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C13orf42 is a
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.
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
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...
which, in humans, is encoded by the gene
In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...
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
A mitochondrion (; ) is an organelle found in the Cell (biology), cells of most Eukaryotes, such as animals, plants and Fungus, fungi. Mitochondria have a double lipid bilayer, membrane structure and use aerobic respiration to generate adenosi ...
, nucleus
Nucleus ( : nuclei) is a Latin word for the seed inside a fruit. It most often refers to:
*Atomic nucleus, the very dense central region of an atom
*Cell nucleus, a central organelle of a eukaryotic cell, containing most of the cell's DNA
Nucle ...
, 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
The alpha helix (α-helix) is a common motif in the secondary structure of proteins and is a right hand-helix conformation in which every backbone N−H group hydrogen bonds to the backbone C=O group of the amino acid located four residues ear ...
.
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 severalpseudogenes
Pseudogenes are nonfunctional segments of DNA that resemble functional genes. Most arise as superfluous copies of functional genes, either directly by DNA duplication or indirectly by reverse transcription of an mRNA transcript. Pseudogenes are ...
along with ribonuclease H2 subunit B (RNASEH2B
Ribonuclease H2, subunit B is a protein that in humans is encoded by the ''RNASEH2B'' gene. RNase H2 is composed of a single catalytic subunit ( A) and two non-catalytic subunits (B and C), and degrades the RNA of RNA:DNA hybrids. The non-cataly ...
), uncharacterized LOC107984554, and family with sequence similarity 124 member A (FAM124A).
Exons
The C13orf42 gene contains 4exons
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 sequencing technique which uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample at a given moment, analyzing the continuously changing c ...
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 lab-on-a-chip. Its purpose is to simultaneously detect the expression of thousands of genes from a sample (e.g. from a tissue). It is a two-dimensional array on a solid substrate—usually a glass slide or silicon t ...
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 variantsvariant 1
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 chargedamino acid
Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha am ...
(lysine and arginine) rich protein. This composition is partially conserved in orthologs.
Tertiary Structure
The C13orf42tertiary 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 may int ...
of the highest confidence predicted by I-Tasser is predicted to have many alpha helices
The alpha helix (α-helix) is a common motif in the secondary structure of proteins and is a right hand-helix conformation in which every backbone N−H group hydrogen bonds to the backbone C=O group of the amino acid located four residues ear ...
. 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 themitochondria
A mitochondrion (; ) is an organelle found in the Cell (biology), cells of most Eukaryotes, such as animals, plants and Fungus, fungi. Mitochondria have a double lipid bilayer, membrane structure and use aerobic respiration to generate adenosi ...
, nucleus
Nucleus ( : nuclei) is a Latin word for the seed inside a fruit. It most often refers to:
*Atomic nucleus, the very dense central region of an atom
*Cell nucleus, a central organelle of a eukaryotic cell, containing most of the cell's DNA
Nucle ...
, 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 ...
, and endoplasmic reticulum
The endoplasmic reticulum (ER) is, in essence, the transportation system of the eukaryotic cell, and has many other important functions such as protein folding. It is a type of organelle made up of two subunits – rough 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
C13orf42antibody
An antibody (Ab), also known as an immunoglobulin (Ig), is a large, Y-shaped protein used by the immune system to identify and neutralize foreign objects such as pathogenic bacteria and viruses. The antibody recognizes a unique molecule of the ...
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 (, plural: nucleoli ) is the largest structure in the nucleus of eukaryotic cells. It is best known as the site of ribosome biogenesis, which is the synthesis of ribosomes. The nucleolus also participates in the formation of sign ...
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
Camp may refer to:
Outdoor accommodation and recreation
* Campsite or campground, a recreational outdoor sleeping and eating site
* a temporary settlement for nomads
* Camp, a term used in New England, Northern Ontario and New Brunswick to descri ...
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 inmammals
Mammals () are a group of vertebrate animals constituting the class Mammalia (), characterized by the presence of mammary glands which in females produce milk for feeding (nursing) their young, a neocortex (a region of the brain), fur or ...
, birds
Birds are a group of warm-blooded vertebrates constituting the class Aves (), characterised by feathers, toothless beaked jaws, the laying of hard-shelled eggs, a high metabolic rate, a four-chambered heart, and a strong yet lightweigh ...
, reptiles
Reptiles, as most commonly defined are the animals in the Class (biology), class Reptilia ( ), a paraphyletic grouping comprising all sauropsid, sauropsids except birds. Living reptiles comprise turtles, crocodilians, Squamata, squamates (lizar ...
, amphibians
Amphibians are four-limbed and ectothermic vertebrates of the class Amphibia. All living amphibians belong to the group Lissamphibia. They inhabit a wide variety of habitats, with most species living within terrestrial, fossorial, arbore ...
, bony fish
Osteichthyes (), popularly referred to as the bony fish, is a diverse superclass of fish that have skeletons primarily composed of bone tissue. They can be contrasted with the Chondrichthyes, which have skeletons primarily composed of cartilag ...
, and cartilaginous fish
Chondrichthyes (; ) is a class that contains the cartilaginous fishes that have skeletons primarily composed of cartilage. They can be contrasted with the Osteichthyes or ''bony fishes'', which have skeletons primarily composed of bone tissue ...
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 withchronic lymphocytic leukemia
Chronic lymphocytic leukemia (CLL) is a type of cancer in which the bone marrow makes too many lymphocytes (a type of white blood cell). Early on, there are typically no symptoms. Later, non-painful lymph node swelling, feeling tired, fever, nigh ...
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 nasa ...
and pronasale face shape in humans.
References
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