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CCDC162P Gene

pseudogene   GIFtS: 23
GCID: GC06P109613

Coiled-Coil Domain Containing 162, Pseudogene

(Previous names: chromosome 6 open reading frame 184, chromosome 6 open reading...)
(Previous symbols: C6orf184, C6orf185, CCDC162)
  Search for CCDC162P
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 162, Pseudogene1 2     Chromosome 6 Open Reading Frame 1851
C6orf1841 2 3     bA425D10.32
C6orf1851 2 3     bA425D10.72
CCDC1621 2 3     Coiled-Coil Domain-Containing Protein 162 Pseudogene3
Chromosome 6 Open Reading Frame 1841     

External Ids:    HGNC: 215651   Entrez Gene: 2212622   Ensembl: ENSG000002037997   UniProtKB: A2VCL23   

Export aliases for CCDC162P 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 CCDC162P Gene:
CCDC162P (coiled-coil domain containing 162, pseudogene) is a pseudogene.


(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_000006.12  NC_018917.2  NT_025741.16  
Regulatory elements:
   Search for regulatory transcription factor binding sites for CCDC162P
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for CCDC162P

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CCDC162P


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

Entrez Gene cytogenetic band: 6q21   Ensembl cytogenetic band:  6q21   HGNC cytogenetic band: 6q21

CCDC162P Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CCDC162P gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P109613:  view genomic region     (about GC identifiers)

Start:
109,612,231 bp from pter      End:
109,676,266 bp from pter
Size:
64,036 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, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: CC162_HUMAN, A2VCL2 (See protein sequence)
Recommended Name: Coiled-coil domain-containing protein 162  
Size: 907 amino acids; 103842 Da
Sequence caution: Sequence=CAI40699.1; Type=Erroneous gene model prediction;
Secondary accessions: A1A4V1 A4QMU0 Q5JSU0 Q5JSU7
Alternative splicing: 3 isoforms:  A2VCL2-3   A2VCL2-1   A2VCL2-2   

Explore the universe of human proteins at neXtProt for CCDC162P: NX_A2VCL2

Explore proteomics data for CCDC162P at MOPED


See CCDC162P Protein Expression from SPIRE MOPED, PaxDB, and MaxQB


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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: A2VCL2


(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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Animal Models:
   inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for CCDC162P
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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 CCDC162P
Interactions:

    Search GeneGlobe Interaction Network for CCDC162P

(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 CCDC162P (CC162)



(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, Primers from OriGene, and/or QIAGEN )
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Unigene Cluster for CCDC162P:

Coiled-coil domain containing 162, pseudogene
Hs.373914  [show with all ESTs]
Unigene Representative Sequence: BC128119
9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000514758 ENST00000422819(uc003ptb.1) ENST00000429614(uc010kdm.1)
ENST00000368966 ENST00000508210 ENST00000506861 ENST00000473454 ENST00000440451
ENST00000368965(uc003ptc.1)
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Additional mRNA sequence: 

BC128118.1 BC128119.1 

4 DOTS entries:

DT.75195215  DT.92417296  DT.65287910  DT.92417297 

12 AceView cDNA sequences:

BU078179 AW189129 BU077934 AI962255 BU681175 BG181290 BG195719 BG190613 
AW130946 BG186897 BU676062 BG189551 

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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CCDC162P expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GGCTCGTCAG
CCDC162P Expression
About this image

CCDC162P Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

CCDC162P Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.373914
    Custom PCR Arrays for CCDC162P
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In Situ
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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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ENSEMBL Gene Tree for CCDC162P (if available)
TreeFam Gene Tree for CCDC162P (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 CCDC162P (see all 333)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 6 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1892770521,2
--109613510(+) TGAGAA/GTGGAT 1 -- us2k10--------
rs77489181,2
C,F,H--109613564(+) AAGACT/CTTGGA 1 -- us2k126Minor allele frequency- C:0.29NS EA NA WA CSA 2772
rs1494400371,2
--109613798(+) CTCAGC/TCGACG 1 -- us2k10--------
rs1809600021,2
--109613813(+) CTCACA/TGCAGG 1 -- us2k10--------
rs1165010511,2
--109613830(+) TGGAAA/GTGGCA 1 -- us2k10--------
rs792506211,2
C,F--109613859(+) GTAAAG/CGATAG 1 -- us2k11Minor allele frequency- C:0.06WA 118
rs15219081,2
C,F,A,H--109613986(+) GTGCCT/CGGATG 1 -- us2k117Minor allele frequency- C:0.50NS EA NA WA CSA 791
rs1849859751,2
--109614036(+) CTCTGA/GGCAGG 1 -- us2k10--------
rs1906619901,2
--109614324(+) AAAAAA/CCAAGG 1 -- us2k10--------
rs2016755991,2
--109614377(+) AAATA-/AATT  
        
AATTA
1 -- us2k10--------

HapMap Linkage Disequilibrium report for CCDC162P (109612231 - 109676266 bp)

Structural Variations
     Database of Genomic Variants (DGV) 1 variation for CCDC162P:    About this table    
Variant IDTypeSubtypePubMed ID
nsv527719CNV Loss19592680

Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing CCDC162P
DNA2.0 Custom Variant and Variant Library Synthesis for CCDC162P

(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 CCDC162P gene integrated from 10 sources:
(articles sorted by number of sources associating them with CCDC162P)
    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. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)1, 2 Mungall A.J.... Beck S. (Nature 2003)
  3. Seventy-five genetic loci influencing the human red blood cell. (PubMed id 23222517)1 van der Harst P....Chambers J.C. (Nature 2012)
  4. Genome-wide association study of hematological and biochemical traits in a Japanese population. (PubMed id 20139978)1 Kamatani Y....Kamatani N. (Nat. Genet. 2010)
  5. Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium. (PubMed id 19862010)1 Ganesh S.K....Lin J.P. (Nat. Genet. 2009)
  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. The sequence of the human genome. (PubMed id 11181995)1 Venter J.C.... Zhu X. (Science 2001)

(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: 221262 HGNC: 21565 AceView: C6orf185 Ensembl:ENSG00000203799 euGenes: HUgn221262
ECgene: CCDC162P H-InvDB: CCDC162P

(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 CCDC162P 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 CCDC162P gene:
Search GeneIP for patents involving CCDC162P

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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