| C12orf42 | |||||||||||||||||||||||||||||||||||||||||||||||||||
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| Aliases | C12orf42 , chromosome 12 open reading frame 42 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| External IDs | MGI: 1923890 HomoloGene: 45695 GeneCards: C12orf42 | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Chromosome 12 Open Reading Frame 42 (C12orf42) is a protein-encoding gene in Homo sapiens.
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| Identifiers | |||||||||||||||||||||||||||||||||||||||||||||||||||
| Aliases | C12orf42 , chromosome 12 open reading frame 42 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| External IDs | MGI: 1923890 HomoloGene: 45695 GeneCards: C12orf42 | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Chromosome 12 Open Reading Frame 42 (C12orf42) is a protein-encoding gene in Homo sapiens.
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]
Fifteen different mRNAs are made by transcription: fourteen alternative splice variants and one unspliced form. [5]
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]
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.
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.
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 ]
| 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] |
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.
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.
C12orf42 gene has only one other member in its gene family, this gene is known as Neuroligin 4, Y linked gene (NLGN4Y). [18]
C12orf42 orthologs are mostly mammals. One exception that was found is the Pelodiscus Sinensis or more commonly known as the Chinese soft-shell turtle.
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 |
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.
Chromosome 9 open reading frame 152 is a protein that in humans is encoded by the C9orf152 gene. The exact function of the protein is not completely understood.
PRR29 is a protein encoded by the PRR29 gene located in humans on chromosome 17 at 17q23.
Uncharacterized protein C2orf73 is a protein that in humans is encoded by the C2orf73 gene. The protein is predicted to be localized to the nucleus.
Chromosome 16 open reading frame 46 is a protein of yet to be determined function in Homo sapiens. It is encoded by the C16orf46 gene with NCBI accession number of NM_001100873. It is a protein-coding gene with an overlapping locus.
Chromosome 1 open reading frame 112, is a protein that in humans is encoded by the C1orf112 gene, and is located at position 1q24.2. C1orf112 encodes for seventeen variants of mRNA, fifteen of which are functional proteins. C1orf112 has a determined precursor molecular weight of 96.6 kDa and an isoelectric point of 5.62. C1orf112 has been experimentally determined to localize to the mitochondria, although it does not contain a mitochondrial targeting sequence.
C15orf39 is a protein that in humans is encoded by the Chromosome 15 open reading frame 15 (C15orf39) gene.
Chromosome 4 open reading frame 51 (C4orf51) is a protein which in humans is encoded by the C4orf51 gene.
Cilia- and flagella-associated protein 299 (CFAP299), is a protein that in humans is encoded by the CFAP299 gene. CFAP299 is predicted to play a role in spermatogenesis and cell apoptosis.
Chromosome 1 open reading frame (C1orf167) is a protein which in humans is encoded by the C1orf167 gene. The NCBI accession number is NP_001010881. The protein is 1468 amino acids in length with a molecular weight of 162.42 kDa. The mRNA sequence was found to be 4689 base pairs in length.
C22orf23 is a protein which in humans is encoded by the C22orf23 gene. Its predicted secondary structure consists of alpha helices and disordered/coil regions. It is expressed in many tissues and highest in the testes and it is conserved across many orthologs.
C5orf46 is a protein coding gene located on chromosome 5 in humans. It is also known as sssp1, or skin and saliva secreted protein 1. There are two known isoforms known in humans, with isoform 2 being the longer of the two. The protein encoded is predicted to have one transmembrane domain, and has a predicted molecular weight of 9,692 Da, and a basal isoelectric point of 4.67.
C1orf122 is a gene in the human genome that encodes the cytosolic protein ALAESM.. ALAESM is present in all tissue cells and highly up-regulated in the brain, spinal cord, adrenal gland and kidney. This gene can be expressed up to 2.5 times the average gene in its highly expressed tissues. Although the function of C1orf122 is unknown, it is predicted to be used for mitochondria localization.
C7orf50 is a gene in humans that encodes a protein known as C7orf50. This gene is ubiquitously expressed in the kidneys, brain, fat, prostate, spleen, among 22 other tissues and demonstrates low tissue specificity. C7orf50 is conserved in chimpanzees, Rhesus monkeys, dogs, cows, mice, rats, and chickens, along with 307 other organisms from mammals to fungi. This protein is predicted to be involved with the import of ribosomal proteins into the nucleus to be assembled into ribosomal subunits as a part of rRNA processing. Additionally, this gene is predicted to be a microRNA (miRNA) protein coding host gene, meaning that it may contain miRNA genes in its introns and/or exons.
Uncharacterized protein C17orf78 is a protein encoded by the C17orf78 gene in humans. The name denotes the location of the parent gene, being at the 78th open reading frame, on the 17th human chromosome. The protein is highly expressed in the small intestine, especially the duodenum. The function of C17orf78 is not well defined.
Chromosome 1 Opening Reading Frame 94 or C1orf94 is a protein in human coded by the C1orf94 gene. The function of this protein is still poorly understood.
C12orf24 is a gene in humans that encodes a protein known as FAM216A. This gene is primarily expressed in the testis and brain, but has constitutive expression in 25 other tissues. FAM216A is an intracellular protein that has been predicted to reside within the nucleus of cells. The exact function of C12orf24 is unknown. FAM216A is highly expressed in Sertoli cells of the testis as well as different stage spermatids.
C6orf136 is a protein in humans encoded by the C6orf136 gene. The gene is conserved in mammals, mollusks, as well some porifera. While the function of the gene is currently unknown, C6orf136 has been shown to be hypermethylated in response to FOXM1 expression in Head Neck Squamous Cell Carcinoma (HNSCC) tissue cells. Additionally, elevated expression of C6orf136 has been associated with improved survival rates in patients with bladder cancer. C6orf136 has three known isoforms.
C11orf98 is a protein-encoding gene on chromosome 11 in humans of unknown function. It is otherwise known as c11orf48. The gene spans the chromosomal locus from 62,662,817-62,665,210. There are 4 exons. It spans across 2,394 base pairs of DNA and produces an mRNA that is 646 base pairs long.
Chromosome 17 open reading frame 75 is a protein that in humans is encoded by the C17orf75 gene. C17orf75 is also known as SRI2 and is a human protein encoding gene located at 17q11.2 on the complementary strand. The protein this gene encodes is also known as NJMU-R1. The C17orf75 gene is ubiquitously expressed at medium-low levels throughout the body and at slightly higher levels in the brain and testes. This protein is thought to be part of a complex associated with golgin-mediated vesicle capture.
Chromosome 5 Open Reading Frame 47, or C5ORF47, is a protein which, in humans, is encoded by the C5ORF47 gene. It also goes by the alias LOC133491. The human C5ORF47 gene is primarily expressed in the testis.