Chromosome 12 open reading frame 71
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Chromosome 12 open reading frame 71
Chromosome 12 open reading frame 71 (c12orf71), is a protein-coding gene in Homo sapiens.
Gene
c12orf71 Gene
The gene is located on the minus strand of chromosome 12 (12p11.23).[1][2] The DNA sequence of the c12orf71 gene is 3071 base pairs long and 8 structural variations have been identified including deletions, duplications, gain- and loss-of-function mutations.[3] c12orf71 gene was determined to be altered (gain of 21 Mb) in the chromosomal region 12p11.21-p13.3 of a male patient with chromosomal aberrations and in a duplication (gain of 411 kb) at chromosome 12p11.23 along with c12orf70, the coding regions of STK38L and ARNTL2 and a portion of PPFIBP1.[4][5] Manual inspection of alignments, has determined that c12orf71 gene is mammalian specific.[6] Furthermore, genome-wide screening has identified c12orf71 as one of 1000 disrupted genes that are positively selected by cisplatin, a chemotherapy drug.[1] c12orf71 gene has been found to be present in a protein-protein interaction (PPI) network of the Carboxypeptidase M (CPM) gene, along with nine more genes.[7]
Orthologs
Orthologs of the c12orf71 gene have been found only in mammals, in particular Theria (marsupials and placentals) including Mus muculus (mouse), Pan troglodytes (chimpanzee) and Canis lupus familiaris (dog) and no paralogs of the gene have been reported.[8] The Canis lupus ortholog of c12orf71, located on chromosome 10, has been localized in proximity to the lysozyme (Lyz) gene.[9]
RNA
c12orf71 Transcript Variant 1
c12orf71 transcript variant 1 mRNA is 1022 nucleotides long and consists of 2 exons. There is one more, slightly longer transcript variant of c12orf71. The mRNA sequence of c12orf71 consists of a coding sequence that spans over the two exons and 2 poly-A signal sequences. [1]
c12orf71 mRNA Expression
In humans c12orf71 has shown a highest expression level in testis, however it is also expressed in the bone marrow, skin, spleen, lymph node and liver. [10] RNA-sequencing analysis has revealed that c12orf71 was expressed at a very low level or not expressed at all in osteoarthritis and non-osteoarthritis hip cartilage. [11] A genome engineering study that studied mice knock-outs has found that c12orf71 has a decreased expression in humans compared to mouse testis, however the absence of the c12orf71 had no effect on mouse fertilization.[12]
Protein
The protein encoded by c12orf71 gene, the uncharacterized c12orf71 protein is 269 amino acids long and has a molecular weight of 30 224 Da. The first 21 amino acids of the coding sequence are comprising a disordered region, followed by a domain of unknown function (DUF4640) which spans almost the whole coding sequence.[13] Additionally, the protein also contains a vacuolar domain (Psort2), is mammal specific and may be modulated by phosphorylation.[2]
c12orf71 Protein Function
It has been found that c12orf71 protein is one of fifteen proteins that are overexpressed in mesenchymal cells of the olfactory epithelium due to a mutation in PSEN1 gene that causes Familial Alzheimer’s disease, however no function has been indicated.[14] Additionally, the protein has been listed as a unique protein that is present in humans but absent in Neanderthals and is a modern human protein with most distinct regions against Neanderthals proteins (265 out of 269 amino acids have been determined as relatively unique).[15]
Clinical Association
There is only one disease associated with c12orf71 gene, common warts.[2] A study of global gene methylation of common warts caused by HPV infection found that c12orf71 gene is differentially methylated in Arab male patients with common warts. In particular, c12orf71 is hypomethylated in skin infected with common warts compared to normal skin.[16] 10 SNPs from the GWAS catalog associate c12orf71 gene with obsolete and androgenic alopecia, healing of bone mineral density and educational attainment.[3]
References
- ^ a b "Homo sapiens chromosome 12 open reading frame 71 (C12orf71), transcript variant 1, mRNA". 2022-06-09.
{{cite journal}}: Cite journal requires|journal=(help) - ^ a b c "AceView: Gene:C12orf71, a comprehensive annotation of human, mouse and worm genes with mRNAs or ESTsAceView". www.ncbi.nlm.nih.gov. Retrieved 2022-09-30.
- ^ a b "C12orf71 Gene - GeneCards | CL071 Protein | CL071 Antibody". www.genecards.org. Retrieved 2022-09-30.
- ^ Gomes, Alexandra Galvão (2014-06-26). Caracterização citogenômica de aberrações cromossômicas (text thesis) (in Brazilian Portuguese). Universidade de São Paulo.
- ^ Pyatt, R. E., & Astbury, C. (2011). Interpretation of Copy Number Alterations Identified Through Clinical Microarray-Comparative Genomic Hybridization. ClinicalKey. https://www-clinicalkey-com.ezp1.lib.umn.edu/#
- ^ Cañas, Villanueva (2015-11-20). Insights into mammalian adaptive evolution through genomics data (Ph.D. Thesis thesis). Universitat Pompeu Fabra.
- ^ Asghari Alashti, Fariborz; Goliaei, Bahram; Minuchehr, Zarrin (2022-01-15). "Analyzing large scale gene expression data in colorectal cancer reveals important clues; CLCA1 and SELENBP1 downregulated in CRC not in normal and not in adenoma". American Journal of Cancer Research. 12 (1): 371–380. ISSN 2156-6976. PMC 8822279. PMID 35141024.
- ^ "C12orf71 orthologs". NCBI. Retrieved 2022-09-30.
- ^ Irwin, David M.; Biegel, Jason M.; Stewart, Caro-Beth (2011-06-15). "Evolution of the mammalian lysozyme gene family". BMC Evolutionary Biology. 11 (1): 166. doi:10.1186/1471-2148-11-166. ISSN 1471-2148. PMC 3141428. PMID 21676251.
{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link) - ^ "C12orf71 chromosome 12 open reading frame 71 [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2022-09-30.
- ^ Johnson, Katherine (2016). Functional analysis of the osteoarthritis susceptibility loci marked by the polymorphisms rs10492367 and rs9350591 (Thesis thesis). Newcastle University.
- ^ Miyata, Haruhiko; Castaneda, Julio M.; Fujihara, Yoshitaka; Yu, Zhifeng; Archambeault, Denise R.; Isotani, Ayako; Kiyozumi, Daiji; Kriseman, Maya L.; Mashiko, Daisuke; Matsumura, Takafumi; Matzuk, Ryan M.; Mori, Masashi; Noda, Taichi; Oji, Asami; Okabe, Masaru (2016-07-12). "Genome engineering uncovers 54 evolutionarily conserved and testis-enriched genes that are not required for male fertility in mice". Proceedings of the National Academy of Sciences. 113 (28): 7704–7710. doi:10.1073/pnas.1608458113. ISSN 0027-8424. PMC 4948324. PMID 27357688.
{{cite journal}}: CS1 maint: PMC format (link) - ^ "uncharacterized protein C12orf71 [Homo sapiens] - Protein - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2022-09-30.
- ^ Hernández, R., & Jhenifer, L. (2019). La mutación A431E en PSEN1 causante de enfermedad de Alzheimer Familiar altera el perfil proteómico de las células mesenquimales del epitelio olfatorio (Master's thesis, Tesis (MC)--Centro de Investigación y de Estudios Avanzados del IPN Departamento de Biomedicina Molecular).
- ^ Hosseini, Morteza; Pratas, Diogo; Pinho, Armando J. (2019-09). "A Probabilistic Method to Find and Visualize Distinct Regions in Protein Sequences". 2019 27th European Signal Processing Conference (EUSIPCO): 1–5. doi:10.23919/EUSIPCO.2019.8902695.
{{cite journal}}: Check date values in:|date=(help) - ^ Alghamdi, Mansour A.; AL-Eitan, Laith N.; Tarkhan, Amneh H.; Al-Qarqaz, Firas A. (2021-01-01). "Global gene methylation profiling of common warts caused by human papillomaviruses infection". Saudi Journal of Biological Sciences. 28 (1): 612–622. doi:10.1016/j.sjbs.2020.10.050. ISSN 1319-562X.