Chromosome 9 open reading frame 50 is a protein that in humans is encoded by the C9orf50 gene.[5] C9orf50 has one other known alias, FLJ35803.[6] 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.

C9orf50
Identifiers
AliasesC9orf50, chromosome 9 open reading frame 50
External IDsMGI: 1923631; HomoloGene: 18859; GeneCards: C9orf50; OMA:C9orf50 - orthologs
Orthologs
SpeciesHumanMouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_199350

NM_198000

RefSeq (protein)

NP_955382

NP_932117

Location (UCSC)Chr 9: 129.61 – 129.62 MbChr 2: 30.68 – 30.69 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse

Gene

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Location

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In humans the gene is located on the negative strand at 9q34.11 and the coding sequence is 8,552 base pairs long.[7] On human chromosome 9, the gene spans bases chr9:132,374,504-132,383,055[8] Near C9orf50 is ASB6 which is the gene directly before C9orf50 on the negative strand and on the positive strand is NTMT1 which is more than double the size of C9orf50.[1][2]

Protein

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C9orf50 Schematic Illustration using Dog2.0. The 431 amino acid is displayed showing regions of disorder in yellow, polyampholyte in red, and DUF4685 in teal. Other motifs are shown and labelled at the correct AA position. Pink circles represent sites of acetylation, teal represents glycation, and blue represents sumoylation.

The C9orf50 protein has a molecular weight of 47,639 kD and consists 431 amino acids with a predicted isoelectric point of 10.38[7] The C9orf50 protein contains the conserved domain in pfam15737- DUF4685, the function of which is not well understood and conserved in vertebrates. The protein is made up of 7 exons.

Isoforms

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C9orf50 has 9 different splice isoforms (SI) and 11 different transcript variants (TV), the most common is isoform 1 and transcript variant 1.[9]

 
C9orf50 Isoform table. Author Hannah Berhow
 
C9orf50 Isoforms and Transcript Variants

Domains

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The protein can be analyzed as a whole as well as split into 3 parts including the N-terminalDomain of 193 residues, DUF4685 of 103 residues, and the C-terminal Domain of 135 residues. The full protein pI is similar to the average pI of the NTD, DUF4685, and CTD. Of these sections the NTD has the highest pI and mW but also has the most residues at 193 of 431.[10][11]

C9orf50 pI mW kD Residues
Human Whole Protein 10.38 47.6 431
NTD 11.14 21.1 193
DUF4685 10.8 11.8 103
CTD 9.47 14.7 135

Composition

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The compositional analysis of the C9orf50 protein reveals low amounts of I, M, Y and FIKMNY relative to humans and high amounts of R, and KR-ED. There are no findings for charge clusters, high scoring charged or uncharged segments, charge runs, patterns, high scoring hydrophobic or transmembrane segments. Three different unique spacings of C were found at positions 161, 190, and 342. C9orf50 is also found to have 3 repetitive structures, the first sequence PRLP_KLT occurs starting at position 30 and then is repeated at position 78. Another repetitive structure is SLLP at positions 99 and 398. The last repeat structure at 250 and 303 made of KAAL.[12]

Tertiary Structure

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Tertiary C9orf50 protein structures can be found using I-Tasser. This tool results in 5 visualized structures, the two with the highest C scores are -3.25 and -1.27.

Gene level regulation

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Promoter

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The promoter region for C9orf50 was found using the Genomatix Gene2Promoter search engine.[13] This resulted in 6 found promoter regions. Only 2 of which were supported by transcripts and cage tags. The most supported promoter region spans 1,962 bases and is conserved in 6 of 8 orthologous loci with 945 cage tags. The transcription start site was determined to be located at 1,503 from a transcript with 7 exons supported by 118 cage tags.[13]

Transcription factor binding sites

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There are hundreds of transcription factors that are predicted to bind the promoter region. The promoter region transcription factors table highlight 20 of these.

Transcript Level Regulation

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C9orf50 5' UTR intermolecular base paired structure with the highest delta G is -323.4 kcal/mol. This is the lowest energy structure predicted for the 5'UTR region.[14] For the 3 ' UTR, the highest dG is -127.5 kcal/mol indicating that it is not as stable as the 5' UTR.

 
C9orf50 3' UTR Stem Loop Structures
 
C9orf50 5' UTR Stem Loop Structures

Tissue expression

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RNA-seq data of C9orf50 has found a low expression level, 25-50th percentile, in most human tissues compared to all human proteins.[15] However, it is most highly expressed in testes, brain and gallbladder.[9] C9orf50 protein expression is higher than the C9orf50 RNA expression.[16] When studying in situ hybridization data, The mouse C9orf50 ortholog, symbol 1700001O22Rik, was used to compare protein expression against Beta-actin which is ubiquitously expressed and the analyses shows similar expression patterns in the mouse brain.[17] During development, the protein can be found in the fetal stages.[18]

Subcelluar expression

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The protein has been located primarily in the nucleus and less so found in mitochondria and cytosol.[19]

 
C9orf50 Promoter Region Transcription Factors

Orthologs

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There are no known paralogs of C9orf50. orthologs of C9orf50 have been found conserved across most subclasses of mammals with the furthest, opossum of the infraclass marsupialia, diverged 159 million years ago.[20] This gene is not found in reptiles, amphibians, birds, or any other organisms evolved before mammals. A list of mammals in which C9orf50 is conserved is shown below.

C9orf50 Orthologs
Common Name Taxonomic Group Divergence from Humans (MYA) NCBI Accession # Protein Length (AA) Sequence Identity to Humans%
Human Hominini 0 NP_955382.3 431 100
Chimpanzee Primates 6.65 XP_016817319.1 431 97.22
Gorilla Primates 9.06 XP_018889539.1 435 93.17
Deer Mouse Rodentia 90 XP_006983488.1 391 46.14
Prairie Vole Rodentia 90 XP_005346778.1 370 45.18
American Pika Lagomorpha 90 XP_004593748.1 579 38.11
Narrow Ridged Finless Porpoise Cetacea 96 XP_024617982.1 473 56.71
Killer Whale Cetacea 96 XP_012388229.1 343 59.34
Alpaca Artiodactyla 96 XP_006205645.1 399 53.83
Black Flying Fox Chiroptera 96 XP_015449607.1 432 53.21
Egyption Fruit bat Chiroptera 96 XP_015989428.1 431 53.01
Goat Artiodactyla 96 XP_017910228.1 438 52.4
Northern Fur Seal Carnivora 96 XP_025744313.1 441 52.36
Grizzly Bear Carnivora 96 XP_026369526.1 447 50.63
European Hedgehog Soricomorpha 96 XP_007527129.1 419 51.42
Star Nosed Mole Proboscidea 96 XP_012576659.1 383 48.68
Southern White Rhinoceros Perissodactyla 96 XP_014637447.1 489 47.25
African Bush Elephant Proboscidea 105 XP_023401069.1 527 49.31
Nine-Banded Armadillo Cingulata 105 XP_023443586.1 476 46.72
Gray short tailed opossum Didelpimorphia 159 XP_007475193.1 583 32.56

Evolution

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C9orf50 is predicted to evolve more quickly than other common proteins including cytochrome C, hemoglobin beta, and fibrinogen alpha chain.

 
C9orf50 Molecular Clock

Amino acid conservation

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Important amino acids are characterized by those that were on the 100% consensus line created in MView of the strict ortholog multiple sequence alignment.[21] Amino Acids in red represent conserved amino acids in DUF4685. 14 of the 22 highly conserved amino acids are found within this domain. Leucine occupies the most conserved positions of the C9orf50 protein.

Conserved Amino Acids C9orf50 AA Position
Proline 33,325
Leucine 147, 155, 158, 280, 285, 321, 328
Phenylalanine 231, 275
Arginine 272, 286
Valine 273, 313
Alanine 267
Aspartic Acid 277
Glutamic Acid 278, 289
Threonine 279
Tyrosine 287
Tryptophan 288

Mutations

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Post Translational Modifications and Secondary Structure of C9orf50. PTMs for C9orf50 were found using the tools posted on the Expasy Protein Modifications site. The secondary structure for C9orf50 was predicted by using analysis from Gor, COILS, CFSSP, JPRED, and SOPMA.[1],[2],[3],[4],[5] Helix indicated by green cylinders, beta sheet indicated by blue arrows, and turn structures indicated by pink arrows were included below in the conceptual translation if they had a high prediction score. All the structures that were found in more than one analysis tool were also kept. The protein has no transmembrane sequences.

Common variants in C9orf50 were found with NCBI SNPGeneView.[22]

dbSNP rs# Cluster ID Function dbSNP Allele Amino Acid Position
rs146521610 Synonymous V → G 317
rs566893379 Synonymous S → T 310
rs111868243 Synonymous S → A 258
rs918165 Missense K → A 248
rs141573674 Missense S → A 201
rs759058008 Frameshift Deleted L 189
rs111606531 Synonymous A → T 86
rs146618124 Missense S → C 52
rs372378735 Synonymous G → A 45
rs751493011 Nonsense Insert T 11

References

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  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000179058Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000044320Ensembl, 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.
  5. ^ "uncharacterized protein C9orf50 [Homo sapiens] - Protein - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2019-02-25.
  6. ^ "Gene: C9orf50 (ENSG00000179058) - Summary - Homo sapiens - Ensembl genome browser 95". uswest.ensembl.org. Retrieved 2019-02-25.
  7. ^ a b "C9orf50 Gene". www.genecards.org. Retrieved 2019-02-25.
  8. ^ "C9orf50 chromosome 9 open reading frame 50 [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2019-02-25.
  9. ^ a b "C9orf50 chromosome 9 open reading frame 50 [Homo sapiens (human)] - Gene - NCBI".
  10. ^ Gene https://www.ncbi.nlm.nih.gov/gene/375759
  11. ^ "ExPASy - Compute pI/Mw tool".
  12. ^ "EBI Tools: Job not available".
  13. ^ a b "Genomatix: Login Page".
  14. ^ "The Mfold Web Server | mfold.rit.albany.edu".
  15. ^ "Gds3113 / 115495".
  16. ^ "Anti-C9orf50 antibody produced in rabbit Prestige Antibodies Powered by Atlas Antibodies, affinity isolated antibody, buffered aqueous glycerol solution | Sigma-Aldrich".
  17. ^ "Gene Detail :: Allen Brain Atlas: Mouse Brain".
  18. ^ "EST Profile - Hs.124223".
  19. ^ "WoLF PSORT: Advanced Protein Subcellular Localization Prediction Tool - GenScript".
  20. ^ "Protein BLAST: search protein databases using a protein query". blast.ncbi.nlm.nih.gov. Retrieved 2019-02-25.
  21. ^ "EBI Tools: Error".
  22. ^ "SNP linked to Gene (geneID:375759) Via Contig Annotation".