FAM120AOS | |||||||||||||||||||||||||||||||||||||||||||||||||||
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Aliases | FAM120AOS , C9orf10OS, family with sequence similarity 120A opposite strand | ||||||||||||||||||||||||||||||||||||||||||||||||||
External IDs | HomoloGene: 131283; GeneCards: FAM120AOS; OMA:FAM120AOS - orthologs | ||||||||||||||||||||||||||||||||||||||||||||||||||
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FAM120AOS, or family with sequence similarity 120A opposite strand, codes for uncharacterized protein FAM120AOS, which currently has no known function. [3] The gene ontology describes the gene to be protein binding. [4] Overall, it appears that the thyroid and the placenta are the two tissues with the highest expression levels of FAM120AOS across a majority of datasets.
The microarray-assessed tissue expression pattern of multiple normal tissues for FAM120AOS in humans was found using GDS3834 data. [5] The three tissues in the 90th percentile and higher for FAM120AOS gene expression are as follows: the bladder, epididymis, and thyroid. The thyroid is in the 91st percentile, while the other two are in the 90th percentile. Since high thyroid expression was also seen across the RNA-seq data, [6] [7] [8] [9] it appears that FAM120AOS expression may be important in the thyroid.
The common aliases for FAM120AOS are C9orf10OS, FLJ31534, LOC158293, and putative FAM120A opposite strand protein. [3]
There are two genomic locations for the gene, the first of which is chr9:93,431,441-93,453,601(GRCh38/hg38) with a length of 22,161 base pairs (bp), oriented on the minus strand of the chromosome. [10] The second genomic location for the gene is at chr9:96,208,776-96,215,874(GRCh37/hg19) with a length of 7,099 bp, also oriented on the minus strand of the chromosome. [10] The genes found upstream of FAM120AOS on chromosome 9 are FGD3, SUSD, C9orf89, WNK2, C9orf129, and NINJ1. [3] The genes found downstream from FAM120AOS on chromosome 9 are FAM120A and PHF2. [3]
The longest isoform of FAM120AOS in humans contains 3 exons. [4]
The mRNA transcript variant that encodes for human FAM120AOS isoform 1 is 5922 bp long and contains an upstream in-frame stop codon (taa) at 807-809 bp. [11]
There are 12 known isoforms of the human FAM120AOS gene. [4] The longest and most common transcript variant is isoform 1, which is 5922 bp in length. [4] [12] Transcript variants 3-12 are all non-coding RNAs, meaning that they do not code for a protein. [4] The only isoforms that are protein-encoding are isoform 1 and 2 of the human FAM120AOS gene. [4]
Isoform 2 is 5008 bp in length and contains an alternate exon in the 5' UTR, is missing a portion of the 5' coding region, and initiates translation at an alternate start codon, in comparison to isoform 1. [4] [13] The variant also has a shorter and more distinct N-terminus in comparison to isoform 1. [4]
All of the following variations mentioned are in comparison to isoform 1 of the human FAM120AOS gene.Isoform 3 is 2199 bp and uses an alternate splice site in the first exon. [4] [14] The transcript variants (e.g. isoforms) 6-12 are all candidates for nonsense-mediated mRNA decay (NMD). [4]
Isoform 4 of the gene is 2320 bp and uses an alternate splice site in the first exon and contains an alternate internal exon. [4] [15] Isoform 5 is 6043 bp and contains an alternate internal exon. Isoform 6 is 5272 bp and contains an alternate first exon and an alternate internal exon. [4] [16] Isoform 7 is 5095 bp and contains an alternate first exon. [4] [17] Isoform 8 is 5129 bp and contains an alternate first exon and alternate internal exon. [4] [18] Isoform 9 is 5151 bp and contains an alternate first exon. [4] [19] Isoform 10 is 5354 bp and contains an alternate first exon. [4] [20] Isoform 11 is 5475 bp and contains an alternate first exon and an alternate internal exon. [4] [21] Lastly, isoform 12 5216 is bp and contains an alternate first exon and an alternate internal exon. [4]
There are two different isoforms of the human FAM120AOS gene that encode a protein, isoforms 1 and 2. [4] The uncharacterized protein FAM120AOS isoform 1 is 256 amino acids long [22] and the uncharacterized protein FAM120AOS isoform 2 is 74 amino acids long. [23] Uncharacterized protein FAM120AOS isoform 1 is the longer and more abundant isoform found in humans, and contains protein domain Q5T035. [4] [10] The isoform also has a protein interactant, Q5T035-F120S_HUMAN, and CRISPR reagents and clone products of the protein available. [10]
Uncharacterized protein FAM120AOS isoform 1 (protein isoform 1) in humans has a calculated molecular weight of 27.8 kDa. [4] A theoretical value of 11.93 for the isoelectric point of the protein was determined through the use of ExPASy. [24] The basic isoelectric point indicates that protein isoform 1 is primarily basic. Table 1 shows the isoelectric points and molecular weights for all the different orthologs of the human FAM120AOS protein 1 across Primates and Artiodactyla. [25] The isoelectric point of the protein remains within a pH of 10.05-11.93 across all orthologs, indicating that the protein is primarily basic. However, the molecular weight of the FAM120AOS protein seems to vary greatly between orthologs, ranging from values of 8.1 kDa to 17.9 kDa, with a maximum value of 29.8 kDa. Many of the sequences with a lower molecular weight were found to be composed of fewer amino acids than the sequences with larger molecular weights. These length differences could also be attributed to possible different isoforms of the FAM120AOS protein being analyzed.
Organism | Taxonomic Group | Isoelectric Point | Molecular Weight (in kDa) |
Homo sapiens | Primates | 11.93 | 27.9 |
Pan troglodytes | Primates | 11.92 | 27.7 |
Pongo abelii | Primates | 11.69 | 27.8 |
Nomascus leucogenys | Primates | 10.32 | 7.9 |
Hylobates moloch | Primates | 10.06 | 8.1 |
Trachypithecus francoisi | Primates | 11.35 | 8.1 |
Rhinopithecus roxellana | Primates | 11.57 | 8.3 |
Macaca nemestrina | Primates | 11.35 | 8.1 |
Papio anubis | Primates | 10.98 | 8.2 |
Carlito syrichta | Primates | 11.36 | 25.8 |
Microcebus murinus | Primates | 11.52 | 29.8 |
Muntiacus muntjak | Artiodactyla | 11.21 | 17.9 |
Protein isoform 1 contains two different internal repeats in its amino acid composition, determined through analysis of the protein sequence using Dotlet JS. [26] The first internal repeat occurs at amino acid positions 41-59 and 88–105. [26] The second internal repeat occurs at amino acid positions 145-153 and 160–168. [26] There is an upstream in-frame stop codon (taa) present at amino acid positions 806–808. [4] There is an alternate polyadenylation site present at amino acid positions 2726–2731. [4] The polyadenylation signal used is present from amino acid positions 5889–5893. [4] The amino acid positions from L206-S211, H213, H215, K219-P225, and K227-C233 were found to be conserved across all of the strict orthologs of the human uncharacterized protein FAM120AOS isoform 1. [27] The amino acid G95 was found to be conserved across all Primates and Artiodactyla for which sequences were identified. [27] The human FAM120AOS protein 1 was found to arginine-rich, and glutamic acid and tyrosine-poor. [28]
The uncharacterized protein FAM120AOS isoform 1 in humans contains the protein domain Q5T035. [10]
Two notable motifs found using a eukaryotic linear motif analysis for the human FAM120AOS protein 1 are TRG_RT_diArg_1 and TRG_NLS_MonoExtN_4. [29] The TRG_RT_diArg_1 motif is a di Arginine retention/retrieving signal that is present on membrane proteins, where it serves for ER localization. [29] The TRG_NLS_MonoExtN_4 is a NLS classical nuclear localization signal, which is possessed by many nuclear proteins, indicating that the human FAM120AOS protein 1 is a nuclear protein.
The secondary structure of the human FAM120AOS protein 1 was predicted by the I-TASSER server and shows 11 alpha helices as follows, in order of position: SER15-TRP18, PRO25-SER27, THR34-TRP40, ALA85-ARG88, LYS111-ALA121, CYS145-ARG155, HIS158-ALA163, LEU169-LYS171, PRO179-ARG198, PRO225-CYS233, and PRO246-PHE252. [30]
The tertiary structure of the human FAM120AOS protein 1 was predicted by the I-TASSER server with a C-score of -4.00. [30] It appears that the outermost parts of the protein are more solvent accessible, while the inner areas are less solvent accessible. [30] The protein appears to be primarily blue, again indicating that it is a basic structure. [30] The protein also indicated the presence of a peripheral likelihood of 1.48 at amino acid position 132. [31] The NUCDISC results indicated the presence of pat 7 PLKKTKS (4) starting at amino acid position 168. [31]
There are four different promoters for the human FAM120AOS protein 1, which are depicted in the table below. [32] The promoter used for further analysis below (GXP_1829163) is 1665 base pairs long from coordinates 93450944–93452608, with five coding transcripts. [32]
Promoter | Size (in base pairs) | Coordinates | Strand | Coding Transcripts |
GXP_9004065 | 1040 | 93437082-93438121 | - | None (non-coding only) |
GXP_228179 | 1040 | 93446357-93447396 | - | None (non-coding only) |
GXP_1829163 | 1665 | 93450944-93452608 | - | 5 |
GXP_2255852 | 1487 | 93453115-93454601 | - | 2 |
The transcription factors described below were identified on the Human FAM120A protein 1 promoter. [33]
Code Name | Full Name | Binding | Matrix Score | Start site | End site |
AP2F | Activator protein 2 | agcGCCAgacggcac | 0.862 | 336 | 350 |
STEM | Motif composed of binding sites for pluripotency or stem cell factors | cccgtctGCATggcccact | 0.912 | 255 | 273 |
ZF20 | C2H2 Zinc finger transcription factors 20 | tgcggttACCA | 0.791 | 447 | 457 |
E2FF | E2F-myc activator/cell cycle regulator | tggacacggGATAatgg | 0.754 | 29 | 45 |
ZF5F | ZF5 POZ domain zinc finger | ccctgaGCGCcccaggc | 0.957 | 28 | 44 |
P53F | P53 tumor suppressor | tgcggttaccaaaggCAAGtcagtg | 0.954 | 312 | 336 |
RXRF | RXR heterodimer binding sites | ttattgacctagGGTCatattatag | 0.857 | 156 | 180 |
EBOX | E-box binding factors | attatccCGTGtccaga | 0.901 | 466 | 482 |
ZF02 | C2H2 Zinc finger transcription factors 2 | caaaagcaCCCCcctacacccgc | 0.933 | 91 | 113 |
AP1R | MAF and AP1 related factors | ttggttGCTGagaaatttctagtag | 0.842 | 356 | 380 |
PLAG | pleomorphic adenoma gene | taggGGGGtgcttttgctttcct | 0.871 | 114 | 136 |
KLFS | Krueppel like transcription factors | agagcttAAAGgattcttc | 0.976 | 118 | 136 |
ETSF | Human and murine ETS1 factors | ttcagtgaGGAAagcaaaagc | 0.933 | 196 | 216 |
An immunohistochemical staining of the FAM120AOS protein in the human prostate using a FAM120AOS polyclonal antibody indicates the presence of FAM120AOS in the nucleus of glandular cells. [34]
In Homo sapiens (humans), the gene exhibits high levels of expression (in RPKM) in the colon, fat, placenta, prostate, and thyroid, as determined through quantitative transcriptomic analysis (RNA-Seq) with the following respective values: 12.598, 11.727, 10.978, 11.277, and 13.511. [6] During human fetal development, the gene exhibits the highest levels of expression in the intestine at 20 weeks and the lungs at 17 weeks, as determined through the use of circular RNA with the following respective mean RPKM values: 5.066 and 4.365. [7] The sequencing of RNA from 20 human tissues showed the highest levels of FAM120AOS expression in the placenta, prostate, and thyroid, with respective mean RPKM values of 7.057, 3.978, and 4.396. [9] Transcription profiling through high throughput sequencing of both individual and mixtures of 16 human tissues RNA also found high levels of FAM120AOS gene expression in the thyroid, with a mean RPKM of 9.518. [8]
There are 4 large stem loops present in the 5' UTR of the human FAM120AOS protein 1. [38] There are 8 miRNA binding sites identified for the human FAM120AOS protein 1. [39]
miRNA Name | miRNA sequence | Target Score | Seed Location |
has-miR-4286 | ACCCCACUCCUGGUACC | 94 | 475 |
has-miR-3059-5p | UUUCCUCUCUGCCCCAUAGGGUGU | 88 | 199, 396 |
has-miR-3152 | UGUGUUAGAAUAGGGGCAAUAA | 87 | 173,735 |
has-miR-4499 | AAGACUGAGAGGAGGGA | 83 | 730 |
has-miR-129-2-3p | AAGCCCUUACCCCAAAAAGCAU | 83 | 1022 |
has-miR-129-1-3p | AAGCCCUUACCCCAAAAAGUAU | 83 | 1022 |
has-miR-6881-3p | AUCCUCUUUCGUCCUUCCCACU | 82 | 199, 395 |
has-miR-10400-3p | CUGGGCUCCCGGACGAGGCGGG | 81 | 337 |
The K-NN prediction results for the human FAM120AOS protein 1 predicted it to be present in the nucleus of cells. [31] There is a possible transmembrane domain for the protein, present from amino acid position 131–148. [40]
There were no paralogs identified for human FAM120AOS. [4] [10] The most distant homolog for human FAM120AOS detectable is the Microcebus murinus , with a 61.17% sequence identity to the human protein. [41] There was a total of 11 orthologs identified for human FAM120AOS protein 1. [42] No proteins with homologous domains to the human FAM120AOS sequence were identified. [43] FAM120AOS seems to be evolving at a moderate rate, in between that of cytochrome c and fibrinogen alpha. [4]
The function and biochemistry of the human FAM120AOS protein are currently unknown. [4] [10] The single nucleotide polymorphisms (SNPs) did not show any mutations in conserved amino acids, so it is lis likely that two copies of the FAM120AOS gene are necessary for proper function.
The FAM120AOS protein is physically associated with the following proteins: MDFI, ELAV1, TRIM25, and APEX1 . [45] [46] [47] [48] [10]
A missense mutation in the FAM120AOS protein from amino acid threonine at position 248 to isoleucine (T248I) has been linked in one whole-of-exome sequencing study to: coarse facial features, scoliosis, pectus excavatum, skin laxity, hypotonia, GERD, hyperreactive airway disease, [lower-alpha 1] and undescended testicles. [49]
Chromosome 16 open reading frame 95 (C16orf95) is a gene which in humans encodes the protein C16orf95. It has orthologs in mammals, and is expressed at a low level in many tissues. C16orf95 evolves quickly compared to other proteins.
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.
The Family with sequence similarity 149 member B1 is an uncharacterized protein encoded by the human FAM149B1 gene, with one alias KIAA0974. The protein resides in the nucleus of the cell. The predicted secondary structure of the gene contains multiple alpha-helices, with a few beta-sheet structures. The gene is conserved in mammals, birds, reptiles, fish, and some invertebrates. The protein encoded by this gene contains a DUF3719 protein domain, which is conserved across its orthologues. The protein is expressed at slightly below average levels in most human tissue types, with high expression in brain, kidney, and testes tissues, while showing relatively low expression levels in pancreas tissues.
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.
FAM71E1, also known as Family With Sequence Similarity 71 Member E1, is a protein that in humans is encoded by the FAM71E1 gene. It is thought to be ubiquitously expressed at low levels throughout the body, and it is conserved in vertebrates, particularly mammals and some reptiles. The protein is localized to the nucleus and can be exported to the cytoplasm.
C11orf42 is an uncharacterized protein in Homo sapiens that is encoded by the C11orf42 gene. It is also known as chromosome 11 open reading frame 42 and uncharacterized protein C11orf42, with no other aliases. The gene is mostly conserved in mammals, but it has also been found in rodents, reptiles, fish and worms.
Chromosome 9 open reading frame 50 is a protein that in humans is encoded by the C9orf50 gene. C9orf50 has one other known alias, FLJ35803. In humans the gene coding sequence is 10,051 base pairs long, transcribing an mRNA of 1,624 bases that encodes a 431 amino acid protein.
C16orf90 or chromosome 16 open reading frame 90 produces uncharacterized protein C16orf90 in homo sapiens. C16orf90's protein has four predicted alpha-helix domains and is mildly expressed in the testes and lowly expressed throughout the body. While the function of C16orf90 is not yet well understood by the scientific community, it has suspected involvement in the biological stress response and apoptosis based on expression data from microarrays and post-translational modification data.
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.
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.
C2orf74, also known as LOC339804, is a protein encoding gene located on the short arm of chromosome 2 near position 15 (2p15). Isoform 1 of the gene is 19,713 base pairs long. C2orf74 has orthologs in 135 different species, including primarily placental mammals and some marsupials.
Chromosome 9 open reading frame 85, commonly known as C9orf85, is a protein in Homo sapiens encoded by the C9orf85 gene. The gene is located at 9q21.13. When spliced, four different isoforms are formed. C9orf85 has a predicted molecular weight of 20.17 kdal. Isoelectric point was found to be 9.54. The function of the gene has not yet been confirmed, however it has been found to show high levels of expression in cells of high differentiation.
The FAM214B, also known as protein family with sequence similarity 214, B (FAM214B) is a protein that, in humans, is encoded by the FAM214B gene located on the human chromosome 9. The protein has 538 amino acids. The gene contain 9 exon. There has been studies that there are low expression of this gene in patients with major depression disorder. In most organisms such as mammals, amphibians, reptiles, and birds, there are high levels of gene expression in the bone marrow and blood. For humans in fetal development, FAM214B is mostly expressed in the brains and bone marrow.
Family with Sequence Similarity 166, member C (FAM166C), is a protein encoded by the FAM166C gene. The protein FAM166C is localized in the nucleus. It has a calculated molecular weight of 23.29 kDa. It also contains DUF2475, a protein of unknown function from amino acid 19–85. The FAM166C protein is nominally expressed in the testis, stomach, and thyroid.
TEKTIP1, also known as tektin-bundle interacting protein 1, is a protein that in humans is encoded by the TEKTIP1 gene.
THAP domain-containing protein 3 (THAP3) is a protein that, in Homo sapiens (humans), is encoded by the THAP3 gene. The THAP3 protein is as known as MGC33488, LOC90326, and THAP domain-containing, apoptosis associated protein 3. This protein contains the Thanatos-associated protein (THAP) domain and a host-cell factor 1C binding motif. These domains allow THAP3 to influence a variety of processes, including transcription and neuronal development. THAP3 is ubiquitously expressed in H. sapiens, though expression is highest in the kidneys.
Chromosome 13 Open Reading Frame 46 is a protein which in humans is encoded by the C13orf46 gene. In humans, C13orf46 is ubiquitously expressed at low levels in tissues, including the lungs, stomach, prostate, spleen, and thymus. This gene encodes eight alternatively spliced mRNA transcript, which produce five different protein isoforms.
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.
Leucine-rich repeat-containing protein 74A (LRRC74A), is a protein encoded by the LRRC74A gene. The protein LRRC74A is localized in the cytoplasm. It has a calculated molecular weight of approximately 55 kDa. The LRRC74A protein is nominally expressed in the testis, salivary gland, and pancreas.
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