C7orf50

Last updated

C7orf50
Identifiers
Aliases C7orf50 , YCR016W, chromosome 7 open reading frame 50
External IDs MGI: 1920462; HomoloGene: 49901; GeneCards: C7orf50; OMA:C7orf50 - orthologs
Orthologs
SpeciesHumanMouse
Entrez

84310

73212

Ensembl

ENSG00000146540

ENSMUSG00000053553

UniProt

Q9BRJ6

Q9CXL3

RefSeq (mRNA)

NM_028469

RefSeq (protein)

NP_082745

Location (UCSC) Chr 7: 1 – 1.14 Mb Chr 5: 139.35 – 139.45 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

C7orf50 (Chromosome 7, Open Reading Frame 50) is a gene in humans ( Homo sapiens ) that encodes a protein known as C7orf50 (uncharacterized protein C7orf50). This gene is ubiquitously expressed in the kidneys, brain, fat, prostate, spleen, among 22 other tissues and demonstrates low tissue specificity. [5] [6] C7orf50 is conserved in chimpanzees, Rhesus monkeys, dogs, cows, mice, rats, and chickens, along with 307 other organisms from mammals to fungi. [7] 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. [8] [9] 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 . [10] [11]

Contents

Gene

Background

C7orf50, also known as YCR016W, MGC11257, and LOC84310, is a protein coding gene of poor characterization in need of further research. This gene can be accessed on NCBI at the accession number NC_000007.14, on HGNC at the ID number 22421, on ENSEMBL at the ID ENSG00000146540, on GeneCards at GCID:GC07M000996, and on UniProtKB at the ID Q9BRJ6.

Location

C7orf50 is located on the short arm of chromosome 7 (7p22.3), starting at base pair (bp) 977,964 and ending at bp 1,138,325. This gene spans 160,361 bps on the minus (-) strand and contains a total of 13 exons. [5]

Gene Neighborhood

Genes within the neighborhood of C7orf50 are the following: LOC105375120, GPR146, LOC114004405, LOC107986755, ZFAND2A, LOC102723758, LOC106799841, COX19, ADAP1, CYP2W1, MIR339, GPER1, and LOC101927021. This neighborhood extends from bp 89700 to bp 1165958 on chromosome 7. [5]

mRNA

Alternative Splicing

C7orf50 has a total of 7 experimentally curated mRNA transcripts. [5] These transcripts are maintained independently of annotated genomes and were not generated computationally from a specific genome build such as the GRCh38.p13 primary assembly; therefore, they are typically more reliable. The longest and most complete of these transcripts (transcript 4) being 2138bp, producing a 194 amino acid-long (aa) protein, and consisting of 5 exons. [12] Of these transcripts, four of them encode for the same 194aa protein (isoform a), [13] only differing in their 5' and 3' untranslated regions (UTRs). The three other transcripts encode isoform b, c, and d, respectively. The table below is representative of these transcripts.

C7orf50 Experimentally Determined

NCBI Reference Sequences (RefSeq) mRNA Transcripts

NameNCBI Accession #Transcript Length# of ExonsProtein LengthIsoform
Transcript Variant 1NM_032350.51311bp5194aaa
Transcript Variant 2NM_001134395.11301bp5194aaa
Transcript Variant 3NM_001134396.11282bp5194aaa
Transcript Variant 4NM_001318252.22138bp5194aaa
Transcript Variant 7NM_001350968.11081bp6193aab
Transcript Variant 8NM_001350969.11500bp5180aac
Transcript Variant 9NM_001350970.11448bp360aad

Alternatively, when the primary genomic assembly, GRCh38.p13, is used for annotation (NCBI: NC_000007.14), there are 10 computationally predicted mRNA transcripts. [5] The most complete and supported of these transcripts (transcript variant X6) is 1896bp, producing a 225aa-long protein. [14] In total, there are 6 different isoforms predicted for C7orf50. Of these transcripts, 5 of them encode for the same isoform (X3). [15] The remaining transcripts encode isoforms X2, X4, X5, X6, and X7 as represented below.

C7orf50 Computationally Determined

NCBI Reference Sequences (RefSeq) mRNA Transcripts

NameNCBI Accession #Transcript LengthProtein LengthIsoform
Transcript Variant X2XM_017012719.11447bp375aaX2
Transcript Variant X3XM_011515582.31192bp225aaX3
Transcript Variant X4XM_024446977.11057bp193aaX4
Transcript Variant X5XM_011515581.31240bp225aaX3
Transcript Variant X6XM_011515584.21896bp225aaX3
Transcript Variant X7XM_017012720.21199bp225aaX3
Transcript Variant X8XM_011515583.21215bp225aaX3
Transcript Variant X9XM_017012721.22121bp211aaX5
Transcript Variant X10XM_024446978.12207bp180aaX6
Transcript Variant X11XM_024446979.1933bp93aaX7

5' and 3' UTR

Based on the experimentally determined C7orf50 mRNA transcript variant 4, the 5' UTR of C7orf50 is 934 nucleotides (nt) long, while the 3' UTR is 619nt. The coding sequence (CDS) of this transcript spans nt 935..1519 for a total length of 584nt and is encoded in reading frame 2. [12] Interestingly, the 5'UTR of C7orf50 contains a uORF in need of further study, ranging from nt 599 to nt 871 also in the second reading frame. [16]

Protein

General Properties

The C7orf50 Isoform a's 194aa protein sequence from NCBI [13] is as follows:

>NP_001127867.1 uncharacterized protein C7orf50 isoform a [Homo sapiens] MAKQKRKVPEVTEKKNKKLKKASAEGPLLGPEAAPSGEGAGSKGEAVLRPGLDAEPELSPEEQRVLERKL 70 KKERKKEERQRLREAGLVAQHPPARRSGAELALDYLCRWAQKHKNWRFQKTRQTWLLLHMYDSDKVPDEH 140 FSTLLAYLEGLQGRARELTVQKAEALMRELDEEGSDPPLPGRAQRIRQVLQLLS                 194

The underlined region within the sequence is indicative of a domain known as DUF2373 ("domain of unknown function 2373"), found in isoforms a, b, and c.

C7orf50 has a predicted molecular weight (Mw) of 22 kDa, making C7orf50 smaller than the average protein (52 kDa). [17] The isoelectric point (theoretical pI) for this isoform is 9.7, meaning that C7orf50 is slightly basic. [18] [19] As for charge runs and patterns within isoform a, there is a significant mixed charge (*) run (-++0++-+++--+) from aa67 to aa79 and an acidic (-) run from aa171 – aa173. It is likely that this mixed charge run encodes the protein-protein interaction (PPI) site of C7orf50. [20] [21]

Domains and Motifs

DUF2373 is a domain of unknown function found in the C7orf50 protein. This is a highly conserved c-terminal region found from fungi to humans. [22] As for motifs, a bipartite nuclear localization signal (NLS) was predicted from aa6 to aa21, meaning that C7orf50 is likely localized in the nucleus. [23] Interestingly, a nuclear export signal (NES) is also found within the C7orf50 protein at the following amino acids: 150, and 153 - 155, suggesting that C7orf50 has function both inside and outside the nucleus. [24] [25]

Schematic Model of C7orf50 Protein. Green region is indicative of nuclear localization signal (NLS), blue of the mixed charge run, and orange of the DUF2373. Marked sites are indicative of post-translational modifications. Image made with Prosite MyDomains tool. C7orf50 Schematic.png
Schematic Model of C7orf50 Protein. Green region is indicative of nuclear localization signal (NLS), blue of the mixed charge run, and orange of the DUF2373. Marked sites are indicative of post-translational modifications. Image made with Prosite MyDomains tool.

Structure

Secondary Structure

The majority of C7orf50 (isoform a) secondary structure is made up of alpha helices, with the remainder being small portions of random coils, beta turns, or extended strands. [26] [27]

Tertiary Structure

The tertiary structure of C7orf50 consists primarily of alpha helices as determined I-TASSER. [9] [28] [29]

Quaternary Structure

The interaction network (quaternary structure) involving the C7orf50 protein has significantly more (p < 1.0e-16) interactions than a randomly selected set of proteins. This indicates that these proteins are partially connected biologically as a group; therefore, they intrinsically depend on each other within their biological pathway. [30] This means that although the function of C7orf50 is uncharacterized, it is most likely to be associated with the same processes and functions as the proteins within its network.

Functional Enrichments within the C7orf50 Network
Biological ProcessesrRNA processingmaturation of 5.8S, LSU, and SSU rRNA
Molecular Functionscatalytic activity, acting on RNAATP-dependent RNA helicase activity
Cellular Componentsnucleoluspreribosomes
Reactome Pathwaysmajor pathway of rRNA processing in the nucleolus and cytosolrRNA modification in the nucleus and cytosol
Protein Domains and Motifshelicase conserved C-terminal domainDEAD/DEAH box helicase

The closest predicted functional partners of C7orf50 are the following proteins: DDX24, DDX52, PES1, EBNA1BP2, RSLD1, NOP14, FTSJ3, KRR1, LYAR, and PWP1. These proteins are predicted to co-express rather than bind directly C7orf50 and each other.

STRING quaternary analysis of C7orf50. Shows protein-protein interactions (direct and indirect) associated with C7orf50. Network nodes (circles) represent proteins. Edges (lines) represent protein-protein associations. C7orf50 QuarternaryStructure.png
STRING quaternary analysis of C7orf50. Shows protein-protein interactions (direct and indirect) associated with C7orf50. Network nodes (circles) represent proteins. Edges (lines) represent protein-protein associations.

Regulation

Gene Regulation

Promoter

C7orf50 has 6 predicted promoter regions. The promoter with the greatest number of transcripts and CAGE tags overall is promoter set 6 (GXP_6755694) on ElDorado by Genomatix. This promoter region is on the minus (-) strand and has a start position of 1,137,965 and an end position of 1,139,325, making this promoter 1,361bp long. It has 16 coding transcripts and the transcript with the greatest identity to C7orf50 transcript 4 is transcript GXT_27788039 with 98746 CAGE tags. [31]

Promoter IDStart PositionEnd PositionLength# of Coding TranscriptsGreatest # of CAGE Tags in Transcripts
GXP_9000582101306310131631101bp0N/A
GXP_6755691102823910300701832bp4169233
GXP_6053282105520610563061101bp1449
GXP_3207505112728811283881101bp1545
GXP_9000584113054111316411101bp0N/A
GXP_6755694113796511393251361bp16100,070

The CpG island associated with this promoter has 75 CpGs (22% of island), and is 676bp long. The C count plus G count is 471, the percentage C or G is 70% within this island, and the ratio of observed to expected CpG is 0.91. [32] [33]

C7orf50 with ElDorado suggested promoters with exons labeled. Gene is on the minus (-) strand, thus promoter (GXP_6755694) transcripts runs 5' to 3' on the bottom strand (R to L). C7orf50 PromoterSchematic.png
C7orf50 with ElDorado suggested promoters with exons labeled. Gene is on the minus (-) strand, thus promoter (GXP_6755694) transcripts runs 5’ to 3’ on the bottom strand (R to L).

Transcription Factor Binding Sites

As determined by MatInspector at Genomatix, the following transcription factor (TFs) families are most highly predicted to bind to C7orf50 in the promoter region. [31]

Transcription FactorDetailed Family Information
NR2F Nuclear receptor subfamily 2 factors
PEROPeroxisome proliferator-activated receptor
HOMFHomeodomain transcription factors
PRDMPR (PRDI-BF1-RIZ1 homologous) domain transcription factor
VTBPVertebrate TATA binding protein factor
HZIPHomeodomain-leucine zipper transcription factors
ZTREZinc transcriptional regulatory element
XBBFX-box binding factors
SP1F GC-Box factors SP1/GC
CAATCCAAT binding factors
ZF57KRAB domain zinc finger protein 57
CTCF CTCF and BORIS gene family, transcriptional regulators with highly conserved zinc finger domains
MYOD Myoblast determining factors
KLFSKrueppel like transcription factors

Expression Pattern

C7orf50 shows ubiquitous expression in the kidneys, brain, fat, prostate, spleen and 22 other tissues and low tissue and immune cell specificity . [5] [6] This expression is very high, 4 times above the average gene; therefore, there is a higher abundance of C7orf50 mRNA than the average gene within a cell. [34] There does not appear to be a definitive cell type in which this gene is not expressed. [35]

Transcription Regulation

Splice Enhancers

The mRNA of C7orf50 is predicted to have exonic splicing enhancers, in which SR proteins can bind, at bp positions 45 (SRSF1 (IgM-BRCA1)), 246 (SRSF6), 703 (SRSF5), 1301 (SRSF1), and 1308 (SRSF2) [36] [37]

Stem Loop Prediction

Both the 5' and 3' UTRs of the mRNA of C7orf50 are predicted to fold into structures such as bulge loops, internal loops, multibranch loops, hairpin loops, and double helices. The 5'UTR has a predicted free energy of -416 kcal/mol with an ensemble diversity of 238. The 3' UTR has a predicted free energy of -279 kcal/mol with an ensemble diversity of 121. [38]

miRNA Targeting

There are many poorly conserved miRNA binding sites predicted within the 3’UTR of C7orf50 mRNA. The notable miRNA families that are predicted to bind to C7orf50 mRNA and regulate/repress transcription are the following: miR-138-5p, miR-18-5p, miR-129-3p, miR-124-3p.1, miR-10-5p, and miR-338-3p. [39] [40] [41]

Protein Regulation

Subcellular Localization

The C7orf50 protein is predicted to localize intercellularly in both the nucleus and cytoplasm, but primarily within the nucleoplasm and nucleoli. [42] [43] [23] [44]

Post-Translational Modification

The C7orf50 protein is predicted to be mucin-type GalNAc o-glycosylated at the following amino acid sites: 12, 23, 36, 42, 59, and 97. [45] [46] Additionally, this protein is predicted to be SUMOylated at aa71 with the SUMO protein binding from aa189 through aa193. [47] [48] [49] C7orf50 is also predicted to be kinase-specific phosphorylated at the following amino acids: 12, 23, 36, 42, 59, 97, 124, 133, 159, and 175. [50] [51] [52] [53] [54] Interestingly, many of these sites overlap with the o-glycosylation sites. Of these phosphorylation sites, the majority are serines (53%) with the remainder being either tyrosines or threonines. The most associated kinases with these sites are the following kinase groups: AGC, CAMK, TKL, and STE. Finally, this protein is predicted to have 8 glycations of the ε amino groups of lysines at the following sites: aa3, 5, 14, 15, 17, 21, 76, and 120. [55] [56]

Homology

Paralogs

No paralogs of C7orf50 have been detected in the human genome; however, there is slight evidence (58% similarity) of a paralogous DUF2373 domain in the protein of KIDINS220. [57]

Orthologs

Below is a table of a variety of orthologs of the human C7orf50 gene. [58] [7] The table includes closely, moderately, and distantly related orthologs. C7orf50 is highly evolutionary conserved from mammals to fungi. When these ortholog sequences are compared, the most conserved portions are those of DUF2373, highlighting this domain's importance in the functioning of C7orf50. C7orf50 has evolved moderately and evenly over time with a divergence rate greater than Hemoglobin but less than Cytochrome C.

Selected Orthologs of C7orf50
Genus and SpeciesCommon NameTaxon ClassDate of Divergence (MYA)Accession #Length (AA)% identity w/ human
Homo sapiens Human Mammalia N/ANM_001318252.2194aa100%
Tupaia chinensisChinese Tree ShrewMammalia82XP_006167949.1194aa76%
Dasypus novemcinctus Nine-banded ArmadilloMammalia105XP_004483895.1198aa70%
Miniopterus natalens Natal Long-fingered BatMammalia96XP_016068464.1199aa69%
Protobothrops mucrosquamatus Brown-spotted Pit Viper Reptilia 312XP_015673296.1196aa64%
Balearica regulorum gibbericeps Grey-crowned Crane Aves 312XP_010302837.1194aa61%
Falco peregrinus Peregrine FalconAves312XP_027635198.1193aa59%
Xenopus laevis African Clawed FrogAmphibia352XP_018094637.1198aa50%
Electrophorus electricus Electric EelActinopterygii435XP_026880604.1195aa53%
Rhincodon typus Whale Shark Chondrichthyes 465XP_020372968.1195aa52%
Ciona intestinalis Sea Vase Ascidiacea 676XP_026696561.1282aa37%
Octopus bimaculoides California Two-spot Octopus Cephalopoda 797XP_014772175.1221aa40%
Priapulus caudatus Priapulus Priapulida 797XP_014663190.1333aa39%
Bombus terrestris Buff-tailed BumblebeeInsecta797XP_012171653.1260aa32%
Actinia tenebrosa Australian Red Waratah Sea Anemone Anthozoa 824XP_031575029.1330aa43%
Trichoplax adhaerens Trichoplax Trichoplacidae 948XP_002110193.1137aa44%
Spizellomyces punctatusBranching Chytrid Fungi Fungi 1105XP_016610491.1412aa29%
Eremothecium cymbalariaeFungiFungi1105XP_003644395.1266aa25%
Quercus suber Cork Oak Tree Plantae 1496XP_023896156.1508aa30%
Plasmopara halstedii Downy Mildew of Sunflower Oomycetes 1768XP_024580369.1179aa26%
Rate of C7orf50 divergence compared to divergence rates of Hemoglobin and Cytochrome C. C7orf50 Divergence.png
Rate of C7orf50 divergence compared to divergence rates of Hemoglobin and Cytochrome C.

Function

The consensus prediction of C7orf50 function (GO terms), as determined by I-TASSER, [59] [28] [29] predicts the molecular function to be protein binding, the biological process to be protein import (specifically into the nucleus), and the associated cellular component to be a pore complex (specifically of the nuclear envelope). It can be predicted that the function of C7orf50 is one in which C7orf50 imports ribosomal proteins into the nucleus in order to be made into ribosomes, but further research is needed to solidify this function.

Interacting Proteins

Proteins Predicted to Interact with C7orf50 [60] [61]
Name of ProteinName of GeneFunctionUniProt Accession #
THAP1 domain-containing protein 1 THAP1 DNA-binding transcription regulator that regulates endothelial cell proliferation and G1/S cell-cycle progression. [62] Q9NVV9
Protein Tax-2 tax Transcriptional activator that activates both the viral long terminal repeat (LTR) and cellular promoters via activation of CREB, NF-kappa-B, SRF and AP-1 pathways. [63] P03410
Major Prion Protein PRNP Its primary physiological function is unclear. May play a role in neuronal development and synaptic plasticity. May be required for neuronal myelin sheath maintenance. May promote myelin homeostasis through acting as an agonist for ADGRG6 receptor. May play a role in iron uptake and iron homeostasis. [64] P04156
Aldehyde dehydrogenase X, mitochondrial ALDH1B1 Pay a major role in the detoxification of alcohol-derived acetaldehyde. They are involved in the metabolism of corticosteroids, biogenic amines, neurotransmitters, and lipid peroxidation. [65] P30837
Cell growth-regulating nucleolar protein LYAR Plays a role in the maintenance of the appropriate processing of 47S/45S pre-rRNA to 32S/30S pre-rRNAs and their subsequent processing to produce 18S and 28S rRNAs. [66] [67] Q9NX58
Coiled-coil domain-containing protein 85B CCDC85B Functions as a transcriptional repressor. [68] [69] Q15834
Nucleolar protein 56 NOP56 Involved in the early to middle stages of 60S ribosomal subunit biogenesis. Core component of box C/D small nucleolar ribonucleoprotein (snoRNP) particles. Required for the biogenesis of box C/D snoRNAs such U3, U8 and U14 snoRNAs. [70] O00567
rRNA 2'-O-methyltransferase fibrillarin FBL Has the ability to methylate both RNAs and proteins. Involved in pre-rRNA processing by catalyzing the site-specific 2'-hydroxyl methylation of ribose moieties in pre-ribosomal RNA. [71] [72] [73] P22087
40S ribosomal protein S6 RPS6 May play an important role in controlling cell growth and proliferation through the selective translation of particular classes of mRNA. [74] P62753

Clinical Significance

C7orf50 has been noted in a variety of genome-wide association studies (GWAS) and has been shown to be associated with type 2 diabetes among sub-Saharan Africans, [75] daytime sleepiness in African-Americans, [76] prenatal exposure to particulate matter, [77] heritable DNA methylation marks associated with breast cancer, [78] DNA methylation in relation to plasma carotenoids and lipid profile, [79] and has significant interactions with prion proteins. [80]

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References

  1. 1 2 3 GRCh38: Ensembl release 89: ENSG00000146540 – Ensembl, May 2017
  2. 1 2 3 GRCm38: Ensembl release 89: ENSMUSG00000053553 – Ensembl, May 2017
  3. ↑ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. ↑ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
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