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C12orf42

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

Gene

Locus

The genomic location for this gene is as follows: starts at 103,237,591 bp and ends 103,496,010 bp.[1] The cytogenetic location for C12orf42 is 12q23.2. It is located on the negative strand[2]

Cytogenetic band: 12q23.2[3]

mRNA

Fifteen different mRNAs are made by transcription: fourteen alternative splice variants and one unspliced form.[2]

Protein

Tertiary structure for C12orf42 protein.[4]

The protein released by this gene is known as uncharacterized protein C12orf42.[1] 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:[5]

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

Secondary structure

C12orf42 protein takes on several secondary structures, such as: alpha helices, beta sheets, and random coils. C12orf42 protein is a soluble.[6] Proteins that are soluble have a hydrophilic outside and hydrophobic interior .[7] Proteins with this type of structure are able to freely float inside a cell, due to the liquid composition of the cytosol.

Subcellular location

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

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[8]

Acetylation Ser2[9]
Sumoylation IPIVS32-36[10]
O-GlcNAc Thr45,Ser58,Ser130,Ser135,Ser205,Ser210,

Ser217,Thr339[11]

Expression

Tissue profiles

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.[12] There is significant expression in the brain, bladder, epididymis, and the helper T cell.[12] Therefore, there is statistically significant expression of C12orf42 gene throughout the nervous system, immune system, and male reproductive system.

In situ hybridization

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.[13] 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[14]
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

Paralog

C12orf42 gene has only one other member in its gene family, this gene is known as Neuroligin 4, Y linked gene (NLGN4Y).[15]

Orthologs

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

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

In an experiment, fine-tiling comparative genomic hybridization (FT-CGH) and ligation-mediated PCR (LM-PCR) were combined.[16] 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.[16]

References

  1. ^ a b "www.genecards.org/cgi-bin/carddisp.pl?gene=C12orf42#proteins". www.genecards.org. Retrieved 2016-02-29.
  2. ^ a b mieg@ncbi.nlm.nih.gov, Danielle Thierry-Mieg and Jean Thierry-Mieg, NCBI/NLM/NIH. "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.{{cite web}}: CS1 maint: multiple names: authors list (link)
  3. ^ "Chromosome 12: 103,237,591-103,496,010 - Region in detail - Homo sapiens - Ensembl genome browser 84". www.ensembl.org. Retrieved 2016-04-26.
  4. ^ "I-TASSER results". zhanglab.ccmb.med.umich.edu. Archived from the original on 2016-04-28. Retrieved 2016-05-03.
  5. ^ "C12orf42 - Uncharacterized protein C12orf42 - Homo sapiens (Human) - C12orf42 gene & protein". www.uniprot.org. Retrieved 2016-05-03.
  6. ^ "SOSUI/submit a protein sequence". harrier.nagahama-i-bio.ac.jp. Retrieved 2016-04-30.
  7. ^ Berg, Jeremy M.; Tymoczko, John L.; Stryer, Lubert (2002-01-01). "Summary". {{cite journal}}: Cite journal requires |journal= (help)
  8. ^ "NetPhos 2.0 Server". www.cbs.dtu.dk. Retrieved 2016-05-03.
  9. ^ "NetAcet 1.0 Server". www.cbs.dtu.dk. Retrieved 2016-05-03.
  10. ^ "GPS-SUMO: Prediction of SUMOylation Sites & SUMO-interaction Motifs". sumosp.biocuckoo.org. Retrieved 2016-05-03.
  11. ^ "YinOYang 1.2 Server". www.cbs.dtu.dk. Retrieved 2016-05-03.
  12. ^ a b "GDS3834 / 17229". www.ncbi.nlm.nih.gov. Retrieved 2016-05-02.
  13. ^ "1700113H08Rik MGI Mouse Gene Detail - MGI:1923890 - RIKEN cDNA 1700113H08 gene". www.informatics.jax.org. Retrieved 2016-05-02.
  14. ^ "Gene Detail :: Allen Brain Atlas: Mouse Brain". mouse.brain-map.org. Retrieved 2016-04-28.
  15. ^ "Human BLAT Search". genome.ucsc.edu. Retrieved 2016-05-03.
  16. ^ a b Przybylski, Grzegorz K.; Dittmann, Kathleen; Grabarczyk, Piotr; Dölken, Gottfried; Gesk, Stefan; Harder, Lana; Landmann, Eva; Siebert, Reiner; Schmidt, Christian A. (2010-11-01). "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. ISSN 1600-0609. PMID 20659153.
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