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'''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.<ref name=":0">{{Cite web|url=https://www.ncbi.nlm.nih.gov/gene?cmd=retrieve&list_uids=84310|title=C7orf50 chromosome 7 open reading frame 50 [Homo sapiens (human)] - Gene - NCBI|website=www.ncbi.nlm.nih.gov|access-date=2020-04-29}}</ref><ref>{{Cite web|url=https://www.proteinatlas.org/ENSG00000146540-C7orf50|title=C7orf50 protein expression summary - The Human Protein Atlas|website=www.proteinatlas.org|access-date=2020-04-29}}</ref> C7orf50 is predicted to be a part of, or associated with, [[Nuclear pore|nuclear pore complexes]] (NPCs), as this protein’s primary molecular function is protein and RNA binding,<ref>{{Cite web|url=https://www.ebi.ac.uk/QuickGO/annotations?geneProductId=Q9BRJ6|title=QuickGO|website=www.ebi.ac.uk|access-date=2020-04-29}}</ref> its associated [[biological process]] involves protein import, and the [[cellular component]] it is most associated with is pore complexes.<ref name=":1">{{Cite journal|last=Zhang|first=Chengxin|last2=Freddolino|first2=Peter L.|last3=Zhang|first3=Yang|date=2017-05-02|title=COFACTOR: improved protein function prediction by combining structure, sequence and protein–protein interaction information|url=http://dx.doi.org/10.1093/nar/gkx366|journal=Nucleic Acids Research|volume=45|issue=W1|pages=W291–W299|doi=10.1093/nar/gkx366|issn=0305-1048}}</ref><ref name=":2">{{Cite journal|last=Yang|first=Jianyi|last2=Zhang|first2=Yang|date=2015-04-16|title=I-TASSER server: new development for protein structure and function predictions|url=http://dx.doi.org/10.1093/nar/gkv342|journal=Nucleic Acids Research|volume=43|issue=W1|pages=W174–W181|doi=10.1093/nar/gkv342|issn=0305-1048}}</ref> More specifically, this protein is predicted to be involved with the import of [[ribosomal protein]]s into the [[Nuclear organization|nucleus]] to be assembled into ribosomal subunits.<ref>{{Cite journal|last=Alberts|first=Bruce|last2=Johnson|first2=Alexander|last3=Lewis|first3=Julian|last4=Raff|first4=Martin|last5=Roberts|first5=Keith|last6=Walter|first6=Peter|date=2002|title=The Transport of Molecules between the Nucleus and the Cytosol|url=https://www.ncbi.nlm.nih.gov/books/NBK26932/|journal=Molecular Biology of the Cell. 4th edition|language=en}}</ref> This gene is also predicted to be a [[microRNA]] (miRNA) protein coding host gene'','' meaning that it may contain miRNA genes in its [[intron]]s and/or [[exon]]s''.''<ref>{{Cite journal|last=Boivin|first=Vincent|last2=Deschamps-Francoeur|first2=Gabrielle|last3=Scott|first3=Michelle S|date=2018-03-01|title=Protein coding genes as hosts for noncoding RNA expression|url=http://dx.doi.org/10.1016/j.semcdb.2017.08.016|journal=Seminars in Cell & Developmental Biology|volume=75|pages=3–12|doi=10.1016/j.semcdb.2017.08.016|issn=1084-9521|via=Elsevier}}</ref><ref>{{Cite web|url=https://www.genenames.org/data/genegroup/#!/group/1691|title=MicroRNA protein coding host genes|last=HUGO Gene Nomenclature Committee|first=|date=|website=GeneNames|url-status=live|archive-url=|archive-date=|access-date=2020-04-29}}</ref>
'''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 [[Kidney|kidneys]], [[brain]], [[fat]], [[prostate]], [[spleen]], among 22 other tissues and demonstrates low tissue specificity.<ref name=":0">{{Cite web|url=https://www.ncbi.nlm.nih.gov/gene?cmd=retrieve&list_uids=84310|title=C7orf50 chromosome 7 open reading frame 50 [Homo sapiens (human)] - Gene - NCBI|website=www.ncbi.nlm.nih.gov|access-date=2020-04-29}}</ref><ref>{{Cite web|url=https://www.proteinatlas.org/ENSG00000146540-C7orf50|title=C7orf50 protein expression summary - The Human Protein Atlas|website=www.proteinatlas.org|access-date=2020-04-29}}</ref> C7orf50 is conserved in [[Chimpanzee|chimpanzees]], [[Rhesus macaque|Rhesus monkeys]], [[Dog|dogs]], [[Cattle|cows]], [[Mouse|mice]], [[Rat|rats]], and [[Chicken|chickens]], along with 307 other [[Organism|organisms]] from [[Mammal|mammals]] to [[Fungus|fungi]].<ref name=":7" /> This protein is predicted to be involved with the import of [[ribosomal protein]]s into the [[Nuclear organization|nucleus]] to be assembled into ribosomal subunits as a part of [[Ribosomal RNA|rRNA]] processing.<ref>{{Cite journal|last=Alberts|first=Bruce|last2=Johnson|first2=Alexander|last3=Lewis|first3=Julian|last4=Raff|first4=Martin|last5=Roberts|first5=Keith|last6=Walter|first6=Peter|date=2002|title=The Transport of Molecules between the Nucleus and the Cytosol|url=https://www.ncbi.nlm.nih.gov/books/NBK26932/|journal=Molecular Biology of the Cell. 4th edition|language=en}}</ref><ref name=":8" /> Additionally, this gene is predicted to be a [[microRNA]] (miRNA) protein coding host gene'','' meaning that it may contain miRNA genes in its [[intron]]s and/or [[exon]]s''.''<ref>{{Cite journal|last=Boivin|first=Vincent|last2=Deschamps-Francoeur|first2=Gabrielle|last3=Scott|first3=Michelle S|date=2018-03-01|title=Protein coding genes as hosts for noncoding RNA expression|url=http://dx.doi.org/10.1016/j.semcdb.2017.08.016|journal=Seminars in Cell & Developmental Biology|volume=75|pages=3–12|doi=10.1016/j.semcdb.2017.08.016|issn=1084-9521|via=Elsevier}}</ref><ref>{{Cite web|url=https://www.genenames.org/data/genegroup/#!/group/1691|title=MicroRNA protein coding host genes|last=HUGO Gene Nomenclature Committee|first=|date=|website=GeneNames|url-status=live|archive-url=|archive-date=|access-date=2020-04-29}}</ref>


== Gene ==
== Gene ==
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=== Location ===
=== Location ===
C7orf50 is located on the [[Locus (genetics)|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 bp on the minus (-) strand and contains a total of 13 exons.<ref name=":0" />
C7orf50 is located on the [[Locus (genetics)|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.<ref name=":0" />
[[File:C7orf50 GenomicLocation.png|thumb|292x292px|The genomic location of C7orf50 on chromosome 7 as indicated by red line. As stated by GeneCards.org, the bands are according to Ensembl, locations according to GeneLoc.]]
[[File:C7orf50 GenomicLocation.png|thumb|638x638px|The genomic location of C7orf50 on chromosome 7 as indicated by red line. As stated by GeneCards.org, the bands are according to Ensembl, locations according to GeneLoc.|alt=|none]]


=== Gene Neighborhood ===
=== Gene Neighborhood ===
Genes within the neighborhood of C7orf50 are the following: LOC105375120, [[GPR146]], LOC114004405, LOC107986755, ZFAND2A, LOC102723758, LOC106799841, COX19, [[ADAP1 (gene)|ADAP1]], [[CYP2W1]], MIR339, GPER1, and LOC101927021. This neighborhood extends from bp 89700 to bp 1165958 on chromosome 7.<ref name=":0" />
Genes within the neighborhood of C7orf50 are the following: LOC105375120, [[GPR146]], LOC114004405, LOC107986755, ZFAND2A, LOC102723758, LOC106799841, COX19, [[ADAP1 (gene)|ADAP1]], [[CYP2W1]], MIR339, GPER1, and LOC101927021. This neighborhood extends from bp 89700 to bp 1165958 on chromosome 7.<ref name=":0" />
[[File:C7orf50 GenomicNeighborhood.png|thumb|The genomic neighborhood of C7orf50, with C7orf50 being indicated on the minus strand with the red arrow. Image from NCBI entry on C7orf50.]]
[[File:C7orf50 GenomicNeighborhood.png|thumb|The genomic neighborhood of C7orf50, with C7orf50 being indicated on the minus strand with the red arrow. Image from NCBI entry on C7orf50.|alt=|none|446x446px]]


== mRNA ==
== mRNA ==


=== Alternative Splicing ===
=== Alternative Splicing ===
C7orf50 has a total of 7 experimentally predicted [[Messenger RNA|mRNA]] [[transcript]]s.<ref name=":0" /> 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. 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.<ref name=":3">{{Cite journal|date=2020-04-25|title=Homo sapiens chromosome 7 open reading frame 50 (C7orf50), transcript variant 4, mRNA|url=http://www.ncbi.nlm.nih.gov/nuccore/NM_001318252.2|language=en-US}}</ref> Of these transcripts, four of them encode for the same 194aa protein ([[Protein isoform|isoform]] a),<ref name=":4">{{Cite web|url=https://www.ncbi.nlm.nih.gov/protein/970919379|title=uncharacterized protein C7orf50 isoform a [Homo sapiens] - Protein - NCBI|website=www.ncbi.nlm.nih.gov|access-date=2020-04-29}}</ref> only differing in their 5' and 3' [[untranslated region]]s (UTRs). The three other transcripts encode isoform b, c, and d, respectively. The table below is representative of these transcripts.
C7orf50 has a total of 7 experimentally predicted [[Messenger RNA|mRNA]] [[transcript]]s.<ref name=":0" /> 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. 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.<ref name=":3">{{Cite journal|date=2020-04-25|title=Homo sapiens chromosome 7 open reading frame 50 (C7orf50), transcript variant 4, mRNA|url=http://www.ncbi.nlm.nih.gov/nuccore/NM_001318252.2|language=en-US}}</ref> Of these transcripts, four of them encode for the same 194aa protein ([[Protein isoform|isoform]] a),<ref name=":4">{{Cite web|url=https://www.ncbi.nlm.nih.gov/protein/970919379|title=uncharacterized protein C7orf50 isoform a [Homo sapiens] - Protein - NCBI|website=www.ncbi.nlm.nih.gov|access-date=2020-04-29}}</ref> only differing in their 5' and 3' [[untranslated region]]s (UTRs). The three other transcripts encode isoform b, c, and d, respectively. The table below is representative of these transcripts.


{| class="wikitable sortable mw-collapsible"
{| class="wikitable sortable mw-collapsible"
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|}
|}
Alternatively, when the primary genomic assembly, GRCh38.p13, is used for annotation (NCBI: NC_000007.14), there are 10 computationally predicted mRNA transcripts.<ref name=":0" /> The most complete and supported of these transcripts (transcript variant X6) is 1896bp, producing a 225aa-long protein.<ref>{{Cite journal|date=2020-03-02|title=PREDICTED: Homo sapiens chromosome 7 open reading frame 50 (C7orf50), transcript variant X6, mRNA|url=http://www.ncbi.nlm.nih.gov/nuccore/XM_011515584.2|language=en-US}}</ref> In total, there are 6 different isoforms predicted for C7orf50. Of these transcripts, 5 of them encode for the same isoform (X3).<ref>{{Cite web|url=https://www.ncbi.nlm.nih.gov/protein/767945960|title=uncharacterized protein C7orf50 isoform X3 [Homo sapiens] - Protein - NCBI|website=www.ncbi.nlm.nih.gov|access-date=2020-04-29}}</ref> The remaining transcripts encode isoforms X2, X4, X5, X6, and X7 as represented below.
Alternatively, when the primary genomic assembly, GRCh38.p13, is used for annotation (NCBI: NC_000007.14), there are 10 computationally predicted mRNA transcripts.<ref name=":0" /> The most complete and supported of these transcripts (transcript variant X6) is 1896bp, producing a 225aa-long protein.<ref>{{Cite journal|date=2020-03-02|title=PREDICTED: Homo sapiens chromosome 7 open reading frame 50 (C7orf50), transcript variant X6, mRNA|url=http://www.ncbi.nlm.nih.gov/nuccore/XM_011515584.2|language=en-US}}</ref> In total, there are 6 different isoforms predicted for C7orf50. Of these transcripts, 5 of them encode for the same isoform (X3).<ref>{{Cite web|url=https://www.ncbi.nlm.nih.gov/protein/767945960|title=uncharacterized protein C7orf50 isoform X3 [Homo sapiens] - Protein - NCBI|website=www.ncbi.nlm.nih.gov|access-date=2020-04-29}}</ref> The remaining transcripts encode isoforms X2, X4, X5, X6, and X7 as represented below.
{| class="wikitable sortable mw-collapsible"
{| class="wikitable sortable mw-collapsible mw-collapsed"
| colspan="5" |C7orf50 Computationally Determined
| colspan="5" |C7orf50 Computationally Determined


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=== 5' and 3' UTR ===
=== 5' and 3' UTR ===
Based on the experimentally determined C7orf50 mRNA transcript variant 4, the 5' UTR of C7orf50 is 934 [[nucleotide]]s (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.<ref name=":3" />
Based on the experimentally determined C7orf50 mRNA transcript variant 4, the 5' UTR of C7orf50 is 934 [[nucleotide]]s (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.<ref name=":3" /> Interestingly, the 5'UTR of C7orf50 contains a [[Upstream open reading frame|uORF]] in need of further study, ranging from nt 599 to nt 871 also in the second reading frame <ref>{{Cite web|title=ORF Finder|url=https://www.bioinformatics.org/sms2/orf_find.html|website=www.bioinformatics.org|access-date=2020-05-03}}</ref>.


== Protein ==
== Protein ==
Line 169: Line 169:


=== Tertiary Structure ===
=== Tertiary Structure ===
The [[Protein tertiary structure|tertiary structure]] of C7orf50 is comprised primarily of alpha helices as determined I-TASSER.<ref>{{Cite web|url=https://zhanglab.ccmb.med.umich.edu/I-TASSER/|title=I-TASSER server for protein structure and function prediction|website=zhanglab.ccmb.med.umich.edu|access-date=2020-04-29}}</ref><ref name=":1" /><ref name=":2" />
The [[Protein tertiary structure|tertiary structure]] of C7orf50 is comprised primarily of alpha helices as determined I-TASSER.<ref name=":8">{{Cite web|url=https://zhanglab.ccmb.med.umich.edu/I-TASSER/|title=I-TASSER server for protein structure and function prediction|website=zhanglab.ccmb.med.umich.edu|access-date=2020-04-29}}</ref><ref name=":1">{{Cite journal|last=Zhang|first=Chengxin|last2=Freddolino|first2=Peter L.|last3=Zhang|first3=Yang|date=2017-05-02|title=COFACTOR: improved protein function prediction by combining structure, sequence and protein–protein interaction information|url=http://dx.doi.org/10.1093/nar/gkx366|journal=Nucleic Acids Research|volume=45|issue=W1|pages=W291–W299|doi=10.1093/nar/gkx366|issn=0305-1048}}</ref><ref name=":2">{{Cite journal|last=Yang|first=Jianyi|last2=Zhang|first2=Yang|date=2015-04-16|title=I-TASSER server: new development for protein structure and function predictions|url=http://dx.doi.org/10.1093/nar/gkv342|journal=Nucleic Acids Research|volume=43|issue=W1|pages=W174–W181|doi=10.1093/nar/gkv342|issn=0305-1048}}</ref>
[[File:C7orf50 TertiaryStructure.jpeg|thumb|Tertiary structure of C7orf50 protein as predicted by I-TASSER. C-score = -3.32. Estimated TM-score = 0.35 ± 0.12. Estimated RMSD = 13.1 ± 4.2 Å. Runs from N-terminal (Red) to C-terminal (Blue).]]
[[File:C7orf50 TertiaryStructure.jpeg|thumb|Tertiary structure of C7orf50 protein as predicted by I-TASSER. C-score = -3.32. Estimated TM-score = 0.35 ± 0.12. Estimated RMSD = 13.1 ± 4.2 Å. Runs from N-terminal (Red) to C-terminal (Blue).|231x231px]]


=== Quaternary structure ===
=== Quaternary structure ===
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=== Orthologs ===
=== Orthologs ===
Below is a table of a variety of [[Sequence homology|orthologs]] of the human C7orf50 gene.<ref>{{Cite web|title=BLAST: Basic Local Alignment Search Tool|url=https://blast.ncbi.nlm.nih.gov/Blast.cgi|website=blast.ncbi.nlm.nih.gov|access-date=2020-05-02}}</ref><ref>{{Cite web|title=C7orf50 orthologs|url=https://www.ncbi.nlm.nih.gov/gene/84310/ortholog/|website=NCBI|language=en|access-date=2020-05-02}}</ref> The table includes closely, moderately, and distantly related orthologs. Orthologs of the human protein C7orf50 are listed in descending order of the date of divergence. C7orf50 is highly evolutionary conserved from [[Mammal|mammals]] to [[Fungus|fungi]]. C7orf50 has evolved moderately and evenly over time with a divergence rate greater than [[Hemoglobin]] but less than [[Cytochrome c|Cytochrome C]].
Below is a table of a variety of [[Sequence homology|orthologs]] of the human C7orf50 gene.<ref>{{Cite web|title=BLAST: Basic Local Alignment Search Tool|url=https://blast.ncbi.nlm.nih.gov/Blast.cgi|website=blast.ncbi.nlm.nih.gov|access-date=2020-05-02}}</ref><ref name=":7">{{Cite web|title=C7orf50 orthologs|url=https://www.ncbi.nlm.nih.gov/gene/84310/ortholog/|website=NCBI|language=en|access-date=2020-05-02}}</ref> The table includes closely, moderately, and distantly related orthologs. Orthologs of the human protein C7orf50 are listed in descending order of the date of divergence. C7orf50 is highly evolutionary conserved from [[Mammal|mammals]] to [[Fungus|fungi]]. C7orf50 has evolved moderately and evenly over time with a divergence rate greater than [[Hemoglobin]] but less than [[Cytochrome c|Cytochrome C]].
[[File:C7orf50 Divergence.png|thumb|Rate of C7orf50 divergence compared to rates of Hemoglobin and Cytochrome C.]]
[[File:C7orf50 Divergence.png|thumb|Rate of C7orf50 divergence compared to rates of Hemoglobin and Cytochrome C.]]
{| class="wikitable"
{| class="wikitable"
Line 581: Line 581:
|''[[Trichoplax|Trichoplax adhaerens]]''
|''[[Trichoplax|Trichoplax adhaerens]]''
|Trichoplax
|Trichoplax
|Trichoplacidae
|[[Trichoplax|Trichoplacidae]]
|948
|948
|XP_002110193.1
|XP_002110193.1
Line 589: Line 589:
|''Spizellomyces punctatus''
|''Spizellomyces punctatus''
|Branching Chytrid Fungi
|Branching Chytrid Fungi
|Fungi
|[[Fungus|Fungi]]
|1105
|1105
|XP_016610491.1
|XP_016610491.1
Line 605: Line 605:
|''[[Quercus suber]]''
|''[[Quercus suber]]''
|Cork Oak Tree
|Cork Oak Tree
|Plantae
|[[Plant|Plantae]]
|1496
|1496
|XP_023896156.1
|XP_023896156.1
Line 613: Line 613:
|''[[Plasmopara halstedii]]''
|''[[Plasmopara halstedii]]''
|Downy Mildew of Sunflower
|Downy Mildew of Sunflower
|Oomycetes
|[[Oomycete|Oomycetes]]
|1768
|1768
|XP_024580369.1
|XP_024580369.1
Line 619: Line 619:
|26%
|26%
|}
|}

<br />
== Function ==
The consensus prediction of C7orf50 function (GO terms), as determined by [[I-TASSER]] <ref>{{Cite web|title=I-TASSER results|url=https://zhanglab.ccmb.med.umich.edu/I-TASSER/output/S533933/|website=zhanglab.ccmb.med.umich.edu|access-date=2020-05-03}}</ref><ref name=":1" /><ref name=":2" />, predicts the molecular function to be [https://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0005515 protein binding], the biological process to be [https://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0017038 protein import] (specifically [https://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0051170 into the nucleus]), and the associated cellular component to be a [https://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0046930 pore complex] (specifically of the [https://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0005635 nuclear envelope]).

=== Interacting Proteins ===
{| class="wikitable"
|+Proteins Predicted to Interact with C7orf50 <ref>{{Cite web|url=https://www.ebi.ac.uk/intact/|website=www.ebi.ac.uk|access-date=2020-05-03}}</ref><ref>{{Cite web|title=CCSB Interactome Database|url=http://interactome.dfci.harvard.edu/index.php?page=home|website=interactome.dfci.harvard.edu|access-date=2020-05-03}}</ref>
!Name of Protein
!Name of Gene
!Function
!UniProt Accession #
|-
|THAP1 domain-containing protein 1
|[[THAP1]]
|DNA-binding transcription regulator that regulates endothelial cell proliferation and G1/S cell-cycle progression.<ref>{{Cite web|title=THAP1 - THAP domain-containing protein 1 - Homo sapiens (Human) - THAP1 gene & protein|url=https://www.uniprot.org/uniprot/Q9NVV9|website=www.uniprot.org|access-date=2020-05-03}}</ref>
|[https://www.uniprot.org/uniprot/Q9NVV9 Q9NVV9]
|-
|Protein Tax-2
|[[Tax gene product|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.<ref>{{Cite web|title=tax - Protein Tax-2 - Human T-cell leukemia virus 2 (HTLV-2) - tax gene & protein|url=https://www.uniprot.org/uniprot/P03410|website=www.uniprot.org|access-date=2020-05-03}}</ref>
|[https://www.uniprot.org/uniprot/P03410 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.<ref>{{Cite web|title=PRNP - Major prion protein precursor - Homo sapiens (Human) - PRNP gene & protein|url=https://www.uniprot.org/uniprot/P04156|website=www.uniprot.org|access-date=2020-05-03}}</ref>
|[https://www.uniprot.org/uniprot/P04156 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.<ref>{{Cite web|title=ALDH1B1 - Aldehyde dehydrogenase X, mitochondrial precursor - Homo sapiens (Human) - ALDH1B1 gene & protein|url=https://www.uniprot.org/uniprot/P30837|website=www.uniprot.org|access-date=2020-05-03}}</ref>
|[https://www.uniprot.org/uniprot/P30837 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.<ref>{{Cite web|title=LYAR - Cell growth-regulating nucleolar protein - Homo sapiens (Human) - LYAR gene & protein|url=https://www.uniprot.org/uniprot/Q9NX58|website=www.uniprot.org|access-date=2020-05-03}}</ref><ref>{{Cite journal|last=Miyazawa|first=Naoki|last2=Yoshikawa|first2=Harunori|last3=Magae|first3=Satomi|last4=Ishikawa|first4=Hideaki|last5=Izumikawa|first5=Keiichi|last6=Terukina|first6=Goro|last7=Suzuki|first7=Ai|last8=Nakamura-Fujiyama|first8=Sally|last9=Miura|first9=Yutaka|last10=Hayano|first10=Toshiya|last11=Komatsu|first11=Wataru|date=2014-04|title=Human cell growth regulator Ly-1 antibody reactive homologue accelerates processing of preribosomal RNA|url=https://www.ncbi.nlm.nih.gov/pubmed/24495227|journal=Genes to Cells: Devoted to Molecular & Cellular Mechanisms|volume=19|issue=4|pages=273–286|doi=10.1111/gtc.12129|issn=1365-2443|pmid=24495227}}</ref>
|[https://www.uniprot.org/uniprot/Q9NX58 Q9NX58]
|-
|Coiled-coil domain-containing protein 85B
|[[CCDC85B]]
|Functions as a transcriptional repressor.<ref>{{Cite journal|last=Du|first=Xiulian|last2=Wang|first2=Qiang|last3=Hirohashi|first3=Yoshihiko|last4=Greene|first4=Mark I.|date=2006-12|title=DIPA, which can localize to the centrosome, associates with p78/MCRS1/MSP58 and acts as a repressor of gene transcription|url=https://www.ncbi.nlm.nih.gov/pubmed/17014843|journal=Experimental and Molecular Pathology|volume=81|issue=3|pages=184–190|doi=10.1016/j.yexmp.2006.07.008|issn=0014-4800|pmid=17014843}}</ref><ref>{{Cite web|title=CCDC85B - Coiled-coil domain-containing protein 85B - Homo sapiens (Human) - CCDC85B gene & protein|url=https://www.uniprot.org/uniprot/Q15834|website=www.uniprot.org|access-date=2020-05-03}}</ref>
|[https://www.uniprot.org/uniprot/Q15834 Q15834]
|-
|Nucleolar protein 56
|[[NOP56 (gene)|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. <ref>{{Cite web|title=NOP56 - Nucleolar protein 56 - Homo sapiens (Human) - NOP56 gene & protein|url=https://www.uniprot.org/uniprot/O00567|website=www.uniprot.org|access-date=2020-05-03}}</ref>
|[https://www.uniprot.org/uniprot/O00567 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. <ref>{{Cite web|title=FBL - rRNA 2'-O-methyltransferase fibrillarin - Homo sapiens (Human) - FBL gene & protein|url=https://www.uniprot.org/uniprot/P22087|website=www.uniprot.org|access-date=2020-05-03}}</ref><ref>{{Cite journal|last=Tessarz|first=Peter|last2=Santos-Rosa|first2=Helena|last3=Robson|first3=Sam C.|last4=Sylvestersen|first4=Kathrine B.|last5=Nelson|first5=Christopher J.|last6=Nielsen|first6=Michael L.|last7=Kouzarides|first7=Tony|date=2014-01-23|title=Glutamine methylation in histone H2A is an RNA-polymerase-I-dedicated modification|url=https://www.ncbi.nlm.nih.gov/pubmed/24352239|journal=Nature|volume=505|issue=7484|pages=564–568|doi=10.1038/nature12819|issn=1476-4687|pmc=3901671|pmid=24352239}}</ref><ref>{{Cite journal|last=Iyer-Bierhoff|first=Aishwarya|last2=Krogh|first2=Nicolai|last3=Tessarz|first3=Peter|last4=Ruppert|first4=Thomas|last5=Nielsen|first5=Henrik|last6=Grummt|first6=Ingrid|date=12 11, 2018|title=SIRT7-Dependent Deacetylation of Fibrillarin Controls Histone H2A Methylation and rRNA Synthesis during the Cell Cycle|url=https://www.ncbi.nlm.nih.gov/pubmed/30540930|journal=Cell Reports|volume=25|issue=11|pages=2946–2954.e5|doi=10.1016/j.celrep.2018.11.051|issn=2211-1247|pmid=30540930}}</ref>
|[https://www.uniprot.org/uniprot/P22087 P22087]
|-
|40S ribosomal protein S6
|[[Ribosomal protein s6|RPS6]]
|May play an important role in controlling cell growth and proliferation through the selective translation of particular classes of mRNA. <ref>{{Cite web|title=RPS6 - 40S ribosomal protein S6 - Homo sapiens (Human) - RPS6 gene & protein|url=https://www.uniprot.org/uniprot/P62753|website=www.uniprot.org|access-date=2020-05-03}}</ref>
|[https://www.uniprot.org/uniprot/P62753 P62753]
|}

=== Clinical Significance ===
C7orf50 has been noted in a variety of genome-wide association studies ([[Genome-wide association study|GWAS]]) and has been shown to be associated with [[type 2 diabetes]] among [[Sub-Saharan Africa|sub-Saharan Africans]] <ref>{{Cite journal|last=Meeks|first=Karlijn A C|last2=Henneman|first2=Peter|last3=Venema|first3=Andrea|last4=Addo|first4=Juliet|last5=Bahendeka|first5=Silver|last6=Burr|first6=Tom|last7=Danquah|first7=Ina|last8=Galbete|first8=Cecilia|last9=Mannens|first9=Marcel M A M|last10=Mockenhaupt|first10=Frank P|last11=Owusu-Dabo|first11=Ellis|date=2019-02-01|title=Epigenome-wide association study in whole blood on type 2 diabetes among sub-Saharan African individuals: findings from the RODAM study|url=https://academic.oup.com/ije/article/48/1/58/5070420|journal=International Journal of Epidemiology|language=en|volume=48|issue=1|pages=58–70|doi=10.1093/ije/dyy171|issn=0300-5771|pmc=PMC6380309|pmid=30107520}}</ref>, daytime sleepiness in [[African Americans|African-Americans]] <ref>{{Cite journal|last=Barfield|first=Richard|last2=Wang|first2=Heming|last3=Liu|first3=Yongmei|last4=Brody|first4=Jennifer A|last5=Swenson|first5=Brenton|last6=Li|first6=Ruitong|last7=Bartz|first7=Traci M|last8=Sotoodehnia|first8=Nona|last9=Chen|first9=Yii-der I|last10=Cade|first10=Brian E|last11=Chen|first11=Han|date=2019-08-01|title=Epigenome-wide association analysis of daytime sleepiness in the Multi-Ethnic Study of Atherosclerosis reveals African-American-specific associations|url=https://academic.oup.com/sleep/article/doi/10.1093/sleep/zsz101/5492629|journal=Sleep|language=en|volume=42|issue=8|pages=zsz101|doi=10.1093/sleep/zsz101|issn=0161-8105|pmc=PMC6685317|pmid=31139831}}</ref>, [[Prenatal development|prenatal]] exposure to [[Particulates|particulate matter]] <ref>{{Cite journal|last=Gruzieva|first=Olena|last2=Xu|first2=Cheng-Jian|last3=Yousefi|first3=Paul|last4=Relton|first4=Caroline|last5=Merid|first5=Simon Kebede|last6=Breton|first6=Carrie V.|last7=Gao|first7=Lu|last8=Volk|first8=Heather E.|last9=Feinberg|first9=Jason I.|last10=Ladd-Acosta|first10=Christine|last11=Bakulski|first11=Kelly|date=2019-05|title=Prenatal Particulate Air Pollution and DNA Methylation in Newborns: An Epigenome-Wide Meta-Analysis|url=https://ehp.niehs.nih.gov/doi/10.1289/EHP4522|journal=Environmental Health Perspectives|language=en|volume=127|issue=5|pages=057012|doi=10.1289/EHP4522|issn=0091-6765|pmc=PMC6792178|pmid=31148503}}</ref>, heritable [[DNA methylation]] marks associated with [[breast cancer]] <ref>{{Cite journal|last=kConFab|last2=Joo|first2=Jihoon E.|last3=Dowty|first3=James G.|last4=Milne|first4=Roger L.|last5=Wong|first5=Ee Ming|last6=Dugué|first6=Pierre-Antoine|last7=English|first7=Dallas|last8=Hopper|first8=John L.|last9=Goldgar|first9=David E.|last10=Giles|first10=Graham G.|last11=Southey|first11=Melissa C.|date=2018-12|title=Heritable DNA methylation marks associated with susceptibility to breast cancer|url=http://www.nature.com/articles/s41467-018-03058-6|journal=Nature Communications|language=en|volume=9|issue=1|pages=867|doi=10.1038/s41467-018-03058-6|issn=2041-1723|pmc=PMC5830448|pmid=29491469}}</ref>, DNA methylation in relation to plasma [[Carotenoid|carotenoids]] and [[lipid profile]] <ref>{{Cite journal|last=Tremblay|first=Bénédicte L.|last2=Guénard|first2=Frédéric|last3=Lamarche|first3=Benoît|last4=Pérusse|first4=Louis|last5=Vohl|first5=Marie-Claude|date=2019-06-04|title=Network Analysis of the Potential Role of DNA Methylation in the Relationship between Plasma Carotenoids and Lipid Profile|url=https://www.mdpi.com/2072-6643/11/6/1265|journal=Nutrients|language=en|volume=11|issue=6|pages=1265|doi=10.3390/nu11061265|issn=2072-6643|pmc=PMC6628241|pmid=31167428}}</ref>, and has significant interactions with [[prion]] proteins <ref>{{Cite journal|last=Satoh|first=J.|last2=Obayashi|first2=S.|last3=Misawa|first3=T.|last4=Sumiyoshi|first4=K.|last5=Oosumi|first5=K.|last6=Tabunoki|first6=H.|date=2009|title=Protein microarray analysis identifies human cellular prion protein interactors|url=https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2990.2008.00947.x|journal=Neuropathology and Applied Neurobiology|language=en|volume=35|issue=1|pages=16–35|doi=10.1111/j.1365-2990.2008.00947.x|issn=1365-2990}}</ref>.

== References ==
== References ==
{{reflist}}
{{reflist}}

Revision as of 16:22, 3 May 2020

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.[1][2] C7orf50 is conserved in chimpanzees, Rhesus monkeys, dogs, cows, mice, rats, and chickens, along with 307 other organisms from mammals to fungi.[3] 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.[4][5] 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.[6][7]

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.[1]

File:C7orf50 GenomicLocation.png
The genomic location of C7orf50 on chromosome 7 as indicated by red line. As stated by GeneCards.org, the bands are according to Ensembl, locations according to GeneLoc.

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.[1]

File:C7orf50 GenomicNeighborhood.png
The genomic neighborhood of C7orf50, with C7orf50 being indicated on the minus strand with the red arrow. Image from NCBI entry on C7orf50.

mRNA

Alternative Splicing

C7orf50 has a total of 7 experimentally predicted mRNA transcripts.[1] 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. 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.[8] Of these transcripts, four of them encode for the same 194aa protein (isoform a),[9] 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

Name NCBI Accession # Transcript Length Protein Length Isoform
Transcript Variant 1 NM_032350.5 1311bp 194aa a
Transcript Variant 2 NM_001134395.1 1301bp 194aa a
Transcript Variant 3 NM_001134396.1 1282bp 194aa a
Transcript Variant 4 NM_001318252.2 2138bp 194aa a
Transcript Variant 7 NM_001350968.1 1081bp 193aa b
Transcript Variant 8 NM_001350969.1 1500bp 180aa c
Transcript Variant 9 NM_001350970.1 1448bp 60aa d

Alternatively, when the primary genomic assembly, GRCh38.p13, is used for annotation (NCBI: NC_000007.14), there are 10 computationally predicted mRNA transcripts.[1] The most complete and supported of these transcripts (transcript variant X6) is 1896bp, producing a 225aa-long protein.[10] In total, there are 6 different isoforms predicted for C7orf50. Of these transcripts, 5 of them encode for the same isoform (X3).[11] The remaining transcripts encode isoforms X2, X4, X5, X6, and X7 as represented below.

C7orf50 Computationally Determined

NCBI Reference Sequences (RefSeq) mRNA Transcripts

Name NCBI Accession # Transcript Length Protein Length Isoform
Transcript Variant X2 XM_017012719.1 1447bp 375aa X2
Transcript Variant X3 XM_011515582.3 1192bp 225aa X3
Transcript Variant X4 XM_024446977.1 1057bp 193aa X4
Transcript Variant X5 XM_011515581.3 1240bp 225aa X3
Transcript Variant X6 XM_011515584.2 1896bp 225aa X3
Transcript Variant X7 XM_017012720.2 1199bp 225aa X3
Transcript Variant X8 XM_011515583.2 1215bp 225aa X3
Transcript Variant X9 XM_017012721.2 2121bp 211aa X5
Transcript Variant X10 XM_024446978.1 2207bp 180aa X6
Transcript Variant X11 XM_024446979.1 933bp 93aa X7

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.[8] 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 [12].

Protein

General Properties

The longest experimentally determined, being recognized as the primary C7orf50 protein isoform, is isoform a.[9] This isoform's 194aa sequence from NCBI 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.

Isoform a has a predicted molecular weight (Mw) of 22.1 kDa, making C7orf50 smaller than the average protein (52 kDa).[13] The isoelectric point (theoretical pI) for this isoform is 9.65, meaning that C7orf50 is slightly basic.[14] 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.[15][16][17]

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.[18] As for motifs, a bipartite nuclear localization signal (NLS) was predicted from aa6 to aa21, meaning that C7orf50 is likely localized in the nucleus.[19] 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.[20][21]

Schematic model of C7orf50 Domains, Motifs, and special regions. First special region is of the mixed charge run. Second special region is of the acidic run. Created using Prosite MyDomains Image Creator.

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.[22][23]

File:C7orf50 SecondaryStructure Consensus.png
Predicted secondary structure of C7orf50 based on Prabi consensus predictor. Blue is indicative of alpha helices. Pink is indicative of ambiguous structure (beta turns and/or extended strands). Yellow/Orange is indicative of random coils.

Tertiary Structure

The tertiary structure of C7orf50 is comprised primarily of alpha helices as determined I-TASSER.[5][24][25]

File:C7orf50 TertiaryStructure.jpeg
Tertiary structure of C7orf50 protein as predicted by I-TASSER. C-score = -3.32. Estimated TM-score = 0.35 ± 0.12. Estimated RMSD = 13.1 ± 4.2 Å. Runs from N-terminal (Red) to C-terminal (Blue).

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.[26] This means that although the function of C7orf50 is unknown, 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 Processes rRNA processing ribosomal large subunit biogenesis maturation of 5.8S, LSU, and SSU rRNA RNA metabolic processing gene expression cellular component organization or biogenesis RNA secondary structure unwinding macromolecule methylation
Molecular Functions catalytic activity, acting on RNA ATP-dependent RNA helicase activity
Cellular Components nucleolus preribosome, large subunit precursor 90S preribosome small-subunit processome
Reactome Pathways major pathway of rRNA processing in the nucleolus and cytosol rRNA modification in the nucleus and cytosol
Protein Domains and Motifs helicase conserved C-terminal domain DEAD/DEAH box helicase RNA helicase, DEAD-box type, Q motif helicase superfamily 1/2, ATP-binding domain

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.

Regulation

Gene Level 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.[27]

Promoter ID Start Position End Position Length # of Coding Transcripts Greatest # of CAGE Tags in Transcripts
GXP_9000582 1013063 1013163 1101bp 0 N/A
GXP_6755691 1028239 1030070 1832bp 4 169233
GXP_6053282 1055206 1056306 1101bp 1 449
GXP_3207505 1127288 1128388 1101bp 1 545
GXP_9000584 1130541 1131641 1101bp 0 N/A
GXP_6755694 1137965 1139325 1361bp 16 100,070
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 factors (TFs) are most highly predicted to bind to C7orf50 in the promoter region.[27]

Transcription Factor Detailed Family Information Detailed Matrix Information Matrix Similarity Binding Sequence
NR2F Nuclear receptor subfamily 2 factors Chicken ovalbumin upstream promoter transcription factor 2 0.878 ctcaggaatccaaaGGTGacaagca
PERO Peroxisome proliferator-activated receptor Peroxisome proliferator-activated receptor gamma 0.908 cctcaggaatccAAAGgtgacaa
HOMF Homeodomain transcription factors Hmx2/Nkx5-2 homeodomain transcription factor 0.895 agtaagTTAAgtgcttggc
PRDM PR (PRDI-BF1-RIZ1 homologous) domain transcription factor PR domain zinc finger protein 4 (PFM1) 0.901 gcatgcTTTCaagtcacccagtaagttaagt
VTBP Vertebrate TATA binding protein factor Muscle TATA box                         0.871 tttttTAAAacagagtc
HOMF Homeodomain transcription factors Hmx2/Nkx5-2 homeodomain transcription factor 0.916 ccgggcttAAACgattttc
HZIP Homeodomain-leucine zipper transcription factors Homeobox and leucine zipper encoding transcription factor 0.908 ggaaaATCGtttaag
ZTRE Zinc transcriptional regulatory element ZTRE motifs (1 bp spacer), ZNF658 binding site 0.829 cccaccccGGGAcgcca
XBBF X-box binding factors Motif bound by regulatory factor X (RFX) proteins 0.993 tggttgccaAGGCaacccg
XBBF X-box binding factors X-box binding protein RFX1 0.988 gggttgccttgGCAAccag
SP1F GC-Box factors SP1/GC Sp4 transcription factor 0.960 acggggGGCGgttccag
CAAT CCAAT binding factors Nuclear factor Y (Y-box binding factor) 0.939 tcgtCCAAtgggagg
ZTRE Zinc transcriptional regulatory element ZTRE motifs (2 bp spacer), ZNF658 binding site 0.831 caCTCCtgaaggcggga
SP1F GC-Box factors SP1/GC Sp2, member of the Sp/XKLF transcription factors with three C2H2 zinc fingers in a conserved carboxyl-terminal domain 0.955 cctgaaggcgGGACtaa
ZF57 KRAB domain zinc finger protein 57 Krueppel-associated box-containing zinc-finger protein 57 (KRAB-ZFP 57) 0.942 tgcTGCCgccgct
CTCF CTCF and BORIS gene family, transcriptional regulators with 11 highly conserved zinc finger domains CCCTC-binding factor (zinc finger protein)-like (BORIS) 0.913 ggtccctgccggaaggcGGCGtccgcg
MYOD Myoblast determining factors Myogenic bHLH protein myogenin (myf4) 0.977 cgtgaaCAGCtgcgtcg
SP1F GC-Box factors SP1/GC Stimulating protein 1, ubiquitous zinc finger transcription factor 0.977 ccccgGGGCgggctccc
SP1F GC-Box factors SP1/GC Sp4 transcription factor 0.982 ggagggGGCGgagcccc
KLFS Krueppel like transcription factors Core promoter-binding protein (CPBP) with 3 Krueppel-type zinc fingers (KLF6, ZF9) 0.987 gtggagGGGGcggagcccc

Expression Pattern

C7orf50 shows ubiquitous expression in the kidneys, brain, fat, prostrate, spleen and 22 other tissues.[1] This expression is very high, 4.3 times above the average gene; therefore, there is a higher abundance of C7orf50 mRNA than the average gene within a cell.[28] There does not appear to be a definitive cell type in which this gene is not expressed.[29]

Transcription Regulation

Splice Enhancers

The mRNA of C7orf50 is predicted to have exonic spliceing enhancers, in which SR proteins can bind, at bp positions 45 (SRSF1 (IgM-BRCA1)), 246 (SRSF6), 703 (SRSF5), 1301 (SRSF1), and 1308 (SRSF2). Additionally, the 5’ splice site is predicted to be at bp 45, the 3’ site at bp 1696, and the branch site at bp 728.[30][31]

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 -415.73 kcal/mol with an ensemble diversity of 237.96. The 3' UTR has a predicted free energy of -278.97 kcal/mol with an ensemble diversity of 120.91.[32]

File:C7orf50 5UTR mRNAFolding.png
5'UTR mRNA Folding
File:C7orf50 3'UTR mRNAFolding.png
3' UTR mRNA Folding

miRNA Targeting

There are many poorly conserved miRNA binding sites predicted within the 3’UTR of C7orf50 mRNA. The notable miRNA familys 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.[33][34][35]

Gene Regulation

Subcellular Localization

The C7orf50 protein is predicted to localize intercellularly in both the nucleus and cytoplasm, but primarily within the nucleoplasm and nucleoli.[36][37][19][38]

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.[39][40] Additionally, this protein is predicted to be SUMOylated at aa71 with the SUMO protein binding from aa189 through aa193.[41][42][43] 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.[44][45][46][47][48] 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 threnonines. 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.[49][50]

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 kinase D-interacting Substrate of 220 kDa.[51]

Orthologs

Below is a table of a variety of orthologs of the human C7orf50 gene.[52][3] The table includes closely, moderately, and distantly related orthologs. Orthologs of the human protein C7orf50 are listed in descending order of the date of divergence. C7orf50 is highly evolutionary conserved from mammals to fungi. C7orf50 has evolved moderately and evenly over time with a divergence rate greater than Hemoglobin but less than Cytochrome C.

Rate of C7orf50 divergence compared to rates of Hemoglobin and Cytochrome C.
Selected Orthologs of C7orf50
Genus and Species Common Name Taxon Class Date of Divergence (MYA) Accession # Length (AA) % identity w/ human
Homo sapiens Human Mammalia N/A NM_001318252.2 194aa 100%
Tupaia chinensis Chinese Tree Shrew Mammalia 82 XP_006167949.1 194aa 76%
Dasypus novemcinctus Nine-banded Armadillo Mammalia 105 XP_004483895.1 198aa 70%
Miniopterus natalens Natal Long-fingered Bat Mammalia 96 XP_016068464.1 199aa 69%
Protobothrops mucrosquamatus Brown-spotted Pit Viper Reptilia 312 XP_015673296.1 196aa 64%
Balearica regulorum gibbericeps Grey-crowned Crane Aves 312 XP_010302837.1 194aa 61%
Falco peregrinus Peregrine Falcon Aves 312 XP_027635198.1 193aa 59%
Xenopus laevis African Clawed Frog Amphibia 352 XP_018094637.1 198aa 50%
Electrophorus electricus Electric Eel Actinopterygii 435 XP_026880604.1 195aa 53%
Rhincodon typus Whale Shark Chondrichthyes 465 XP_020372968.1 195aa 52%
Ciona intestinalis Sea Vase Ascidiacea 676 XP_026696561.1 282aa 37%
Octopus bimaculoides California Two-spot Octopus Cephalopoda 797 XP_014772175.1 221aa 40%
Priapulus caudatus Priapulus Priapulida 797 XP_014663190.1 333aa 39%
Bombus terrestris Buff-tailed Bumblebee Insecta 797 XP_012171653.1 260aa 32%
Actinia tenebrosa Australian Red Waratah Sea Anemone Anthozoa 824 XP_031575029.1 330aa 43%
Trichoplax adhaerens Trichoplax Trichoplacidae 948 XP_002110193.1 137aa 44%
Spizellomyces punctatus Branching Chytrid Fungi Fungi 1105 XP_016610491.1 412aa 29%
Eremothecium cymbalariae Fungi Fungi 1105 XP_003644395.1 266aa 25%
Quercus suber Cork Oak Tree Plantae 1496 XP_023896156.1 508aa 30%
Plasmopara halstedii Downy Mildew of Sunflower Oomycetes 1768 XP_024580369.1 179aa 26%

Function

The consensus prediction of C7orf50 function (GO terms), as determined by I-TASSER [53][24][25], 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).

Interacting Proteins

Proteins Predicted to Interact with C7orf50 [54][55]
Name of Protein Name of Gene Function UniProt Accession #
THAP1 domain-containing protein 1 THAP1 DNA-binding transcription regulator that regulates endothelial cell proliferation and G1/S cell-cycle progression.[56] 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.[57] 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.[58] 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.[59] 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.[60][61] Q9NX58
Coiled-coil domain-containing protein 85B CCDC85B Functions as a transcriptional repressor.[62][63] 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. [64] 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. [65][66][67] 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. [68] 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 [69], daytime sleepiness in African-Americans [70], prenatal exposure to particulate matter [71], heritable DNA methylation marks associated with breast cancer [72], DNA methylation in relation to plasma carotenoids and lipid profile [73], and has significant interactions with prion proteins [74].

References

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