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CCDC96 Gene

protein-coding   GIFtS: 40
GCID: GC04M007042

Coiled-Coil Domain Containing 96

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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 961 2
Coiled-Coil Domain-Containing Protein 962

External Ids:    HGNC: 269001   Entrez Gene: 2572362   Ensembl: ENSG000001730137   UniProtKB: Q2M3293   

Export aliases for CCDC96 gene to outside databases

Previous GC identifer: GC04M007093


(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 CCDC96 Gene:
CCDC96 (coiled-coil domain containing 96) 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_000004.11  NC_018915.2  NT_006051.19  
Regulatory elements:
   Regulatory transcription factor binding sites in the CCDC96 gene promoter:
         Evi-1   GATA-1   CREB   Ik-2   FOXO4   deltaCREB   FOXO1a   SEF-1 (1)   TGIF   FOXO1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCCDC96 promoter sequence
   Search Chromatin IP Primers for CCDC96

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CCDC96


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

Entrez Gene cytogenetic band: 4p16.1   Ensembl cytogenetic band:  4p16.1   HGNC cytogenetic band: 4p16.1

CCDC96 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CCDC96 gene location

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04M007042:  view genomic region     (about GC identifiers)

Start:
7,042,576 bp from pter      End:
7,044,728 bp from pter
Size:
2,153 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., 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: CCD96_HUMAN, Q2M329 (See protein sequence)
Recommended Name: Coiled-coil domain-containing protein 96  
Size: 555 amino acids; 62711 Da
Secondary accessions: Q8N2I7

Explore the universe of human proteins at neXtProt for CCDC96: NX_Q2M329

Explore proteomics data for CCDC96 at MOPED


See CCDC96 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_699207.1  
ENSEMBL proteins: 
 ENSP00000309285  

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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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1 InterPro protein domain:
 IPR025254 DUF4201

Graphical View of Domain Structure for InterPro Entry Q2M329

ProtoNet protein and cluster: Q2M329


Find genes that share domains with CCDC96           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:
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hsa-mir-25-3p (MIRT050295)

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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
nucleus3
cytosol2

(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 CCDC96
Interactions:

    Search GeneGlobe Interaction Network for CCDC96

(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 CCDC96 (CCD96)



(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 CCDC96 gene: 
NM_153376.2  

Unigene Cluster for CCDC96:

Coiled-coil domain containing 96
Hs.656757  [show with all ESTs]
Unigene Representative Sequence: NM_153376
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000310085(uc003gjv.2)
miRNA
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  QuantiFast Probe-based Assays in human, mouse, rat CCDC96

Additional mRNA sequence: 

AK075056.1 BC105055.1 BC112274.1 

2 DOTS entries:

DT.40199523  DT.95301489 

17 AceView cDNA sequences:

CK300202 NM_153376 BQ009685 BQ015371 AI352352 AK075056 BE550360 AI453089 
BU101619 BX091584 AI862332 AI609755 BQ188733 BE504875 R27422 AI828177 
AW449605 

GeneLoc Exon Structure


(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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CCDC96 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GAGAACGCGT
CCDC96 Expression
About this image

CCDC96 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

CCDC96 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.656757
    Custom PCR Arrays for CCDC96
Primer
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In Situ
Assay Products:
 

 
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(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 CCDC96 gene from Selected species (see all 12)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Ccdc961 , 5 coiled-coil domain containing 961, 5 76.74(n)1
71.94(a)1
  5 (19.14 cM)5
667171  NM_025725.21  NP_080001.11 
 364845885 
chicken
(Gallus gallus)
Aves CCDC961 coiled-coil domain containing 96 55.38(n)
40.44(a)
  100859647  XM_003641227.1  XP_003641275.1 
lizard
(Anolis carolinensis)
Reptilia CCDC966
coiled-coil domain containing 96
43(a)
1 ↔ 1
4(79463369-79466783)
African clawed frog
(Xenopus laevis)
Amphibia Xl.114742 Xenopus laevis transcribed sequence with weak similarity more 71.01(n)    48057799 
zebrafish
(Danio rerio)
Actinopterygii ccdc966
coiled-coil domain containing 96
35(a)
1 ↔ 1
7(41124054-41131186) ENSDARG00000035963


ENSEMBL Gene Tree for CCDC96 (if available)
TreeFam Gene Tree for CCDC96 (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 CCDC96 (see all 117)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 4 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1858738291,2
--6969312(+) TTTCAC/TTGAAA 1 -- int10--------
rs76594361,2
C,F,A,H--6969360(+) ATCATC/TTCTCC 1 -- int19Minor allele frequency- T:0.01NS EA NA 1036
rs2002787441,2
--6969414(+) CATAT-/AAAAAA 1 -- int10--------
rs774427931,2
C,F--6969423(+) AAAAAT/ATTTTT 1 -- int12Minor allele frequency- A:0.13WA NA 238
rs577000041,2
C--6969441(+) CAAGAA/GTCTCG 1 -- int10--------
rs1440828831,2
--6969446(+) GTCTCA/GCTCTG 1 -- int10--------
rs1464872601,2
--6969454(+) CTGTCA/GCCCAG 1 -- int10--------
rs1892805951,2
--6969499(+) AAGCTC/TTGCCT 1 -- int10--------
rs68152941,2
C,F,A--6969564(+) cgcccG/Accacc 1 -- int13Minor allele frequency- A:0.33NA 6
rs68471011,2
C--6969704(+) ccaccG/Tagccc 1 -- int16Minor allele frequency- T:0.02WA NA EA 364

HapMap Linkage Disequilibrium report for CCDC96 (7042576 - 7044728 bp)

Structural Variations
     Database of Genomic Variants (DGV) Selected variations for CCDC96 (see all 11):    About this table    
Variant IDTypeSubtypePubMed ID
nsv878532CNV Loss21882294
esv34033CNV Loss18971310
esv26516CNV Loss19812545
nsv4217CNV Loss18451855
nsv878530CNV Loss21882294
nsv878531CNV Loss21882294
nsv878533CNV Loss21882294
nsv428436CNV Gain18775914
nsv469847CNV Complex16826518
dgv1568e1CNV Complex17122850

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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 CCDC96 gene integrated from 10 sources:
(articles sorted by number of sources associating them with CCDC96)
    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. 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)
  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. (Genome Res. 2006)
  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)

(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: 257236 HGNC: 26900 AceView: FLJ90575 Ensembl:ENSG00000173013 euGenes: HUgn257236
ECgene: CCDC96 H-InvDB: CCDC96

(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 CCDC96 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 CCDC96 gene:
Search GeneIP for patents involving CCDC96

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, 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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The GeneCards human gene database gene index: 1 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 


Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

Hot genes      Disease genes      CCDC96 gene at Home site.
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