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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

C9orf50 Gene

protein-coding   GIFtS: 35
GCID: GC09M132374

chromosome 9 open reading frame 50
  Search for C9orf50
in
MalaCards
our new
 Human Malady Compendium 
Biological research products
for C9orf50    

Aliases
for C9orf50 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Chromosome 9 Open Reading Frame 501 2
FLJ358031
Uncharacterized Protein C9orf502

External Ids:    HGNC: 236771   Entrez Gene: 3757592   Ensembl: ENSG000001790587   UniProtKB: Q5SZB43   

Export aliases for C9orf50 gene to outside databases

Previous GC identifers: GC09M129455 GC09M131414 GC09M101973


Summaries
for C9orf50 gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
  --

Genomic Views
for C9orf50 gene

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000009.11  NC_018920.1  NT_008470.19  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the C9orf50 gene promoter:
         Egr-3   Pax-5   SREBP-1c   C/EBPalpha   SREBP-1b   GATA-1   E47   POU2F1   SREBP-1a   POU2F1a   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for C9orf50

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat C9orf50


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 9q34.11   Ensembl cytogenetic band:  9q34.11   HGNC cytogenetic band: 9q34.2

C9orf50 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C9orf50 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09M132374:  view genomic region     (about GC identifiers)

Start:
 132,374,504 bp from pter      End:
 132,383,055 bp from pter
Size:
 8,552 bases      Orientation:
 minus strand

Proteins
for C9orf50 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB/Swiss-Prot: CI050_HUMAN, Q5SZB4 (See protein sequence)
Recommended Name: Uncharacterized protein C9orf50  
Size: 431 amino acids; 47639 Da
Sequence caution: Sequence=AK093122; Type=Erroneous termination; Positions=378; Note=Translated as Gln;
Secondary accessions: Q2M1I2 Q8NA65

Explore the universe of human proteins at neXtProt for C9orf50: NX_Q5SZB4

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q5SZB4

    • C9orf50 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_955382.3  
    ENSEMBL proteins: 
     ENSP00000361556  

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    Protein Domains /
    Families
    for C9orf50 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    ProtoNet protein and cluster: Q5SZB4


    Function
    for C9orf50 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    miRNA
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    Pathways & Interactions
    for C9orf50 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for C9orf50

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    1 Interacting protein for C9orf50 (ENSP000003615564) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PPP1CCENSP000003350844STRING: ENSP00000335084
    About this table

    Drugs & Compounds
    for C9orf50 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
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    Browse Tocris compounds for C9orf50
    Search CenterWatch for drugs/clinical trials and news about C9orf50 / CI050 

    Transcripts
    for C9orf50 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
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    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    REFSEQ mRNAs for C9orf50 gene: 
    NM_199350.3  

    Unigene Cluster for C9orf50:

    Chromosome 9 open reading frame 50
    Hs.124223  [show with all ESTs]
    Unigene Representative Sequence: NM_199350
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000372478(uc004byc.4 uc022boo.1)

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    Inhib. RNA
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    Primer
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    Additional cDNA sequence: 

    AK093122.1 BC112353.1 JF442034.1 

    1 DOTS entry:

    DT.107442 

    19 AceView cDNA sequences:

    AX747938 AW118229 AA770485 AA628303 AI393130 NM_199350 AA459682 AK093122 
    AW958565 BX953457 AW958564 BX096497 BF941893 AA459803 AW291326 AA894604 
    AW468767 AA382330 AW084476 

    GeneLoc Exon Structure


    Expression
    for C9orf50 gene

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    C9orf50 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GGCCAGGCAA

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    C9orf50 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    1 LifeMap In Vivo Development Anatomical Compartment/Cell 
    Tissue Anatomical Compartment CellCategory (developmental path)
    EyeInner Nuclear LayerGABAergic Amacrine CellsAmacrine, Retina
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See C9orf50 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for C9orf50

    SOURCE GeneReport for Unigene cluster: Hs.124223
        SABiosciences Custom PCR Arrays for C9orf50
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    In Situ
    Assay Products:     
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    Orthologs
    for C9orf50 gene

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section
    This gene was present in the common ancestor of human and mouse.

    Orthologs for C9orf50 gene from 1/5 species (see all 5)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    mouse
    (Mus musculus)    		 Mammalia 1700001O22Rik1 , 5 RIKEN cDNA 1700001O22 gene1, 5 65.03(n)1
    49.45(a)1    		   2 (21.74 cM)5
    735981  NM_198000.31  NP_932117.21 
     307947695 


    ENSEMBL Gene Tree for C9orf50 (if available)
    TreeFam Gene Tree for C9orf50 (if available) 

    Paralogs
    for C9orf50 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    		  --

    Genomic Variants
    for C9orf50 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/230 NCBI SNPs in C9orf50 are shown (see all 230)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 9 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs12207011,2
    		C,F,A,H,--132374013(-) GAAACC/TCAAAA 1 -- ds500120Minor allele frequency- T:0.23NS EA NA CSA WA 2343
    rs1173374861,2
    		F,--132374071(+) CTCTCG/TCCCAG 1 -- ds50011Minor allele frequency- T:0.06EA 120
    rs1505641431,2
    		--132374090(+) GCAGTG/TGCGGG 1 -- ds50010--------
    rs126836571,2
    		C,A,H,--132374166(+) acctgG/Tggcta 1 -- ds50014Minor allele frequency- T:0.23NA EA 244
    rs1395647321,2
    		--132374270(+) GCCATA/CCTCCC 1 -- ds50010--------
    rs1822369241,2
    		--132374311(+) GGCATA/GGACCA 1 -- ds50010--------
    rs1447686701,2
    		--132374501(+) AGAAAA/GGCTTG 1 -- ds50010--------
    rs788334351,2
    		C,F,--132374601(+) GTGTGC/ACCCTG 1 -- ut314Minor allele frequency- A:0.18NA EA EU 379
    rs1486118771,2
    		C,F--132374629(+) GTTCAC/TCTCTT 2 R syn12Minor allele frequency- T:0.00NA EU 5353
    rs1420450191,2
    		F--132374634(+) CCTCTT/CATCTG 2 /K /E mis11Minor allele frequency- C:0.00NA 4518

    HapMap Linkage Disequilibrium report for C9orf50 (132374504 - 132383055 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for C9orf50: --

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    Disorders / Diseases
    for C9orf50 gene

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    		   --

    Publications
    for C9orf50 gene

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for C9orf50 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with C9orf50)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    2. Pharmacogenomic study of side-effects for antidepressa nt treatment options in STAR*D. (PubMed id 22041458)1 Clark S.L....van den Oord E.J. (2012)
    3. Identification of the human testis protein phosphatase 1 interactome. (PubMed id 21382349)1 Fardilha M....Silva E.F. (2011)
    4. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
    5. DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)2 Humphray S.J.... Dunham I. (2004)
    6. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)
    7. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)

    External Searches for C9orf50 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  
      Query String
    		PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    Genome Databases showing C9orf50 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 375759 HGNC: 23677 AceView: LOC375759 Ensembl:ENSG00000179058 euGenes: HUgn375759
    ECgene: C9orf50 H-InvDB: C9orf50

    Other Databases showing C9orf50 gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing C9orf50 gene

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for C9orf50 Pharmacogenomics, SNPs, Pathways

    Intellectual Property
    for C9orf50 gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		Patent Information for C9orf50 gene:
    Search GeneIP for patents involving C9orf50

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    Products
    for C9orf50 gene

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    About This Section

     
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