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CCDC171 Gene

protein-coding   GIFtS: 33
GCID: GC09P015554

Coiled-Coil Domain Containing 171

(Previous name: chromosome 9 open reading frame 93)
(Previous symbol: C9orf93)
  Search for CCDC171
at  

(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
Coiled-Coil Domain Containing 1711 2     bA536D16.12
C9orf931 2 3     bA778P13.12
Myosin Tail Domain Containing Protein1 2     Coiled-Coil Domain-Containing Protein 1712
Chromosome 9 Open Reading Frame 931     

External Ids:    HGNC: 298281   Entrez Gene: 2032382   Ensembl: ENSG000001649897   UniProtKB: Q6TFL33   

Export aliases for CCDC171 gene to outside databases


(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 CCDC171 Gene:
CCDC171 (coiled-coil domain containing 171) 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:
NC_000009.12  NT_008413.19  NC_018920.2  
Regulatory elements:
   Search for regulatory transcription factor binding sites for CCDC171
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for CCDC171

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CCDC171


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

Entrez Gene cytogenetic band: 9p22.3   Ensembl cytogenetic band:  9p22.3   HGNC cytogenetic band: 9p22.2

CCDC171 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CCDC171 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09P015554:  view genomic region     (about GC identifiers)

Start:
15,552,895 bp from pter      End:
16,061,661 bp from pter
Size:
508,767 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: CC171_HUMAN, Q6TFL3 (See protein sequence)
Recommended Name: Coiled-coil domain-containing protein 171  
Size: 1326 amino acids; 152810 Da
Sequence caution: Sequence=BAC04370.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=BAC04823.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAC87511.1;
Type=Erroneous initiation; Note=Translation N-terminally extended;
Secondary accessions: B7ZM22 Q5SU58 Q6P1W1 Q6ZR13 Q8N1Z4 Q8N8L3 Q8TBR2
Alternative splicing: 3 isoforms:  Q6TFL3-1   Q6TFL3-3   Q6TFL3-4   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for CCDC171: NX_Q6TFL3

Explore proteomics data for CCDC171 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See CCDC171 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_775821.2  
    ENSEMBL proteins: 
     ENSP00000370077   ENSP00000409055   ENSP00000399526   ENSP00000297641   ENSP00000438838  

    CCDC171 Human Recombinant Protein Products:

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    ProtoNet protein and cluster: Q6TFL3


    (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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003700sequence-specific DNA binding transcription factor activity ----
    GO:0004871signal transducer activity ----
         
    CCDC171 for ontologies           About GeneDecksing


    Phenotypes:
         2 GenomeRNAi human phenotypes for CCDC171:
     Increased gamma-H2AX phosphory  Synthetic lethal with Ras 

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for CCDC171
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    Browse Sino Biological Human cDNA Clones
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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      --

    (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 CCDC171
    Interactions:

        Search GeneGlobe Interaction Network for CCDC171

    Gene Ontology (GO): 2 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006355regulation of transcription, DNA-templated ----
    GO:0007165signal transduction ----

    CCDC171 for ontologies           About GeneDecksing



    (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 CCDC171 (CC171)



    (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,
    Conferences by KenesGroup, 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, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for CCDC171 gene: 
    NM_173550.2  

    Unigene Cluster for CCDC171:

    Coiled-coil domain containing 171
    Hs.17267  [show with all ESTs]
    Unigene Representative Sequence: CR936775
    11 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000380701(uc003zmd.3 uc003zme.3 uc011lmu.2) ENST00000474193
    ENST00000449575 ENST00000432954(uc003zmf.1) ENST00000470191 ENST00000498725
    ENST00000486641 ENST00000472806(uc003zmg.3) ENST00000478913 ENST00000297641(uc010mih.1)
    ENST00000535968(uc003zmc.2)
    miRNA
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      QuantiTect SYBR Green Assays in human, mouse, rat CCDC171
      QuantiFast Probe-based Assays in human, mouse, rat CCDC171

    Additional mRNA sequence: 

    AF440401.1 AK094506.1 AK096586.1 AK128581.1 AK308284.1 AL832443.1 AY422473.1 BC026063.2 
    BC040738.1 BC064849.1 BC144214.1 BC150600.1 BX537933.1 CR936775.1 

    11 DOTS entries:

    DT.99942588  DT.92414693  DT.101967351  DT.91664811  DT.70105105  DT.100017630  DT.40276605  DT.205466 
    DT.40235805  DT.97788108  DT.91757792 

    Selected AceView cDNA sequences (see all 68):

    BC026063 AA732460 AK128581 BC064849 N33749 CA429396 AY422473 AW297965 
    AI239947 NM_173550 AA639185 BG197895 BE165539 AA393656 AI243499 AA234608 
    BG183926 W73161 BG217818 AA236524 BX537933 AW305150 AW188326 AF440401 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for CCDC171    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20a · 20b ^ 21 ^ 22 ^ 23a · 23b ^
    SP1:                                                        -                                                                                                   
    SP2:        -                                                                                                                                                   
    SP3:                                                                                                                                                            
    SP4:                                                                                                                                                            

    ExUns: 24 ^ 25a · 25b ^ 26 ^ 27a · 27b
    SP1:              -                     
    SP2:                                    
    SP3:                                    
    SP4:        -     -     -               


    ECgene alternative splicing isoforms for CCDC171

    (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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    CCDC171 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    CCDC171 Expression
    About this image

    CCDC171 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    CCDC171 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.17267
        Custom PCR Arrays for CCDC171
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CCDC171

    (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 chordates.

    Orthologs for CCDC171 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ccdc1711 , 5 RIKEN cDNA 4930473A06 gene5
    coiled-coil domain containing 1711
    85.22(n)1
    87.29(a)1
      4 (39.46 cM)5
    3202261  NM_001081012.11  NP_001074481.11 
     835255455 
    chicken
    (Gallus gallus)
    Aves C9ORF931 chromosome Z open reading frame, human C9orf93 72.97(n)
    63.54(a)
      427242  XM_004949115.1  XP_004949172.1 
    lizard
    (Anolis carolinensis)
    Reptilia CCDC1716
    coiled-coil domain containing 171
    67(a)
    1 ↔ 1
    2(35089607-35307382)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia Str.181782 Transcribed sequences 72.7(n)    BX757414.1 
    zebrafish
    (Danio rerio)
    Actinopterygii si:ch211-116m6.41 si:ch211-116m6.4 49.39(n)
    38.99(a)
      100330004  XM_002665826.3  XP_002665872.3 


    ENSEMBL Gene Tree for CCDC171 (if available)
    TreeFam Gene Tree for CCDC171 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for CCDC171 gene
    3 SIMAP similar genes for CCDC171 using alignment to 3 protein entries:     CC171_HUMAN (see all proteins):
    DKFZp686I0230    DKFZp762M154    FOXP2

    CCDC171 for paralogs           About GeneDecksing



    (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 CCDC171 (see all 10399)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs752595231,2
    C,Funtested115744607(+) TCAAAG/AGATTG 2 /R /G mis11Minor allele frequency- A:0.03EA 120
    rs1830683751,2
    --15551146(+) ATATAA/GTACAT 1 -- us2k10--------
    rs132927711,2
    A--15551239(+) gagtcC/Gcgctc 1 -- us2k10--------
    rs1859894201,2
    --15551266(+) GTGCAC/GTGACG 1 -- us2k10--------
    rs1908896061,2
    --15551291(+) TGCAAA/GCTCCA 1 -- us2k10--------
    rs754809681,2
    C,F--15551293(+) CAAGCG/TCCACC 1 -- us2k11Minor allele frequency- T:0.50WA 2
    rs1878550961,2
    --15551340(+) GAGTAC/GCTGGG 1 -- us2k10--------
    rs1924237101,2
    --15551457(+) CCGCCA/CACCTC 1 -- us2k10--------
    rs1154891721,2
    F--15551507(+) CGCCCG/AGCCAA 1 -- us2k11Minor allele frequency- A:0.03WA 118
    rs3698774521,2
    C--15551673(+) AAAAA-/GAAAAA 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for CCDC171 (15552895 - 15802895 bp, first 250kb of CCDC171)

    Structural Variations
          Database of Genomic Variants (DGV) variations for CCDC171: --
    Human Gene Mutation Database (HGMD): CCDC171
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing CCDC171
    DNA2.0 Custom Variant and Variant Library Synthesis for CCDC171

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    CCDC171 for disorders           About GeneDecksing


    Export disorders for CCDC171 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 CCDC171 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with CCDC171)
        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, 3 Ota T.... Sugano S. (Nat. Genet. 2004)
    2. DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)1, 2 Humphray S.J.... Dunham I. (Nature 2004)
    3. 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)
    4. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
    5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    6. 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. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    7. (PubMed id )2 

    (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: 203238 HGNC: 29828 AceView: C9orf93 Ensembl:ENSG00000164989 euGenes: HUgn203238
    ECgene: CCDC171 H-InvDB: CCDC171

    (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 CCDC171 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 CCDC171 gene:
    Search GeneIP for patents involving CCDC171

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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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