C13orf42 is a

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...

which, in humans, is encoded by the

gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...

chromosome 13

open reading frame In molecular biology, reading frames are defined as spans of DNA sequence between the start and stop codons. Usually, this is considered within a studied region of a prokaryotic DNA sequence, where only one of the six possible reading frames ...

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 A mitochondrion () is an organelle found in the cells of most eukaryotes, such as animals, plants and fungi. Mitochondria have a double membrane structure and use aerobic respiration to generate adenosine triphosphate (ATP), which is us ...

, nucleus, and

cytosol The cytosol, also known as cytoplasmic matrix or groundplasm, is one of the liquids found inside cells ( intracellular fluid (ICF)). It is separated into compartments by membranes. For example, the mitochondrial matrix separates the mitochondri ...

. Tertiary structure predictions for C13orf42 indicate multiple

alpha helices An alpha helix (or α-helix) is a sequence of amino acids in a protein that are twisted into a coil (a helix). The alpha helix is the most common structural arrangement in the secondary structure of proteins. It is also the most extreme type of l ...

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

pseudogene Pseudogenes are nonfunctional segments of DNA that resemble functional genes. Pseudogenes can be formed from both protein-coding genes and non-coding genes. In the case of protein-coding genes, most pseudogenes arise as superfluous copies of fun ...

s along with ribonuclease H2 subunit B ( RNASEH2B), uncharacterized LOC107984554, and family with sequence similarity 124 member A (FAM124A). C13orf42_exon_diagram_to_scale

Exons

The C13orf42 gene contains 4

exon An exon is any part of a gene that will form a part of the final mature RNA produced by that gene after introns have been removed by RNA splicing. The term ''exon'' refers to both the DNA sequence within a gene and to the corresponding sequence ...

Expression

RNA sequencing RNA-Seq (named as an abbreviation of RNA sequencing) is a technique that uses next-generation sequencing to reveal the presence and quantity of RNA molecules in a biological sample, providing a snapshot of gene expression in the sample, also kn ...

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 A microarray is a multiplex (assay), multiplex lab-on-a-chip. Its purpose is to simultaneously detect the expression of thousands of biological interactions. It is a two-dimensional array on a Substrate (materials science), solid substrate—usu ...

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 1variant 2variant 3
an
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 Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although over 500 amino acids exist in nature, by far the most important are the 22 α-amino acids incorporated into proteins. Only these 22 a ...

(lysine and arginine) rich protein. This composition is partially conserved in orthologs.

Tertiary Structure

The C13orf42

tertiary structure Protein tertiary structure is the three-dimensional shape of a protein. The tertiary structure will have a single polypeptide chain "backbone" with one or more protein secondary structures, the protein domains. Amino acid side chains and the ...

of the highest confidence predicted by I-Tasser is predicted to have many

. 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. Predicted_C13orf42_tertiary_structure_with_conserved_amino_acids_labeled

Predicted_C13orf42_tertiary_structure_with_conserved_amino_acids_labeled

C13orf42_structure_predicted_by_I-Tasser_and_annotated_in_Chimera

Subcellular Localization

Human C13orf42 is predicted to be localized to the

, nucleus,

, and

endoplasmic reticulum The endoplasmic reticulum (ER) is a part of a transportation system of the eukaryote, eukaryotic cell, and has many other important functions such as protein folding. The word endoplasmic means "within the cytoplasm", and reticulum is Latin for ...

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 An antibody (Ab) or immunoglobulin (Ig) is a large, Y-shaped protein belonging to the immunoglobulin superfamily which is used by the immune system to identify and neutralize antigens such as pathogenic bacteria, bacteria and viruses, includin ...

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 The nucleolus (; : nucleoli ) is the largest structure in the nucleus of eukaryotic cells. It is best known as the site of ribosome biogenesis. The nucleolus also participates in the formation of signal recognition particles and plays a ro ...

localization in HeLa cells.

Post translational Modifications

Human_C13orf42_predicted_post_translational_modification_illustration

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

Graph of C13orf42 evolution compared to Cytochrome C and Fibrinogen Alpha

Orthologs

C13orf42 has orthologs in

mammals A mammal () is a vertebrate animal of the class Mammalia (). Mammals are characterised by the presence of milk-producing mammary glands for feeding their young, a broad neocortex region of the brain, fur or hair, and three middle e ...

birds Birds are a group of warm-blooded vertebrates constituting the class (biology), class Aves (), characterised by feathers, toothless beaked jaws, the Oviparity, laying of Eggshell, hard-shelled eggs, a high Metabolism, metabolic rate, a fou ...

reptiles Reptiles, as commonly defined, are a group of tetrapods with an ectothermic metabolism and Amniotic egg, amniotic development. Living traditional reptiles comprise four Order (biology), orders: Testudines, Crocodilia, Squamata, and Rhynchocepha ...

amphibians Amphibians are ectothermic, anamniote, anamniotic, tetrapod, four-limbed vertebrate animals that constitute the class (biology), class Amphibia. In its broadest sense, it is a paraphyletic group encompassing all Tetrapod, tetrapods, but excl ...

bony fish Osteichthyes ( ; ), also known as osteichthyans or commonly referred to as the bony fish, is a Biodiversity, diverse clade of vertebrate animals that have endoskeletons primarily composed of bone tissue. They can be contrasted with the Chondricht ...

, and

cartilaginous fish Chondrichthyes (; ) is a class of jawed fish that contains the cartilaginous fish or chondrichthyans, which all have skeletons primarily composed of cartilage. They can be contrasted with the Osteichthyes or ''bony fish'', which have skeleto ...

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

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 Chronic lymphocytic leukemia (CLL) is a type of cancer that affects the blood and bone marrow. In CLL, the bone marrow makes too many lymphocytes, which are a type of white blood cell. In patients with CLL, B cell lymphocytes can begin to colle ...

which lead to ATM inactivation. Xiong et. al indicated SNP rs7325564 to be significantly associated with

nasion The nasion () is the most anterior point of the frontonasal suture that joins the nasal part of the frontal bone and the nasal bones. It marks the midpoint at the intersection of the frontonasal suture with the internasal suture joining the na ...

and pronasale face shape in humans.

References

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