Gene
Locus
The gene is located on the short arm of chromosome 16 at 16p13.1. [5] Its genomic sequence begins on the plus strand at 4,734,242 bp and ends at 4,749,396 bp. [1]
Uncharacterized protein Chromosome 16 Open Reading Frame 71 is a protein in humans, encoded by the C16orf71 gene. [1] The gene is expressed in epithelial tissue of the respiratory system, adipose tissue, and the testes. [2] Predicted associated biological processes of the gene include regulation of the cell cycle, cell proliferation, apoptosis, and cell differentiation in those tissue types. [3] 1357 bp of the gene are antisense to spliced genes ZNF500 and ANKS3, indicating the possibility of regulated alternate expression. [4]
The gene is located on the short arm of chromosome 16 at 16p13.1. [5] Its genomic sequence begins on the plus strand at 4,734,242 bp and ends at 4,749,396 bp. [1]
Three different protein encoding transcript variants, or isoforms, have been identified for C16orf71. [7] One non-protein coding transcript variant was identified for the gene. [8]
| Name | Length (bp) | Protein (aa) | Mass (kDa) | Biotype |
|---|---|---|---|---|
| Uncharacterized protein C16orf71 (primary assembly) [7] | 2716 | 520 | 55.7 | Protein coding |
| Uncharacterized protein C16orf71 isoform X2 [9] | 2324 | 136 | 14.6 | Protein coding |
| Uncharacterized protein C16orf71 isoform X3 [10] | 2435 | 156 | 16.8 | Protein coding |
| Uncharacterized protein C16orf71 isoform X1 [11] | 2562 | 537 | 57.5 | Protein coding |
| Uncharacterized protein C16orf71 Transcript-003 [8] | 3705 | No protein | – | Retained intron |
The primary encoded protein consists of 520 amino acid residues, 11 total exons, and is 15.14 kb long, with a molecular weight of approximately 55.68 kDa. [1] The predicted isoelectric point was reported to be 4.81, indicating it is relatively unstable. [13] The gene was reported to be well expressed, at 1.1 times the average gene level. [4]
Alanine was the most abundant amino acid, contributing to 11.54% of the molecular weight of the protein. [13] Serine was the second most abundant, contributing 10.19% to the overall molecular weight. [13] The average Alanine frequency in vertebrate proteins is approximately 7.4% and the average Serine frequency is approximately 8.1%. [14]
C16orf71 has one identified domain of unknown function, DUF4701, that is conserved in all mammals and some species of reptiles and birds. [1] DUF4701 spans from amino acid residue 21 to 520 in the protein. [1]
C16orf71 is predicted to undergo multiple post-translational modifications such as phosphorylation, N-glycosylation, and amidation.
Experimentation with C16orf71 has revealed interactions with four other proteins, ARHGAP1, ZNFX1, PLVAP, and MBTPS1. [15] ARHGAP1, ZNFX1, and MBTPS1 are associated with regulation in signaling and metabolism while PLVAP is associated with the formation of small lipid rafts in the plasma membrane of vertebrate endothelial and adipose cells. [3]
The majority of the predicted interactions involved with the protein related to regulation of mitotic processes, cellular differentiation, proliferation, metabolism, and signaling. [3] Additional related processes included the formation and differentiation of B cells, T cells, endothelial cells, endoderm, and endocrine glands. [3]
| Interactor [3] | Function [3] |
|---|---|
| CREB1 (cAMP responsive element binding protein 1) | Induction of growth, differentiation, migration, adhesion, and cell survival in epidermal cells Mediation of growth, differentiation, survival, and migration in early developmental stages Mediation of metabolic functions, tissue repair, and regeneration in mature adult tissue |
| TYK2 (tyrosine kinase 2) | Cellular differentiation, migration, and proliferation in immune cells |
| TNIP2 (TNPAIP3 interacting protein 2) | Negative regulation of apoptosis for endothelial cells |
| OBSL1 (obscurin-like 1) | Mitotic regulation, cytoskeleton and microtubule organization and assembly |
| DUSP3 (dual specificity phosphatase 3) | Negative regulation of multiple enzymatic cascades and signaling pathways Positive regulation of the mitotic cell cycle |
| FGFRL1 (fibroblast growth factor receptor-like 1) | Fibroblast growth activity |
| GNPAT (glyceronephosphate O-acyltransferase) | Involved in multiple metabolic and biosynthesis processes for cellular lipids, ether lipids, glycerophospholipids, phosphatidic acid, and phospholipids |
| AURKA (aurora kinase A) | Regulation for G2/M transition, nuclear division, mitotic spindle organization, the centrosome cycle, cytokinesis, and spindle stabilization |
| NAMPT (nicotinamide phosphoribosyltransferase) | Adipose tissue development, regulation of nicotinamide metabolism, signal transduction, cell-cell signaling, and vitamin metabolism. |
C16orf71 was observed in nuclear speckles of the nucleus through experimental protocols involving fluorescent in situ hybridization with antibodies. [2] Nuclear speckles, also known as interchromatin granule clusters, are enriched in pre-mRNA splicing factors. [16] These highly dynamic structures are located in interchromatin regions of the nucleoplasm in mammalian cells and have been observed to cycle throughout various nuclear regions and active transcription sites. [16]
The secondary structure of C16orf71 is predicted to consist primarily of coils, with small regions of alpha helices and two segments of beta sheets throughout the span of the protein. [13] [17]
Protein sequences of the gene's mammalian orthologs were analyzed to reveal similar results, while distant reptilian and avian ortholog sequences predicted more regions of beta sheets. [18] [19]
Human expression for the gene has been observed primarily in respiratory epithelial tissue, specifically the trachea, larynx, nasopharynx, and bronchus. [2] C16orf71 is also moderately expressed in adipose tissue and testes. [2]
DNA microarray analysis from various experiments provided information on the expression levels of C16orf71 in unique, varying conditions.
The gene appears to have higher levels of expression in the omental adipose tissue of obese subjects compared to non-obese subjects. [20]
C16orf71 was also observed to have decreased expression when there was a depletion of HIF-1 alpha, HIF-2 beta, or both. HIF, or hypoxia-inducible factors, are responsible for the mediation of hypoxia effects within the body. [23] In addition, HIFs promote clotting and restoration of various epithelial tissues and are vital in the development of mammalian embryos, sperm, and ova. [24]
Data from an experiment also indicated noticeably lower expression of the gene in sperm affected with teratozoospermia, a condition where sperm have abnormal morphology affecting the fertility in males, compared to normal sperm. [22]
C16orf71 was observed to be present in all stages of development, with similar levels of expression throughout. [25]
Three chemicals, bisphenol A, butyraldehyde, and polychlorinated biphenyls, have been experimentally tested with C16orf71 for evidence of interaction. [26]
Bisphenol A is suspected to cause impairment in male reproduction. [27] An experiment utilizing seminiferous tubule culture was conducted to observe the effects on meiosis and potential germ-line abnormalities. [27] Gene expression analysis revealed decrease expression for C16orf71 when exposed to the chemical. [27]
Butyraldehyde has been observed to affect inflammatory responses in bronchial airway tissue on a genetic level. [28] Microarray analysis was used to determine levels of expression in human alveolar epithelial cells after exposure to the compound. [28] Results indicated decreased expression for C16orf71 when exposed to the chemical. [28]
Polychlorinated biphenyl was used in an experiment to determine its effects on external male genital development. [29] Human fetal corpora cavernosa cells were used as the model tissue. [29] Toxicogenomic analysis indicated the chemical affected all genes involved with genitourinary development and revealed lowered expression levels for C16orf71. [29]
1357 bp of the gene are antisense to spliced genes ZNF500 and ANKS3, indicating possibility of regulated alternate expression. [4] A ZNF500 transcription factor binding domain was found on the minus strand within the promoter region of the gene. [30] ZNF500 is predicted to play a role in gene regulation, transcription, and cellular differentiation. [31]
The beginning of the promoter region was predicted to be 117 bp upstream from the 5' UTR of C16orf71 and is 1371 bp long. [30] The region was analyzed for predicted transcription factors and regulatory elements. Predicted transcription factors in the promoter region related to the regulation of the cell cycle, proliferation, apoptosis, and differentiation of sperm and epithelial tissue components. [3]
| Transcription factor [30] | Associated functions [30] |
|---|---|
| Ascl1 (Mammaliam achaete scute homolog 1) | B-cell differentiation, maturation, and development Negative regulation of transcription and apoptosis Positive regulation of cell cycle and cellular differentiation Response to hypoxia and epidermal growth factor Regulation of epithelial cell differentiation |
| ZNF500 (Zinc finger with KRAB and SCAN domains 3) | Cartilage development Negative regulation of gene expression and cellular senescence T-cell and stem cell differentiation Positive regulation of transcription |
| SMAD4 transcription factor involved in TGF-beta signaling | Regulation of apoptosis, T-cell and endothelial cell activation Endoderm formation and development Negative regulation of cell growth and death Response to hypoxia Thyroid gland development Tissue morphogenesis |
| Cysteine-serine-rich nuclear protein 1 | TGF-beta induced apoptosis Regulation of early development and differentiation Extracellular matrix formation |
Orthologs have been identified in most mammals for which complete genome data is available. [32] C16orf71 and its domain of unknown function, DUF4701, was present in mammals. [32] The most distant orthologs identified were reptilian. [32] [33]
The m value, or number of corrected amino acid changes per 100 residues, for the gene C16orf71 was plotted against the divergence of species in millions of years. When compared to the data of hemoglobin, fibrinopeptides, and cytochrome C, it was determined that the gene has the closest progression to fibrinopeptides, suggesting a relatively rapid pace of evolution. M values for C16orf71 were derived from percentage of identity of species mRNA sequences compared to the human sequence using the formula derived from the Molecular Clock Hypothesis.
METTL26, previously designated C16orf13, is a protein-coding gene for Methyltransferase Like 26, also known as JFP2. Though the function of this gene is unknown, various data have revealed that it is expressed at high levels in various cancerous tissues. Underexpression of this gene has also been linked to disease consequences in humans.
TMEM156 is a gene that encodes the transmembrane protein 156 (TMEM156) in Homo sapiens. It has the clone name of FLJ23235.
PRR29 is a protein encoded by the PRR29 gene located in humans on chromosome 17 at 17q23.
OCC-1 is a protein, which in humans is encoded by the gene C12orf75. The gene is approximately 40,882 bp long and encodes 63 amino acids. OCC-1 is ubiquitously expressed throughout the human body. OCC-1 has shown to be overexpressed in various colon carcinomas. Novel splice variant of this gene was also detected in various human cancer types; in addition to encoding a novel smaller protein, OCC-1 gene produces a non-protein coding RNA splice variant lncRNA.
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.
Cardiac-enriched FHL2-interacting protein (CEFIP) is a protein encoded by the gene C10orf71 on chromosome 10 open reading frame 71. It is primarily understood that this gene is moderately expressed in muscle tissue and cardiac tissue.
Chromosome 6 open reading frame 62 (C6orf62), also known as X-trans-activated protein 12 (XTP12), is a gene that encodes a protein of the same name. The encoded protein is predicted to have a subcellular location within the cytosol.
Chromosome 19 open reading frame 18 (c19orf18) is a protein which in humans is encoded by the c19orf18 gene. The gene is exclusive to mammals and the protein is predicted to have a transmembrane domain and a coiled coil stretch. This protein has a function that is not yet fully understood by the scientific community.
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.
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 9 open reading frame 43 is a protein that in humans is encoded by the C9orf43 gene. The gene is also known as MGC17358 and LOC257169. C9orf43 contains DUF 4647 and a polyglutamine repeat region although protein function is not well understood.
Chromosome 19 open reading frame 44 is a protein that in humans is encoded by the C19orf44 gene. C19orf44 is an uncharacterized protein with an unknown function in humans. C19orf44 is non-limiting implying that the protein exists in other species besides human. The protein contains one domain of unknown function (DUF) that is highly conserved throughout its orthologs. This protein is most highly expressed in the testis and ovary, but also has significant expression in the thyroid and parathyroid. Other names for this protein include: LOC84167.
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.
ProteinFAM89A is a protein which in humans is encoded by the FAM89A gene. It is also known as chromosome 1 open reading frame 153 (C1orf153). Highest FAM89A gene expression is observed in the placenta and adipose tissue. Though its function is largely unknown, FAM89A is found to be differentially expressed in response to interleukin exposure, and it is implicated in immune responses pathways and various pathologies such as atherosclerosis and glioma cell expression.
TMEM275 is a protein that in humans is encoded by the TMEM275 gene. TMEM275 has two, highly-conserved, helical trans-membrane regions. It is predicted to reside within the plasma membrane or the endoplasmic reticulum's membrane.
C14orf180 is found on chromosome 14 in humans: 14q32.33. It consists of 1832 bp and 160 amino acids post translation. There is a total number of 6 exons. C14orf180 is also known as NRAC, C14orf77, and Chromosome 14 Open Reading Frame 180.
RING Finger Protein 227, also known as RNF227 and LINC02581, is a protein which in humans is encoded by the RNF227 gene. According to DNA microarray data, it is found in at least 15 tissues.
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.
C12orf29 is a protein that in humans is encoded by chromosome 12 open reading frame 29. The gene is ubiquitously expressed in various tissues. The protein has 325 amino acids. The biological process of C12orf29 has been annotated as hematopoietic progenitor cell differentiation. The molecular and cellular functions of C12orf29 gene have not yet well understood by the scientific community.