C12orf42
C12orf42 | |||||||||||||||||||||||||||||||||||||||||||||||||||
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Identifiers | |||||||||||||||||||||||||||||||||||||||||||||||||||
Aliases | C12orf42, chromosome 12 open reading frame 42 | ||||||||||||||||||||||||||||||||||||||||||||||||||
External IDs | MGI: 1923890; HomoloGene: 45695; GeneCards: C12orf42; OMA:C12orf42 - orthologs | ||||||||||||||||||||||||||||||||||||||||||||||||||
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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.
Type of Modification | Amino Acid Position |
---|---|
Phosphorylation | Ser44,Ser47,Ser58,Ser74,Ser113,Ser115,Ser118,Ser123,Ser130,Ser134,Ser135,Ser205,Ser210,Ser217,
Ser226,Ser238, Ser302,Thr17,Thr45,Thr145,Thr150,Thr228, Thr240,Thr240,Thr291,Thr339,Thr344,Tyr124[11] |
Acetylation | Ser2[12] |
Sumoylation | IPIVS32-36[13] |
O-GlcNAc | Thr45,Ser58,Ser130,Ser135,Ser205,Ser210,
Ser217,Thr339[14] |
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.
Mammalia Class | genus | species | common name | Date of divergence | accession # | seq length | seq ident | seq similar | Taxa/Paralog |
---|---|---|---|---|---|---|---|---|---|
1 | Homo | H.Sapiens | Human | --------------- | NP_001157710 | 256aa | 89.80% | ***** | Paralog |
2 | Papio | P.Anubis | Olive Baboon | 27.3 mya | XP_009179812 | 353aa | 90% | 93% | Order Primate |
3 | Ovis | O. Aries | Sheep | 95.0 mya | XP_012026728 | 177aa | 64.00% | 68% | Order Artiodactyla |
4 | Oryctolagus | O. Cuniculus | European Rabbit | 90.1 mya | XP_008255213 | 346aa | 61% | 70% | Order Lagomorpha |
5 | Equus | E. Caballus | Horse | 95.0 mya | XP_005606608 | 293aa | 60% | 68% | Order Perissodactyla |
6 | Orcinus | O. Orca | Killer Whale | 95.0 mya | XP_012388341.1 | 322aa | 59% | 67% | Order Cetacea |
7 | Galeopterus | G.Variegatus | Sunda flying lemur | 83.0 mya | XP_008574769.1 | 289aa | 56% | 64% | Order Dermoptera |
8 | Trichechus | T.Manatus | West Indian Manatee | 102.0 mya | XP_012410246 | 348aa | 55% | 63% | Order Sirenia |
9 | Loxodonta | L. Africana | African bush elephant | 102.0 mya | XP_010599824 | 288aa | 54% | 62% | Order Proboscidea |
10 | Pteropus | P.Alecto | Black flying fox | 95.0 mya | ELK10322.1 | 300aa | 52% | 64% | Order Chiroptera |
11 | Condylura | c.Cristata | Star-nose mole | 95.0 mya | XP_004676538.1 | 306aa | 52% | 64% | Order Insectivora |
12 | Ailuropoda | A. Melanoleuca | Giant Panda | 95.0 mya | XP_011218367.1 | 305aa | 51% | 61% | Order Carnivora |
13 | orycteropus | O. Afer | Aardvarks | 102.0 mya | XP_007950592 | 283aa | 49% | 59% | Order Tubulidentata |
14 | Elephantulus | E. Edwardii | Cape Elephant Shrew | 102.0 mya | XP_006888639 | 114aa | 47% | 60% | Order Macroscelidea |
15 | Mus | M. Musculus | Mouse | 90.1 mya | NP_083961 | 327aa | 45% | 57% | Order Rodentia |
16 | Canis | C. Lupus | Dog | 95.0 mya | XP_013974742 | 206aa | 44% | 56% | Order Carnivora |
17 | Dasypus | D. Novemcinctus | Nine-banded armadillo | 102.0 mya | XP_012377498 | 360aa | 41% | 49% | Order Edentata |
Reptillia Class | genus | species | common name | Date of divergence | accession # | seq length | seq ident | seq similar | NOTES |
1 | Pelodiscus | P. Sinensis | Chinese Soft-Shell Turtle | 320.5 mya | XP_014436518 | 618aa | 32% | 42% | Order Testudines |
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]- ^ a b c GRCh38: Ensembl release 89: ENSG00000179088 – Ensembl, May 2017
- ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
- ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
- ^ a b "www.genecards.org/cgi-bin/carddisp.pl?gene=C12orf42#proteins". www.genecards.org. Retrieved 2016-02-29.
- ^ a b Thierry-Miegn D, Thierry-Mieg J. "AceView: Gene:C12orf42, a comprehensive annotation of human, mouse and worm genes with mRNAs or ESTsAceView". www.ncbi.nlm.nih.gov. Retrieved 2016-05-03.
- ^ "Chromosome 12: 103,237,591-103,496,010 - Region in detail - Homo sapiens - Ensembl genome browser 84". www.ensembl.org. Retrieved 2016-04-26.
- ^ "I-TASSER results". zhanglab.ccmb.med.umich.edu. Archived from the original on 2016-04-28. Retrieved 2016-05-03.
- ^ "C12orf42 - Uncharacterized protein C12orf42 - Homo sapiens (Human) - C12orf42 gene & protein". www.uniprot.org. Retrieved 2016-05-03.
- ^ "SOSUI/submit a protein sequence". harrier.nagahama-i-bio.ac.jp. Retrieved 2016-04-30.
- ^ Berg JM, Tymoczko JL, Stryer L (2002-01-01). Summary.
- ^ "NetPhos 2.0 Server". www.cbs.dtu.dk. Retrieved 2016-05-03.
- ^ "NetAcet 1.0 Server". www.cbs.dtu.dk. Retrieved 2016-05-03.
- ^ "GPS-SUMO: Prediction of SUMOylation Sites & SUMO-interaction Motifs". sumosp.biocuckoo.org. Archived from the original on 2013-05-10. Retrieved 2016-05-03.
- ^ "YinOYang 1.2 Server". www.cbs.dtu.dk. Retrieved 2016-05-03.
- ^ a b "GDS3834 / 17229". www.ncbi.nlm.nih.gov. Retrieved 2016-05-02.
- ^ "1700113H08Rik MGI Mouse Gene Detail - MGI:1923890 - RIKEN cDNA 1700113H08 gene". www.informatics.jax.org. Retrieved 2016-05-02.
- ^ "Gene Detail :: Allen Brain Atlas: Mouse Brain". mouse.brain-map.org. Retrieved 2016-04-28.
- ^ "Human BLAT Search". genome.ucsc.edu. Retrieved 2016-05-03.
- ^ a b Przybylski GK, Dittmann K, Grabarczyk P, Dölken G, Gesk S, Harder L, et al. (November 2010). "Molecular characterization of a novel chromosomal translocation t(12;14)(q23;q11.2) in T-lymphoblastic lymphoma between the T-cell receptor delta-deleting elements (TRDREC and TRAJ61) and the hypothetical gene C12orf42". European Journal of Haematology. 85 (5): 452–456. doi:10.1111/j.1600-0609.2010.01508.x. PMID 20659153. S2CID 23351975.