3] RNA sequencing of human fetal tissue shows C13orf42 expression starting at 20 weeks in the intestine, 16 weeks in the kidney, 10 weeks in the lung, and expression in the stomach is seen at 16 weeks but not 10, 18, or 20 weeks. [3] Recorded RNA expression is very low, with all results being lower than 0.5 reads per kilobase of transcript per million reads mapped (RPKM). Microarray data from NCBI geo (GDS425) shows expression in additional tissues including bone marrow, liver, skeletal muscle, spinal cord, and pancreas. [6]

Transcript

Variants

C13orf42 produces four known transcript variants, variant 1, variant 2, variant 3, and variant X1. Transcript variant 3 (accession number: NM_001351589.3) is the longest high-quality mRNA at 3075 nucleotides. [10] Transcript variant 3 contains 4 exons and encodes a 325 amino acid protein.

Transcript variants 1, 2, and X1 all lack the first exon but align with exons 2, 3, and 4 of transcript variant 3. Variants 1 and 2 are not protein encoding, while variants 3 and X1 are protein coding. Variant X1 is 2717 nucleotides long and encodes a 189 amino acid protein which aligns with the last 187 amino acids of the longer protein encoded by transcript variant 3 and differs in its first two amino acids. [11] [12]

Protein

Isoforms

There are two known proteins encoded by the isoforms of C13orf42. [13] Transcript variant 3 encodes the longest protein at 325 amino acids long. [13] Transcript variant X1 encodes a 189 amino acid long protein. [13] This protein aligns with exons 2, 3, and 4 of the 325 amino acid protein, but is missing exon 1. [12]

Protein Composition

C13orf42 has a predicted isoelectric point of 9.3 and a predicted molecular weight of 37.4 kDa. [14] Human C13orf42 is a serine rich and positively charged amino acid (lysine and arginine) rich protein. [15] This composition is partially conserved in orthologs.

Tertiary Structure

The C13orf42 tertiary structure of the highest confidence predicted by I-Tasser is predicted to have many alpha helices. [5] In the structure below, residues indicated to be present in C13orf42 in higher amounts (serine, lysine and arginine) are annotated. [16] A space filling model and a charge model is also shown for C13orf42.

Tertiary structure of C13orf42 predicted by I-Tasser and annotated in NCBI iCn3D. The protein is shown in space filling form and highly conserved amino acids are labeled in yellow. Predicted C13orf42 tertiary structure with conserved amino acids labeled.png
Tertiary structure of C13orf42 predicted by I-Tasser and annotated in NCBI iCn3D. The protein is shown in space filling form and highly conserved amino acids are labeled in yellow.
Tertiary structure of C13orf42 predicted by I-Tasser and annotated in NCBI iCn3D. Charge is indicated with blue being positive and red being negative residues. Highly conserved amino acids are labeled in yellow. Predicted C13orf42 structure with charge and conserved amino acids.png
Tertiary structure of C13orf42 predicted by I-Tasser and annotated in NCBI iCn3D. Charge is indicated with blue being positive and red being negative residues. Highly conserved amino acids are labeled in yellow.
C13orf42 structure predicted by I-Tasser and annotated in Chimera with residues indicated to be present in higher-than-average amounts highlighted. (Serine = blue, Lysine = green, Arginine = orange) C13orf42 structure predicted by I-Tasser and annotated in Chimera.png
C13orf42 structure predicted by I-Tasser and annotated in Chimera with residues indicated to be present in higher-than-average amounts highlighted. (Serine = blue, Lysine = green, Arginine = orange)

Subcellular Localization

Human C13orf42 is predicted to be localized to the mitochondria, nucleus, cytosol, and endoplasmic reticulum with the ER predicted at a low percentage (<5%). [4] Orthologs show similar predicted subcellular localization with mitochondria, nucleus, and cytosol being the top predicted locations, however, predicted percentages vary. [4]

Immunohistochemistry

C13orf42 antibody B-4 (catalog number: sc-376095) shows cytoplasmic and nuclear staining in seminiferous ducts and Lyedig cells of testis tissue. [18] C13orf42 antibody E-3 (catalog number: sc-374567) shows cytoplasmic staining in seminiferous ducts and Lyedig cells of testis tissue, and cytoplasmic and nucleolar localization in HeLa cells. [19]

Post translational Modifications

Predicted post translational modifications shown on human C13orf42. Diagram was created using Illustrator for Biological Sciences. Human C13orf42 predicted post translational modification illustration.png
Predicted post translational modifications shown on human C13orf42. Diagram was created using Illustrator for Biological Sciences.

C13orf42 is predicted to have 10 highly conserved (in over 70% of analyzed orthologs from table below) phosphorylation sites. [20] Phosphorylation sites include one CK2 phosphorylation, one TYR phosphorylation, two cAMP phosphorylation sites, and six PKC phosphorylation sites. There are three predicted O-β-GlcNAc sites and two predicted yin-yang sites in C13orf42 which are fully conserved in orthologs. [21] A yin-yang site occurs when O-β-GlcNAc and phosphorylation are predicted for the same site. C13orf42 is not predicted to have myristylation sites as it does not contain an N-terminal glycine. [22]

Domains

C13orf42 has no identified domains with high confidence or conservation in orthologs.

Homology and evolution

Corrected Divergence vs. Date of Divergence (MYA) of C13orf42 compared to Cytochrome C and Fibrinogen alpha. Graph of C13orf42 evolution compared to Cytochrome C and Fibrinogen Alpha.jpg
Corrected Divergence vs. Date of Divergence (MYA) of C13orf42 compared to Cytochrome C and Fibrinogen alpha.

Orthologs

C13orf42 has orthologs in mammals, birds, reptiles, amphibians, bony fish, and cartilaginous fish as shown in the ortholog table below. [23] No orthologs were found in jawless fish, invertebrates, plants, fungi, viruses, or bacteria. [23] All mammals contain the same 4 exons as the human C13orf42 protein, and nonmammals are missing exon 4. Mammalian orthologs have a high percent identity to human C13orf42, each having over 62% identity. The furthest orthologs (cartilaginous fish) have sequence identities around 33%. Human C13orf42 does not have paralogs. [8]

Ortholog Table

Table depicting genus and species, common name, taxonomic class, date of divergence, accession number, length, percent identity, and percent similarity of C13orf42 and its orthologs. Default sorting is by date of divergence then percent sequence identity. [13] [12]
Genus and SpeciesCommon NameTaxonomic ClassDate of Divergence (MYA) [24] Accession NumberLength (amino acids)Percent Identity to Homo sapiensPercent Similarity to Homo sapiens
Homo sapiens HumanPrimates0NP_001338518.1325100100
Mus musculus MouseDasyuromorphia87XP_030104110.131876.984
Tursiops truncatus Common bottlenose dolphinCetacea94XP_033699576.131982.887.7
Equus caballus HorsePerissodactyla94XP_023477317.132682.690.2
Mustela putorius European polecatCarnivora94XP_004775284.132679.485
Pipistrellus kuhlii Kuhl's pipistrelle (bat)Chiroptera94XP_036312978.132579.186.8
Ursus maritimus Polar bearUrsidae94XP_040478472.132877.282.7
Elephas maximus indicus Indian elephantProboscidea99XP_049709344.132679.486.2
Dasypus novemcinctus Nine-banded armadilloCingulata99XP_023446856.132872.881.4
Dromiciops gliroides Monito del monteMicrobiotheria160XP_043849658.132667.979.5
Trichosurus vulpecula Common brushtail possumDiprotodontia160XP_036599801.132666.779.5
Sarcophilus harrisii Tasmanian devilDasyuromorphia160XP_023355407.132666.480.1
Ornithorhynchus anatinus PlaytpusMonotremes180XP_028904285.133062.373
Alligator sinensis Chinese alligatorCrocodilian319XP_025062978.126648.661.7
Dromaius novaehollandiae EmuCasuariiformes319XP_025964173.126848.259.8
Gallus gallus ChickenGalliformes319XP_004938779.126847.661.3
Camarhynchus parvulus Small tree finchThraupidae319XP_030802909.126447.160.9
Pelodiscus sinensis Chinese softshell turtleTestudines319XP_014429996.12674760.6
Phasianus colchicus Common pheasantGalliformes319XP_031471701.127246.459.9
Varanus komodoensis Komodo dragonSquamata319XP_044300138.126945.960.1
Python bivittatus Burmese pythonSquamata319XP_025026122.126944.158
Pantherophis guttatus Corn snakeSquamata319XP_034287884.126742.756.4
Rhinatrema bivittatum Two-lined caecilianRhinatrematidae353XP_029459031.127345.459.5
Xenopus tropicalis Western clawed frogAnura353XP_031752228.126043.557.4
Bufo gargarizans Asiatic toadAnura353XP_044141363.126240.756.8
Bufo bufo Common toadAnura353XP_040278366.139130.942
Protopterus annectens West african lungfishLepidosireniformes408XP_043927617.126937.853.5
Polyodon spathula PaddlefishAcipenseriformes431XP_041127510.127533.852.4
Danio rerio ZebrafishCypriniformes431XP_021329868.128730.244.7
Clupea harengus Atlantic herringClupeiformes431XP_042559186.13062941.7
Callorhinchus milii Australian ghostsharkChimaeriformes464XP_042189981.126735.553.3
Amblyraja radiata Thorny skateRajiformes464XP_032889397.12673347.5
Scyliorhinus canicula Small-spotted catsharkCarcharhiniformes464XP_038658253.126432.550.4

Phylogeny

A phylogenetic tree shows human C13orf42 is most related its mammalian orthologs, and most distantly related to cartilaginous fish orthologs. [25]

A phylogenetic tree of the C13orf42 protein made using NCBI protein to collect sequences and phylogeny.fr to generate the tree. Phylogenetic Tree of C13orf42.pdf
A phylogenetic tree of the C13orf42 protein made using NCBI protein to collect sequences and phylogeny.fr to generate the tree.

Function

Clinical significance

Kanagal-Shamanna et. al identified an ATM fusion with C13orf42 in a patient with chronic lymphocytic leukemia which lead to ATM inactivation. [26]

Xiong et. al indicated SNP rs7325564 to be significantly associated with nasion and pronasale face shape in humans. [27]

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References

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  18. ↑ "C13orf42 Antibody (B-4)". www.scbt.com.
  19. ↑ "C13orf42 Antibody (E-3)". www.scbt.com.
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  24. ↑ Kumar S, Suleski M, Craig JM, Kasprowicz AE, Sanderford M, Li M, et al. (August 2022). "TimeTree 5: An Expanded Resource for Species Divergence Times". Molecular Biology and Evolution. 39 (8): msac174. doi:10.1093/molbev/msac174. PMC   9400175 . PMID   35932227.
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  26. ↑ Kanagal-Shamanna R, Bao H, Kearney H, Smoley S, Tang Z, Luthra R, et al. (April 2022). "Molecular characterization of Novel ATM fusions in chronic lymphocytic leukemia and T-cell prolymphocytic leukemia". Leukemia & Lymphoma. 63 (4): 865–875. doi:10.1080/10428194.2021.2010061. PMID   34898335. S2CID   245131979.
  27. ↑ Xiong Z, Dankova G, Howe LJ, Lee MK, Hysi PG, de Jong MA, et al. (November 2019). McCarthy MI, Morris AP, Cha S (eds.). "Novel genetic loci affecting facial shape variation in humans". eLife. 8: e49898. doi: 10.7554/eLife.49898 . PMC   6905649 . PMID   31763980.
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