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CCDC17 Gene

protein-coding   GIFtS: 40
GCID: GC01M046086

Coiled-Coil Domain Containing 17

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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
Coiled-Coil Domain Containing 171 2
Coiled-Coil Domain-Containing Protein 172

External Ids:    HGNC: 265741   Entrez Gene: 1494832   Ensembl: ENSG000001595887   UniProtKB: Q96LX73   

Export aliases for CCDC17 gene to outside databases

Previous GC identifers: GC01M045755 GC01M045858 GC01M044196


(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 CCDC17 Gene:
CCDC17 (coiled-coil domain containing 17) 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_000001.10  NT_032977.10  NC_018912.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the CCDC17 gene promoter:
         STAT4   STAT1beta   Nkx2-5   POU3F2   STAT1alpha   PPAR-gamma1   FAC1   STAT2   STAT3   PPAR-gamma2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCCDC17 promoter sequence
   Search Chromatin IP Primers for CCDC17

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CCDC17


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

Entrez Gene cytogenetic band: 1p34.1   Ensembl cytogenetic band:  1p34.1   HGNC cytogenetic band: 1p34.1

CCDC17 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CCDC17 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M046086:  view genomic region     (about GC identifiers)

Start:
46,085,716 bp from pter      End:
46,089,731 bp from pter
Size:
4,016 bases      Orientation:
minus 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., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: CCD17_HUMAN, Q96LX7 (See protein sequence)
Recommended Name: Coiled-coil domain-containing protein 17  
Size: 622 amino acids; 67721 Da
Sequence caution: Sequence=BAB71539.1; Type=Miscellaneous discrepancy; Note=Incompletely spliced mRNA;
Secondary accessions: A1A4Y7 B4DNX7 B4E1Q5 C9J8L2 Q0P683 Q5T629
Alternative splicing: 4 isoforms:  Q96LX7-4   Q96LX7-5   Q96LX7-2   Q96LX7-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for CCDC17: NX_Q96LX7

Explore proteomics data for CCDC17 at MOPED


See CCDC17 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (2 alternative transcripts): 
NP_001108410.2  NP_001177111.1  

ENSEMBL proteins: 
 ENSP00000361114   ENSP00000389415   ENSP00000432172   ENSP00000411335   ENSP00000437072  
 ENSP00000341451  

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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: Q96LX7


(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:
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SwitchGear 3'UTR luciferase reporter plasmidCCDC17 3' UTR sequence
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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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Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
cytosol2
nucleus2
peroxisome1

(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 CCDC17
Interactions:

    Search GeneGlobe Interaction Network for CCDC17

1 Interacting protein for CCDC17 (Q96LX73) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
FGFR3P226073I2D: score=3 
About this table

(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 CCDC17 (CCD17)



(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 CCDC17 gene (3 alternative transcripts): 
NM_152500.2  NM_001114938.2  NM_001190182.1  

Unigene Cluster for CCDC17:

Coiled-coil domain containing 17
Hs.18912  [show with all ESTs]
Unigene Representative Sequence: NM_001114938
10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000372044 ENST00000482416 ENST00000491755(uc010olt.2) ENST00000421127(uc010ols.2)
ENST00000528266 ENST00000445048 ENST00000479529 ENST00000464739 ENST00000525599
ENST00000343901(uc001com.4 uc001con.4 uc009vxz.3)
miRNA
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6 qRT-PCR Assays for microRNAs that regulate CCDC17:
hsa-miR-181c hsa-miR-589* hsa-miR-181a hsa-miR-181d hsa-miR-181b hsa-miR-4262
SwitchGear 3'UTR luciferase reporter plasmidCCDC17 3' UTR sequence
Inhib. RNA
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Additional mRNA sequence: 

AK298104.1 AK303939.1 BC029888.1 BC128177.1 BC128178.1 

4 DOTS entries:

DT.108418  DT.95366533  DT.95366534  DT.91935752 

Selected AceView cDNA sequences (see all 25):

BC065201 AK057646 NM_152500 BM982802 CA450000 BI825081 BX282368 BX114295 
BC029888 BI820653 BM981839 AI560239 AI186852 AW946466 BM982784 BI772657 
AA702960 BU677500 AA010540 AI829420 AW946509 CA311428 BF846269 AA010539 

GeneLoc Exon Structure

4 Alternative Splicing Database (ASD) splice patterns (SP) for CCDC17    About this scheme

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13a · 13b
SP1:                    -                                                                                       
SP2:                                                                                            -               
SP3:                    -     -                                                                                 
SP4:                                                                                                            


ECgene alternative splicing isoforms for CCDC17

(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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CCDC17 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TTCTGACATT
CCDC17 Expression
About this image

CCDC17 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

CCDC17 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.18912
    Custom PCR Arrays for CCDC17
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CCDC17

(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 CCDC17 gene from Selected species (see all 9)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Ccdc171 , 5 coiled-coil domain containing 171, 5 71.62(n)1
65.59(a)1
  4 (53.24 cM)5
6226651  NM_001037916.31  NP_001033005.11 
 1165966545 
lizard
(Anolis carolinensis)
Reptilia CCDC176
coiled-coil domain containing 17
42(a)
1 ↔ 1
4(110092305-110098567)
zebrafish
(Danio rerio)
Actinopterygii CR854855.26
Uncharacterized protein
27(a)
1 ↔ 1
6(33596046-33609470) ENSDARG00000090480


ENSEMBL Gene Tree for CCDC17 (if available)
TreeFam Gene Tree for CCDC17 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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(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 CCDC17 (see all 203)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 1 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs2007135731,2
--46085239(+) AACTC-/ATATGGT 2 -- int10--------
rs773770651,2
C--46085241(+) CTCAT-/ACGGTTG 2 -- int10--------
rs617899881,2
C--46085242(+) CTCATA/C/GGTTGC 2 -- int11NA 2
rs782426231,2
F--46085287(+) TCCTGA/GTGTTG 2 -- int11Minor allele frequency- G:0.01NA 120
rs15479251,2
C,F,O,A,H--46085356(+) AGTCAT/CGATGT 2 -- int134Minor allele frequency- C:0.31NS EA NA WA CSA 2921
rs1445766571,2
--46085378(+) AGGCAC/TTTGAC 2 -- int10--------
rs1841068001,2
--46085501(+) AGTACA/GTAAGG 2 -- int10--------
rs1887981521,2
--46085522(+) TTCCTC/GTTTAT 2 -- int10--------
rs22750841,2
C,F,H--46085639(+) GAATTT/GAAAGT 2 -- int110Minor allele frequency- G:0.04EA NS NA 2758
rs1160783841,2
F--46085681(+) CCTTTC/TGGAGA 2 -- int11Minor allele frequency- T:0.02WA 118

HapMap Linkage Disequilibrium report for CCDC17 (46085716 - 46089731 bp)

Structural Variations
     Database of Genomic Variants (DGV) 3 variations for CCDC17:    About this table    
Variant IDTypeSubtypePubMed ID
nsv829726CNV Loss17160897
nsv822509CNV Loss20364138
nsv871928CNV Gain21882294

Site Specific Mutation Identification with PCR Assays
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(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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(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 CCDC17 gene integrated from 10 sources:
(articles sorted by number of sources associating them with CCDC17)
    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. (Nat. Genet. 2004)
  2. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)2 Gregory S.G.... Bentley D.R. (Nature 2006)
  3. A human protein-protein interaction network: a resource for annotating the proteome. (PubMed id 16169070)1 Stelzl U.... Wanker E.E. (Cell 2005)
  4. 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. (Genome Res. 2004)
  5. 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)
  6. Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)1 Bonaldo M.F.... Soares M.B. (Genome Res. 1996)

(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: 149483 HGNC: 26574 AceView: FLJ33084 Ensembl:ENSG00000159588 euGenes: HUgn149483
ECgene: CCDC17 H-InvDB: CCDC17

(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 CCDC17 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 CCDC17 gene:
Search GeneIP for patents involving CCDC17

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, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, 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 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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