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C12orf42

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C12orf42
Identifiers
AliasesC12orf42, chromosome 12 open reading frame 42
External IDsMGI: 1923890; HomoloGene: 45695; GeneCards: C12orf42; OMA:C12orf42 - orthologs
Orthologs
SpeciesHumanMouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_029685

RefSeq (protein)

NP_001092806
NP_001265348
NP_001265349
NP_940923

n/a

Location (UCSC)Chr 12: 103.24 – 103.5 Mbn/a
PubMed search[2][3]
Wikidata
View/Edit HumanView/Edit Mouse

Chromosome 12 Open Reading Frame 42 (C12orf42) is a protein-encoding gene in Homo sapiens.

Gene

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Locus

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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]

Cytogenetic band: 12q23.2[6]

mRNA

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

Protein

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Tertiary structure for C12orf42 protein.[7]

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

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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

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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.

This protein cartoon illustrates the location of, the domain DUF4607 and two nuclear localization sequences.

Post-translation modification

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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

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Tissue profiles

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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

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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.

Location in mouse brain Area in Brain[17]
Area #1 Crus 1, granular layer
Crus 2, granular layer
Paramedian lobule, molecular
Area #2 Paraflocculus, granular layer
Flocculus, granular layer
Area #3 Field CA1, pyramidal layer
Field CA2, pyramidal layer
Field CA3, pyramidal layer
Area #4 Piriform area, pyramidal layer
Piriform-amygdalar area, pyramidal layer
Area #5 Cortical amygdalar area, posterior part, lateral zone, layer 2
Cortical amygdalar area, posterior part, Imedial zone, layer 2

Homology

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Paralog

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

Orthologs

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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

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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

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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.

Illustrates the translocation that occurred that led to a deletion in chromosome 12. Where chromosome 12q23 cross-fused with TRDREC and TRAJ61 segment. This interfered with C12orf42 gene.[19]

References

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  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000179088Ensembl, May 2017
  2. ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  3. ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. ^ a b "www.genecards.org/cgi-bin/carddisp.pl?gene=C12orf42#proteins". www.genecards.org. Retrieved 2016-02-29.
  5. ^ 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.
  6. ^ "Chromosome 12: 103,237,591-103,496,010 - Region in detail - Homo sapiens - Ensembl genome browser 84". www.ensembl.org. Retrieved 2016-04-26.
  7. ^ "I-TASSER results". zhanglab.ccmb.med.umich.edu. Archived from the original on 2016-04-28. Retrieved 2016-05-03.
  8. ^ "C12orf42 - Uncharacterized protein C12orf42 - Homo sapiens (Human) - C12orf42 gene & protein". www.uniprot.org. Retrieved 2016-05-03.
  9. ^ "SOSUI/submit a protein sequence". harrier.nagahama-i-bio.ac.jp. Retrieved 2016-04-30.
  10. ^ Berg JM, Tymoczko JL, Stryer L (2002-01-01). Summary.
  11. ^ "NetPhos 2.0 Server". www.cbs.dtu.dk. Retrieved 2016-05-03.
  12. ^ "NetAcet 1.0 Server". www.cbs.dtu.dk. Retrieved 2016-05-03.
  13. ^ "GPS-SUMO: Prediction of SUMOylation Sites & SUMO-interaction Motifs". sumosp.biocuckoo.org. Archived from the original on 2013-05-10. Retrieved 2016-05-03.
  14. ^ "YinOYang 1.2 Server". www.cbs.dtu.dk. Retrieved 2016-05-03.
  15. ^ a b "GDS3834 / 17229". www.ncbi.nlm.nih.gov. Retrieved 2016-05-02.
  16. ^ "1700113H08Rik MGI Mouse Gene Detail - MGI:1923890 - RIKEN cDNA 1700113H08 gene". www.informatics.jax.org. Retrieved 2016-05-02.
  17. ^ "Gene Detail :: Allen Brain Atlas: Mouse Brain". mouse.brain-map.org. Retrieved 2016-04-28.
  18. ^ "Human BLAT Search". genome.ucsc.edu. Retrieved 2016-05-03.
  19. ^ 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.