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. The C13orf42 protein is predicted to be localized in the mitochondria, nucleus, and cytosol. Tertiary structure predictions for C13orf42 indicate multiple alpha helices.

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

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

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).

Exons The C13orf42 gene contains 4 exons.

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. 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. 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.

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. 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.

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

Protein Composition C13orf42 has a predicted isoelectric point of 9.3 and a predicted molecular weight of 37.4 kDa. Human C13orf42 is a serine rich and positively charged amino acid (lysine and arginine) rich protein. 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. In the structure below, residues indicated to be present in C13orf42 in higher amounts (serine, lysine and arginine) are annotated. A space filling model and a charge model is also shown for C13orf42.

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%). Orthologs show similar predicted subcellular localization with mitochondria, nucleus, and cytosol being the top predicted locations, however, predicted percentages vary.

Immunohistochemistry C13orf42 antibody B-4 (catalog number: sc-376095) shows cytoplasmic and nuclear staining in seminiferous ducts and Lyedig cells of testis tissue. 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.

Post translational Modifications

C13orf42 is predicted to have 10 highly conserved (in over 70% of analyzed orthologs from table below) phosphorylation sites. 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. 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.

Domains

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

Homology and evolution

Orthologs C13orf42 has orthologs in mammals, birds, reptiles, amphibians, bony fish, and cartilaginous fish as shown in the ortholog table below. No orthologs were found in jawless fish, invertebrates, plants, fungi, viruses, or bacteria. 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.

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. Genus and species Common Name Taxonomic Class Date of Divergence (MYA) Accession Number Length (amino acids) Percent identity to Homo sapiens Percent Similarity to Homo sapiensHomo sapiens Human Primates 0 NP_001338518.1 325 100 100Mus musculus Mouse Dasyuromorphia 87 XP_030104110.1 318 76.9 84Tursiops truncatus Common bottlenose dolphin Cetacea 94 XP_033699576.1 319 82.8 87.7Equus caballus Horse Perissodactyla 94 XP_023477317.1 326 82.6 90.2Mustela putorius European polecat Carnivora 94 XP_004775284.1 326 79.4 85Pipistrellus kuhlii Kuhl's pipistrelle (bat) Chiroptera 94 XP_036312978.1 325 79.1 86.8Ursus maritimus Polar bear Ursidae 94 XP_040478472.1 328 77.2 82.7Elephas maximus indicus Indian elephant Proboscidea 99 XP_049709344.1 326 79.4 86.2Dasypus novemcinctus Nine-banded armadillo Cingulata 99 XP_023446856.1 32872.8 81.4Dromiciops gliroides Monito del monte Microbiotheria 160 XP_043849658.1 326 67.9 79.5Trichosurus vulpecula Common brushtail possum Diprotodontia 160 XP_036599801.1 326 66.7 79.5Sarcophilus harrisii Tasmanian devil Dasyuromorphia 160 XP_023355407.1 326 66.4 80.1Ornithorhynchus anatinus Playtpus Monotremes 180 XP_028904285.1 330 62.3 73Alligator sinensis Chinese alligator Crocodilian 319 XP_025062978.1 266 48.6 61.7Dromaius novaehollandiae Emu Casuariiformes 319 XP_025964173.1 268 48.2 59.8Gallus gallus Chicken Galliformes 319 XP_004938779.1 268 47.6 61.3Camarhynchus parvulus Small tree finch Thraupidae 319 XP_030802909.1 264 47.1 60.9Pelodiscus sinensis Chinese softshell turtle Testudines 319 XP_014429996.1 267 47 60.6Phasianus colchicus Common pheasant Galliformes 319 XP_031471701.1 272 46.4 59.9Varanus komodoensis Komodo dragon Squamata 319 XP_044300138.1 269 45.9 60.1Python bivittatus Burmese python Squamata 319 XP_025026122.1 269 44.1 58Pantherophis guttatus Corn snake Squamata 319 XP_034287884.1 267 42.7 56.4Rhinatrema bivittatum Two-lined caecilian Rhinatrematidae 353 XP_029459031.1 273 45.4 59.5Xenopus tropicalis Western clawed frog Anura 353 XP_031752228.1 260 43.5 57.4Bufo gargarizans Asiatic toad Anura 353 XP_044141363.1 262 40.7 56.8Bufo bufo Common toad Anura 353 XP_040278366.1 391 30.9 42Protopterus annectens West african lungfish Lepidosireniformes 408 XP_043927617.1 269 37.8 53.5Polyodon spathula Paddlefish Acipenseriformes 431 XP_041127510.1 275 33.8 52.4Danio rerio Zebrafish Cypriniformes 431 XP_021329868.1 287 30.2 44.7Clupea harengus Atlantic herring Clupeiformes 431 XP_042559186.1 306 29 41.7Callorhinchus milii Australian ghostshark Chimaeriformes 464 XP_042189981.1 267 35.5 53.3Amblyraja radiata Thorny skate Rajiformes 464 XP_032889397.1 267 33 47.5Scyliorhinus canicula Small-spotted catshark Carcharhiniformes 464 XP_038658253.1 264 32.5 50.4

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

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.

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

References