C12orf60 | |||||||||||||||||||||||||||||||||||||||||||||||||||
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Identifiers | |||||||||||||||||||||||||||||||||||||||||||||||||||
Aliases | C12orf60 , chromosome 12 open reading frame 60 | ||||||||||||||||||||||||||||||||||||||||||||||||||
External IDs | MGI: 3605234; HomoloGene: 52193; GeneCards: C12orf60; OMA:C12orf60 - orthologs | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Uncharacterized protein C12orf60 is a protein that in humans ( Homo sapiens ) is encoded by the C12orf60 gene. The gene is also known as LOC144608 or MGC47869. The protein lacks transmembrane domains and helices, but it is rich in alpha-helices. It is predicted to localize in the nucleus. [5]
The C12orf60 mature mRNA transcript is 1139 nucleotides long [6] and encodes a protein containing 245 amino acids. [7] The protein lacks transmembrane domains and helices, but it is rich in alpha-helices. It is predicted to localize in the nucleus, but its function is not yet well understood by the scientific community. The gene was listed as a potential biomarker for detecting the efficacy of allergen immunotherapy. [8]
The gene is highly expressed in the testes and colon, but it is also expressed in the kidney, breast carcinomas, brain, and various endocrine glands. [9]
C12rf60 is located on Chromosome 12 beginning at 14,803,572 bp and ending at 14,823,858 bp, spanning 20,287 base pairs [10] It is located on the forward/positive strand between the 12p12.3 and 12p13.1 cytogenic bands. [11] Other genes that are within 100 kilobases of this gene include: [12]
C12orf60 is also known as LOC144608 and MGC47869.
A total of 22 exons exist within the gene.5 From these exons, there are 13 transcript variants. 12 of these transcript variants are predicted, and only a further 7 of these are predicted to encode a protein. Furthermore, they are predicted to encode the same protein.
The notable features of the mRNA sequence include two polyadenylation signals in the 3' untranslated region (UTR), and it is the target of several RNA-binding proteins (RBP) including RBP-MBNL1 in the 5' UTR. A single intron splice site exists in the primary transcript, as does an upstream in-frame stop codon.
C12orf60 has a predicted isoelectric point of 8.19 and a molecular weight of 27.6 kilodaltons. Glycine and tyrosine residues are relatively less prevalent compared to other proteins in the human proteome, while methionine is more prevalent.
The protein product is predicted to have multiple α-helices, coiled coil, and one β-sheet. It is suggested that the protein does not contain transmembrane regions or helices, meaning that the protein is not anchored to the cell membrane nor an intracellular membrane like the Golgi apparatus. [14]
In the predicted protein product, C12orf60 contains a conserved protein domain of 225 amino acids. This domain (DUF4533) is within the pfam15047 family of proteins. Only one other gene is listed within this family: C12orf69 , which is also known as SMOC3 (single-pass membrane protein with coiled-coil domains 3). [15]
Analysis of human C12orf60 and 9 of its orthologs reveals a highly conserved ERL motif starting at the 10th residue of the human protein sequence. It is not known whether this motif occurs in other proteins.
Other conserved residues are Asp25, Ser28, Phe37, Met41, Glu69, Leu85, Lys88, Leu143, Pro147, Ile148, Leu151, Gln164, Lys189, Leu191, Ala207, and Glu212, Leu225, and Lys227. Furthermore, these residues lie within DUF4533, suggesting that these conserved amino acids are important for the function of the domain. Also, the region between the 100 and 150 residues are not conserved. Thus, this region is not likely vital to the protein's function.
Since it is predicted that the protein product is intracellular, extracellular modifications are not predicted to occur on C12orf60. Other modifications such as acetylation, phosphorylation, picornaviral protease cleavage, sumoylation, and O-beta-GlcNAcylation are predicted to occur on C12orf60 as well as several of its orthologous proteins. There are two amino acids that serve as sites of both phosphorylation and O-beta-GlcNAcylation, which may indicate a site of protein activation or inactivation.
C12orf60 is predicted to be localized in the nucleus, cytoplasm, or outside the cell. [16] [17] [18] [19] [20] [21] However, current literature supports its localization in the nucleus.
Expression of C12orf60 is regulated. The gene is highly expressed in the testes and colon, but it is also expressed in the kidney, breast carcinomas, various endocrine glands, and some regions of the brain. [23] [24] [25] It is also expressed in the embryo body and fetus during development. [23]
The promoter GXP_71811 regulates the expression of C12orf60. The promoter is 1373 base pairs long and is also located on the positive strand. There are over 400 transcription factors that are possible matches for binding to this promoter, including those of the SOX/SRY-sex/testis determining, human and murine ETS, and homeodomain transcription factors. [10]
Rolland et al. found that C12orf60 interacts with BMP4 (bone morphogenetic protein 4). [26] BMP4 induces bone and cartilage formation. It also acts in mesoderm induction and fracture repair.
Several other proteins might also interact with C12orf60, [27] and some are predicted to be co-expressed with the protein. [28] Possible protein interactions include L3MBTL4, C3orf67, FAM78A, and PXDC1. Rats that overexpressed L3MBTL4 had higher blood pressure and heart rate. [29]
Proteins that are thought to be co-expressed alongside C12orf60 include ELMOD2, TTC30B, and BCDIN3D. ELMOD2 is thought to be involved in antiviral responses and causing familial idiopathic pulmonary fibrosis. [30] TTC30B is involved in the organelle biogenesis and maintenance pathway as well as intraflagellar transport. BCDIN3D is a methyltransferase and serves as a negative regulator of miRNA processing. [31] As there is no agreement from various sources on any protein-protein interaction, it is difficult to determine if any of these interactions actually occur.
There are no known paralogs to this gene within the human genome, and no paralogs of C12orf60 were found within the selected species that have a C12orf60 protein ortholog.
Many orthologs are found in mammals and a couple of bird species.
Genus and Species | Common Name | Estimated Time Since LCA of Protein (MY) | Accession # (mRNA) | Accession # (Protein) | Corrected Protein Sequence Identity Deviation (%) |
---|---|---|---|---|---|
Homo sapiens | Humans | 0 | NM_175874.3 | NP_787070.2 | 0 |
Pongo abelii | Sumatran orangutan | 15.76 | XM_002822980.2 | XP_002823026.1 | 2.94 |
Rhinopithecus bieti | Black snub-nosed monkey | 29.44 | XM_017873538.1 | XP_017729027.1 | 9.87 |
Cebus capucinus imitator | White-headed capuchin | 43.2 | XM_017528453.1 | XP_017383942.1 | 9.87 |
Saimiri boliviensis boliviensis | Bolivian squirrel monkey | 43.2 | XM_003934554.2 | XP_003934603.1 | 10.3 |
Propithecus coquereli | Coquerel's sifaka | 74 | XM_012652172.1 | XP_012507626.1 | 28.6 |
Ceratotherium simum simum | Southern white rhinoceros | 96 | XM_004435503.2 | XP_004435560.1 | 33.1 |
Physeter catodon | Sperm whale | 96 | XM_007107758.1 | XP_007107820.1 | 35.4 |
Equus caballus | Horse | 96 | XM_001497318.3 | XP_001497368.1 | 38.3 |
Miniopterus natalensis | Natal long-fingered bat | 96 | XM_016197505.1 | XP_016052991.1 | 40.8 |
Felis catus | Domestic cat | 96 | XM_003988472.3 | XP_003988521.1 | 41.4 |
Ovis aries | Sheep | 96 | XM_004007552.3 | XP_004007601.1 | 43.9 |
Ursus maritimus | Polar bear | 96 | XM_008707031.1 | XP_008705253.1 | 44.0 |
Choloepus hoffmanni | Hoffman's two-toed sloth | 105 | N/A | N/A | 44.5 |
Canis lupus familiaris | Dog | 96 | XM_005637113.2 | XP_005637170.1 | 48.1 |
Erinaceus europaeus | Western European hedgehog | 96 | XM_007533153.1 | XP_007533215.1 | 48.8 |
Dasypus novemcinctus | Nine-banded armadillo | 105 | XM_004460316.1 | XP_004460373.1 | 56.0 |
Echinops telfairi | Small Madagascar hedgehog | 105 | XM_004713800.1 | XP_004713857.1 | 56.0 |
Ochotona princeps | American pika | 90 | XM_004592653.2 | XP_004592710.1 | 56.7 |
Myotis brandtii | Brandt's bat | 96 | XM_005866788.2 | XP_005866850.1 | 59.2 |
Mus musculus | House mouse | 90 | NM_178776.3 | NP_848891.2 | 62.0 |
Rattus norvegicus | Norway rat | 90 | NM_001037797.1 | NP_001032886.1 | 67.3 |
Sorex araneus | European shrew | 96 | XM_004611368.1 | XP_004611425.1 | 75.1 |
Leptosomus discolor | Cuckoo roller | 312 | XM_009947218.1 | XP_009945520.1 | 129 (100%) |
Melopsittacus undulatus | Budgerigar | 312 | N/A | N/A | 160 (100%) |
The gene is within 1 Mb of SNPs that were associated with obesity, height, and weight. [32]
The gene was listed along with two other genes in a patent as a potential biomarker for detecting the efficacy of allergen immunotherapy. [8] Specifically, detection of 3 copies of C12orf60 meant that immunotherapy was ineffective.
In one study, the gene was among several identified genes that were translocated in a single patient with recurrent acute lymphoblastic leukemia. [33] This translocation was associated with apoptosis and tumorigenesis.
Another study found that the gene is upregulated by at least 1.5 fold in cells that expressed Constitutive Myocyte Enhancer Factor 2 (MEF2CA). [34] MEF2CA is expressed naturally in the brain.
One study stated the gene contains a “perfect potential antioxidant protein 1 (ATOX1) DNA interaction site in the promoter region.” [35]
C8orf48 is a protein that in humans is encoded by the C8orf48 gene. C8orf48 is a nuclear protein specifically predicted to be located in the nuclear lamina. C8orf48 has been found to interact with proteins that are involved in the regulation of various cellular responses like gene expression, protein secretion, cell proliferation, and inflammatory responses. This protein has been linked to breast cancer and papillary thyroid carcinoma.
Ankyrin repeat domain-containing protein 24 is a protein in humans that is coded for by the ANKRD24 gene. The gene is also known as KIAA1981. The protein's function in humans is currently unknown. ANKRD24 is in the protein family that contains ankyrin-repeat domains.
The coiled-coil domain containing 142 (CCDC142) is a gene which in humans encodes the CCDC142 protein. The CCDC142 gene is located on chromosome 2, spans 4339 base pairs and contains 9 exons. The gene codes for the coiled-coil domain containing protein 142 (CCDC142), whose function is not yet well understood. There are two known isoforms of CCDC142. CCDC142 proteins produced from these transcripts range in size from 743 to 665 amino acids and contain signals suggesting protein movement between the cytosol and nucleus. Homologous CCDC142 genes are found in many animals including vertebrates and invertebrates but not fungus, plants, protists, archea, or bacteria. Although the function of this protein is not well understood, it contains a coiled-coil domain and a RINT1_TIP1 motif located within the coiled-coil domain.
PRR29 is a protein encoded by the PRR29 gene located in humans on chromosome 17 at 17q23.
Coiled-coil domain containing protein 180 (CCDC180) is a protein that in humans is encoded by the CCDC180 gene. This protein is known to localize to the nucleus and is thought to be involved in regulation of transcription as are many proteins containing coiled-coil domains. As it is expressed most highly in the testes and is regulated by SRY and SOX transcription factors, it could be involved in sex determination.
Chromosome 10 open reading frame 67 (C10orf67), also known as C10orf115, LINC01552, and BA215C7.4, is an un-characterized human protein-coding gene. Several studies indicate a possible link between genetic polymorphisms of this and several other genes to chronic inflammatory barrier diseases such as Crohn's Disease and sarcoidosis.
Uncharacterized protein Chromosome 16 Open Reading Frame 71 is a protein in humans, encoded by the C16orf71 gene. The gene is expressed in epithelial tissue of the respiratory system, adipose tissue, and the testes. Predicted associated biological processes of the gene include regulation of the cell cycle, cell proliferation, apoptosis, and cell differentiation in those tissue types. 1357 bp of the gene are antisense to spliced genes ZNF500 and ANKS3, indicating the possibility of regulated alternate expression.
Leukocyte Receptor Cluster Member 9 is an uncharacterized protein encoded by the LENG9 gene. In humans, LENG9 is predicted to play a role in fertility and reproductive disorders associated with female endometrium structures.
BEND2 is a protein that in humans is encoded by the BEND2 gene. It is also found in other vertebrates, including mammals, birds, and reptiles. The expression of BEND2 in Homo sapiens is regulated and occurs at high levels in the skeletal muscle tissue of the male testis and in the bone marrow. The presence of the BEN domains in the BEND2 protein indicates that this protein may be involved in chromatin modification and regulation.
C17orf53 is a gene in humans that encodes a protein known as C17orf53, uncharacterized protein C17orf53. It has been shown to target the nucleus, with minor localization in the cytoplasm. Based on current findings C17orf53 is predicted to perform functions of transport, however further research into the protein could provide more specific evidence regarding its function.
Chromosome 21 Open Reading Frame 58 (C21orf58) is a protein that in humans is encoded by the C21orf58 gene.
Forkhead-associated domain containing protein 1 (FHAD1) is a protein encoded by the FHAD1 gene.
C15orf39 is a protein that in humans is encoded by the Chromosome 15 open reading frame 15 (C15orf39) gene.
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.
Single-pass membrane and coiled-coil domain-containing protein 3 is a protein that is encoded in humans by the SMCO3 gene.
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.
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.
Family with sequence 98, member C or FAM98C is a gene that encodes for FAM98C has two aliases FLJ44669 and hypothetical protein LOC147965. FAM98C has two paralogs in humans FAM98A and FAM98B. FAM98C can be characterized for being a Leucine-rich protein. The function of FAM98C is still not defined. FAM98C has orthologs in mammals, reptiles, and amphibians and has a distant orhtologs in Rhinatrema bivittatum and Nanorana parkeri.
Secernin-3 (SCRN3) is a protein that is encoded by the human SCRN3 gene. SCRN3 belongs to the peptidase C69 family and the secernin subfamily. As a part of this family, the protein is predicted to enable cysteine-type exopeptidase activity and dipeptidase activity, as well as be involved in proteolysis. It is ubiquitously expressed in the brain, thyroid, and 25 other tissues. Additionally, SCRN3 is conserved in a variety of species, including mammals, birds, fish, amphibians, and invertebrates. SCRN3 is predicted to be an integral component of the cytoplasm.