C12orf42

C12orf42
Identifiers
Aliases	C12orf42, chromosome 12 open reading frame 42
External IDs	MGI: 1923890 HomoloGene: 45695 GeneCards: C12orf42
Gene location (Human) Chr. Chromosome 12 (human)[1] Band 12q23.2-q23.3 Start 103,237,591 bp[1] End 103,495,978 bp[1]
RNA expression pattern Bgee Human Mouse (ortholog) Top expressed in sperm spleen lymph node appendix blood bone marrow cells endothelial cell thymus sural nerve prefrontal cortex n/a More reference expression data BioGPS n/a
Orthologs Species Human Mouse Entrez 374470 76640 Ensembl ENSG00000179088 n/a UniProt Q96LP6 n/a RefSeq (mRNA) NM_001099336 NM_001278419 NM_001278420 NM_198521 NM_001386867 NM_001386868 NM_001386869 NM_001386871 NM_001386872 NM_029685 RefSeq (protein) NP_001092806 NP_001265348 NP_001265349 NP_940923 n/a Location (UCSC) Chr 12: 103.24 – 103.5 Mb n/a PubMed search [2] [3]
Wikidata
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Chromosome 12 Open Reading Frame 42 (C12orf42) is a protein-encoding gene in Homo sapiens.

Gene[edit]

Locus[edit]

The genomic location for this gene is as follows: starts at 103,237,591 bp and ends 103,496,010 bp.^[4] The cytogenetic location for C12orf42 is 12q23.2. It is located on the negative strand^[5]

mRNA[edit]

Fifteen different mRNAs are made by transcription: fourteen alternative splice variants and one unspliced form.^[5]

Protein[edit]

The protein released by this gene is known as uncharacterized protein C12orf42.^[4] There are three isoforms for this protein produced by alternative splicing. The first isoform is a conical sequence. The second Isoform differs form the first in that it doesn't contain 1-95 aa in its sequence. The third isoform differs from the conical sequence in two ways:^[8]

• 87-107 aa is the sequence GSHHGQATQKLQGAMVLHLEE instead of VFPERTQNSMACKRLLHTCQY
• the entire sequence 108-360 aa doesn't exist in this isoform

Secondary structure[edit]

C12orf42 protein takes on several secondary structures, such as: alpha helices, beta sheets, and random coils. C12orf42 protein is a soluble.^[9] Proteins that are soluble have a hydrophilic outside and hydrophobic interior .^[10] Proteins with this type of structure are able to freely float inside a cell, due to the liquid composition of the cytosol.

Subcellular location[edit]

C12orf42 is an intracellular protein. This is known by the lack of transmembrane domains or signal peptides. This suggests that it is predicted to be a nuclear protein, given the nuclear localization signal (NSL) found: PRDRRPQ at 292 aa and a bipartite KRLIKVCSSAPPRPTRR at 325 aa.

Post-translation modification[edit]

Predicted post-translation modification sites are seen below in the table. Nuclear proteins are known for having phosphorylation, acetylation, sumoylation, and O-GlcNAc as types of modifications:^{[citation needed]}

• Phosphorylation affects proteins-protein interaction and the stability of the protein.^{[citation needed]}
• Acetylation promotes protein folding and improves stability.
• Sumoylation is involved in nuclear-cytosolic transport and DNA repair.^{[citation needed]}
• Glycosylation (known as O-GlcNAc while in the nucleus) promotes protein folding and stability.

Expression[edit]

Tissue profiles[edit]

Microarray data shows expression of the C12orf42 gene in different tissues throughout the human body. There is high expression in the lymph node, spleen, and thymus.^[15] There is significant expression in the brain, bladder, epididymis, and the helper T cell.^[15] Therefore, there is statistically significant expression of C12orf42 gene throughout the nervous system, immune system, and male reproductive system.

In situ hybridization[edit]

The table below shows the areas in the mouse brain where C12orf42 is expressed. The gene name for the mouse is 1700113H08Rik, it is the human homolog of C12orf42.^[16] Area one and two of the brain manages body and skeletal movement. Areas three and four in the brain are for sensory functions; area four specializes in perception of smell. Area five in the brain functions in emotional learning and memory.

Homology[edit]

Paralog[edit]

C12orf42 gene has only one other member in its gene family, this gene is known as Neuroligin 4, Y linked gene (NLGN4Y).^[18]

Orthologs[edit]

C12orf42 orthologs are mostly mammals. One exception that was found is the Pelodiscus Sinensis or more commonly known as the Chinese soft-shell turtle.

Conserved domain structure[edit]

The domain structure that is most important is DUF4607, it is conserved in the Eutheria clade in the Mammalia class. The order that it is conserved in is as follows: Artiodactyla, Carnivora, Chiroptera, Lagomorpha, Perissodactyla, Primates, Proboscidea, and Rodentia.

Clinical significance[edit]

In an experiment, fine-tiling comparative genomic hybridization (FT-CGH) and ligation-mediated PCR (LM-PCR) were combined.^[19] This resulted in the finding of a chromosomal translocation t(12;14)(q23;q11.2) in  T-lymphoblastic lymphoma (T-LBL). The chromosomal translocation occurs during T-receptor delta gene-deleting rearrangement, which is important in T-cell differentiation. This translocation disrupts C12orf42 and it brings the gene ASCL1 closer to the T-cell receptor alpha (TRA) enhancer. As a result, the cross-fused gene encodes vital transcription factors that are found in medullary thyroid cancer and small-cell lung cancer.

References[edit]