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C9orf85 Gene

protein-coding   GIFtS: 40
GCID: GC09P074526

Chromosome 9 Open Reading Frame 85

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Chromosome 9 Open Reading Frame 851 2
Uncharacterized Protein C9orf852

External Ids:    HGNC: 287841   Entrez Gene: 1382412   Ensembl: ENSG000001556217   UniProtKB: Q96MD73   

Export aliases for C9orf85 gene to outside databases

Previous GC identifers: GC09P069983 GC09P071755 GC09P073716 GC09P044349


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for C9orf85 Gene:
C9orf85 (chromosome 9 open reading frame 85) is a protein-coding 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000009.11  NC_018920.2  NT_008470.20  
Regulatory elements:
   Regulatory transcription factor binding sites in the C9orf85 gene promoter:
         STAT5B   Max1   USF1   USF2   Pax-2   USF-1:USF-2   Pax-2a   C/EBPalpha   CHOP-10   Cart-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for C9orf85

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C9orf85


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

Entrez Gene cytogenetic band: 9q21.13   Ensembl cytogenetic band:  9q21.13   HGNC cytogenetic band: 9q21.2

C9orf85 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C9orf85 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09P074526:  view genomic region     (about GC identifiers)

Start:
74,526,423 bp from pter      End:
74,600,970 bp from pter
Size:
74,548 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: CI085_HUMAN, Q96MD7 (See protein sequence)
Recommended Name: Uncharacterized protein C9orf85  
Size: 179 amino acids; 20166 Da
Sequence caution: Sequence=CAH72769.1; Type=Erroneous gene model prediction;
Secondary accessions: Q5W0N1 Q5W0N3 Q6PJW9 Q86U95
Alternative splicing: 3 isoforms:  Q96MD7-3   Q96MD7-1   Q96MD7-2   (May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay)

Explore the universe of human proteins at neXtProt for C9orf85: NX_Q96MD7

Explore proteomics data for C9orf85 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See C9orf85 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_872311.2  
    ENSEMBL proteins: 
     ENSP00000433086   ENSP00000334289   ENSP00000366230   ENSP00000434838   ENSP00000431527  
     ENSP00000366226  

    C9orf85 Human Recombinant Protein Products:

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    OriGene Purified Protein for C9orf85
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    Novus Biologicals C9orf85 Lysate
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for C9orf85

     
    Search eBioscience for Proteins for C9orf85 

    C9orf85 Antibody Products:

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    C9orf85 Assay Products:

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    Cloud-Clone Corp. ELISAs for C9orf85
    Cloud-Clone Corp. CLIAs for C9orf85
    Search eBioscience for ELISAs for C9orf85 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR019351 DUF2039

    Graphical View of Domain Structure for InterPro Entry Q96MD7

    ProtoNet protein and cluster: Q96MD7


    Find genes that share domains with C9orf85           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for C9orf85
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for C9orf85
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for C9orf85

    miRNA
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    miRTarBase miRNAs that target C9orf85:
    hsa-mir-124-3p (MIRT022127)

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    2 qRT-PCR Assays for microRNAs that regulate C9orf85:
    hsa-miR-1304 hsa-miR-2116
    SwitchGear 3'UTR luciferase reporter plasmidC9orf85 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat C9orf85

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    GenScript: all cDNA clones in your preferred vector: C9orf85 (NM_182505)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for C9orf85
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat C9orf85

    Cell Line
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for C9orf85


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus2
    cytosol1
    extracellular1

    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, 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 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for C9orf85
    Interactions:

        Search GeneGlobe Interaction Network for C9orf85

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for C9orf85 (CI085)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for C9orf85 gene (2 alternative transcripts): 
    NM_198394.1  NM_182505.3  

    Unigene Cluster for C9orf85:

    Chromosome 9 open reading frame 85
    Hs.534190  [show with all ESTs]
    Unigene Representative Sequence: AK307186
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000479413 ENST00000334731(uc004ain.3 uc004aio.3) ENST00000377031
    ENST00000473252 ENST00000486911(uc010mou.2 uc010mov.2) ENST00000377027

    miRNA
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    Block miRNA regulation of human, mouse, rat C9orf85 using miScript Target Protectors
    2 qRT-PCR Assays for microRNAs that regulate C9orf85:
    hsa-miR-1304 hsa-miR-2116
    SwitchGear 3'UTR luciferase reporter plasmidC9orf85 3' UTR sequence
    Inhib. RNA
    Products:
         
    OriGene RNAi products in human, mouse, rat for C9orf85
    Predesigned siRNA for gene silencing in human, mouse, rat C9orf85
    Clone
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    OriGene clones in human, mouse for C9orf85 (see all 7)
    OriGene ORF clones in mouse, rat for C9orf85
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: C9orf85 (NM_182505)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for C9orf85
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat C9orf85
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for C9orf85
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat C9orf85
      QuantiTect SYBR Green Assays in human, mouse, rat C9orf85
      QuantiFast Probe-based Assays in human, mouse, rat C9orf85

    Additional mRNA sequence: 

    AK307186.1 AK311206.1 BC052375.1 

    7 DOTS entries:

    DT.310853  DT.201591  DT.209378  DT.99975922  DT.121146096  DT.121150025  DT.210039 

    Selected AceView cDNA sequences (see all 67):

    AA687136 NM_198394 BU177451 AA978069 AW149895 BM923611 NM_182505 CA420108 
    AA862415 AA824363 AA332945 AA442437 CB113688 BC028019 BM723311 AW015572 
    W03368 AW020306 AW296111 AA970520 BQ020559 AA463332 BC010179 BQ431408 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for C9orf85 (see all 8)    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8a · 8b · 8c · 8d · 8e
    SP1:                    -     -                                                               
    SP2:                    -     -                 -     -     -                                 
    SP3:                          -           -     -     -     -                                 
    SP4:                    -     -           -     -     -                                       
    SP5:                    -     -           -     -     -     -                                 


    ECgene alternative splicing isoforms for C9orf85

    (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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    C9orf85 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    C9orf85 Expression
    About this image

    C9orf85 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    C9orf85 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.534190
        Custom PCR Arrays for C9orf85
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for C9orf85
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat C9orf85
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for C9orf85

    (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)
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    This gene was present in the common ancestor of animals.

    Orthologs for C9orf85 gene from Selected species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia 1110059E24Rik1 , 5 RIKEN cDNA 1110059E24 gene1, 5 84.52(n)1
    82.58(a)1
      19 (15.54 cM)5
    662061  NM_025423.21  NP_079699.11 
     215812025 
    chicken
    (Gallus gallus)
    Aves CZH9orf851 chromosome Z open reading frame, human C9orf85 69.95(n)
    69.7(a)
      770483  XM_001233820.3  XP_001233821.2 
    lizard
    (Anolis carolinensis)
    Reptilia C9orf856
    chromosome 9 open reading frame 85
    54(a)
    1 ↔ 1
    2(48304019-48329936)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.142782 Xenopus laevis transcribed sequence with weak similarity more 74.53(n)    BJ067524.1 
    zebrafish
    (Danio rerio)
    Actinopterygii zgc:1010161 zgc:101016 65.93(n)
    61.76(a)
      445497  NM_001004001.2  NP_001004001.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG86751 CG8675 52.48(n)
    53.47(a)
      32716  NM_132981.2  NP_573209.1 


    ENSEMBL Gene Tree for C9orf85 (if available)
    TreeFam Gene Tree for C9orf85 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for C9orf85 gene
    Selected SIMAP similar genes for C9orf85 using alignment to 4 protein entries:     CI085_HUMAN (see all proteins) (see all similar genes):
    OK/SW-cl.41    ELP4    CALM2    FP6778    LINC00269    NR5A2
    CLTA    ZNF66    SEPSECS    C3orf64    TM4SF19    DSERG1
    SLC35E3    HC6    IDNK    RTBDN    C14orf105    LSM12

    Find genes that share paralogs with C9orf85           About GenesLikeMe


    2 Pseudogenes.org Pseudogenes for C9orf85
    PGOHUM00000240646 PGOHUM00000237889


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for C9orf85 (see all 1078)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs601263321,2
    C--44376936(+) TAAAATT/-TCTAT 1 -- int11Minor allele frequency- -:0.50CSA 2
    rs1386732051,2
    --74412325(+) ACCTGA/TGATCT 1 -- int10--------
    rs802429811,2
    F--74412348(+) CTCTTT/CCTTTC 1 -- int11Minor allele frequency- C:0.07WA 118
    rs1845726821,2
    --74412411(+) GTTCAG/TAGGTA 1 -- int10--------
    rs70379511,2
    C,F--74412450(+) ttcacG/Agagtt 1 -- int12Minor allele frequency- A:0.06WA 120
    rs1415196231,2
    --74412547(+) CTCAGC/TAAGGG 1 -- int10--------
    rs1895535611,2
    --74412624(+) GAATGA/CAAACC 1 -- int10--------
    rs1461838291,2
    C--74412730(+) TCTGCA/GTCTTG 1 -- int10--------
    rs1807462691,2
    --74412746(+) TCTTAA/CCCTAA 1 -- int10--------
    rs1837305441,2
    --74412799(+) TTTTCA/GTAAAA 1 -- int10--------

    HapMap Linkage Disequilibrium report for C9orf85 (74526423 - 74600970 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for C9orf85:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv273935CNV Insertion20981092
    esv267786CNV Insertion20981092
    nsv831618CNV Loss17160897
    nsv521672CNV Loss19592680

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing C9orf85
    DNA2.0 Custom Variant and Variant Library Synthesis for C9orf85

    (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.)
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    Find genes that share disorders with C9orf85           About GenesLikeMe

    Genetic Association Database (GAD): C9orf85

    Export disorders for C9orf85 gene to outside databases

    (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)
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    PubMed articles for C9orf85 gene, integrated from 10 sources (see all 11):
    (articles sorted by number of sources associating them with C9orf85)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    3. DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)1, 2 Humphray S.J.... Dunham I. (Nature 2004)
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    5. N-terminal acetylome analyses and functional insights of the N- terminal acetyltransferase NatB. (PubMed id 22814378)2 Van Damme P....Aldabe R. (Proc. Natl. Acad. Sci. U.S.A. 2012)
    6. Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions. (PubMed id 19690332)2 Mayya V.... Han D.K. (Sci. Signal. 2009)
    7. A quantitative atlas of mitotic phosphorylation. (PubMed id 18669648)2 Dephoure N.... Gygi S.P. (Proc. Natl. Acad. Sci. U.S.A. 2008)
    8. Framingham Heart Study 100K Project: genome-wide associations for blood pressure and arterial stiffness. (PubMed id 17903302)4 Levy D....Mitchell G.F. (BMC Med. Genet. 2007)
    9. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (Genomics 2007)
    10. A genome-wide association for kidney function and endocrine-related traits in the NHLBI's Framingham Heart Study. (PubMed id 17903292)4 Hwang S.J....Fox C.S. (BMC Med. Genet. 2007)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 138241 HGNC: 28784 AceView: C9orf85 Ensembl:ENSG00000155621 euGenes: HUgn138241
    ECgene: C9orf85 H-InvDB: C9orf85

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for C9orf85 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for C9orf85 gene:
    Search GeneIP for patents involving C9orf85

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