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CCDC163P Gene

pseudogene   GIFtS: 27
GCID: GC01M045959

Coiled-Coil Domain Containing 163, Pseudogene

(Previous name: chromosome 1 open reading frame 231)
(Previous symbol: C1orf231)
  See related diseases
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 163, Pseudogene1 2
C1orf2311 2
Chromosome 1 Open Reading Frame 2311
CDNA FLJ548864
Protein CCDC163P4

External Ids:    HGNC: 270031   Entrez Gene: 1266612   Ensembl: ENSG000002366247   UniProtKB: B4DV034   UniProtKB: E9PLD64   
UniProtKB: E9PN014   UniProtKB: E9PNU94   UniProtKB: E9PPK74   UniProtKB: F2Z3K34   

Export aliases for CCDC163P gene to outside databases

Previous GC identifers: GC01M045733 GC01M044071


(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 CCDC163P Gene:
CCDC163P (coiled-coil domain containing 163, pseudogene) is a pseudogene. Diseases associated with CCDC163P include retinitis, and cerebritis.


(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_000001.11  NC_018912.2  NT_032977.10  
Regulatory elements:
   Search for regulatory transcription factor binding sites for CCDC163P
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for CCDC163P

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CCDC163P


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

CCDC163P Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CCDC163P gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M045959:  view genomic region     (about GC identifiers)

Start:
45,959,538 bp from pter      End:
45,965,751 bp from pter
Size:
6,214 bases      Orientation:
minus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for CCDC163P

(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/TrEMBL: B4DV03 (See protein sequence)
Recommended Name: HCG1780060, isoform CRA_b  
Size: 118 amino acids; 13258 Da

UniProtKB/TrEMBL: E9PLD6 (See protein sequence)

Recommended Name: Protein CCDC163P  
Size: 118 amino acids; 13216 Da
Caution: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered
as preliminary data

UniProtKB/TrEMBL: E9PN01 (See protein sequence)

Recommended Name: Protein CCDC163P  
Size: 66 amino acids; 7236 Da
Caution: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered
as preliminary data

UniProtKB/TrEMBL: E9PNU9 (See protein sequence)

Recommended Name: Protein CCDC163P  
Size: 97 amino acids; 10553 Da
Caution: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered
as preliminary data

UniProtKB/TrEMBL: E9PPK7 (See protein sequence)

Recommended Name: Protein CCDC163P  
Size: 164 amino acids; 18127 Da
Caution: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered
as preliminary data

UniProtKB/TrEMBL: F2Z3K3 (See protein sequence)

Recommended Name: Protein CCDC163P  
Size: 145 amino acids; 16203 Da
Caution: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered
as preliminary data

Explore proteomics data for CCDC163P at MOPED


See CCDC163P Protein Expression from SPIRE MOPED, PaxDB, and MaxQB


ENSEMBL proteins: 
 ENSP00000431736   ENSP00000434894   ENSP00000435181   ENSP00000435596   ENSP00000432738  
 ENSP00000432622  

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Browse CLIAs at Cloud-Clone Corp.


(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: B4DV03


(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 CCDC163P
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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
cytosol1
endoplasmic reticulum1
extracellular1
nucleus1
peroxisome1
plasma membrane1

(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 CCDC163P
Interactions:

    Search GeneGlobe Interaction Network for CCDC163P

(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 CCDC163P



(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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REFSEQ mRNAs for CCDC163P gene: 
NM_001102601.1  

Unigene Cluster for CCDC163P:

Coiled-coil domain containing 163, pseudogene
Hs.461300  [show with all ESTs]
Unigene Representative Sequence: NR_033298
8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000415578(uc001cnu.3 uc001cnw.3 uc001cnv.3 uc009vxt.2 uc009vxu.2)
ENST00000515561 ENST00000502793(uc001cnt.3) ENST00000490551 ENST00000432082
ENST00000514299 ENST00000486476 ENST00000488405
miRNA
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Primer
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  QuantiFast Probe-based Assays in human, mouse, rat CCDC163P

Additional mRNA sequence: 

AK054714.1 AK300867.1 BC036618.2 BC047421.1 BC101254.2 BC101255.2 BC101256.1 BC101257.1 
BC113060.1 BC113061.1 NR_033296.1 NR_033297.1 NR_033298.1 

6 DOTS entries:

DT.100778057  DT.91755512  DT.103347  DT.121402060  DT.100748619  DT.121402063 

Selected AceView cDNA sequences (see all 40):

AI268516 BC047421 BF437861 CR606750 AI792796 BM920413 AK054714 BX393447 
D12074 BI666957 BI833152 BI596838 BM906246 BE904870 CD672203 BC036618 
BX350367 D12075 N46903 AA928930 BF355394 BF355392 AI792797 BX117044 

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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CCDC163P expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: CCTAGCCCCA
CCDC163P Expression
About this image


CCDC163P expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 4) fully expand
 
 Brain (Nervous System)    fully expand to see all 9 entries
         Thalamus
 
 Eye (Sensory Organs)
         Retina
 
 Neural Tube (Nervous System)
         Telencephalon
 
 Testis (Reproductive System)
CCDC163P Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

CCDC163P Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.461300
    Custom PCR Arrays for CCDC163P
Primer
Products:
OriGene qSTAR qPCR primer pairs in human, mouse for CCDC163P
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CCDC163P

(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 human and mouse.

Orthologs for CCDC163P gene from Selected species (see all 5)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Ccdc1635 coiled-coil domain containing 163   --   4 (53.29 cM) 116708509 


ENSEMBL Gene Tree for CCDC163P (if available)
TreeFam Gene Tree for CCDC163P (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 CCDC163P (see all 119)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 1 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs107894641,2
C,F,A,H--45959102(+) GATCTC/TTTGAG 3 -- ds50018Minor allele frequency- T:0.30WA NA EA 368
rs1826139321,2
--45959202(+) ATGCCC/TGTAGT 3 -- ds50010--------
rs1508554701,2
C--45959306(+) AAGTAC/TAAAAA 3 -- ds50010--------
rs783145291,2
C--45959505(+) GTTCCG/TTGTTG 3 -- ds50010--------
rs1415156551,2
C--45959636(+) CAGTT-/AATA  
        
AATCT
3 -- nc-transcript-variant0--------
rs1181579821,2
C,F--45959799(+) AGGATG/AATGTG 3 -- nc-transcript-variant1Minor allele frequency- A:0.05EA 120
rs1875814781,2
--45959841(+) AAGCTA/GGGGCT 3 -- nc-transcript-variant0--------
rs1393253091,2
C--45960411(+) ATCACC/TTGAGG 3 -- nc-transcript-variant0--------
rs412691091,2
C--45960484(+) ATTAGC/TGCACA 3 -- nc-transcript-variant2Minor allele frequency- T:0.06CSA EA 122
rs1911939771,2
--45960548(+) GAGGCA/GGAGGT 3 -- nc-transcript-variant0--------

HapMap Linkage Disequilibrium report for CCDC163P (45959538 - 45965751 bp)

Structural Variations
     Database of Genomic Variants (DGV) 4 variations for CCDC163P:    About this table    
Variant IDTypeSubtypePubMed ID
esv2747808CNV Deletion23290073
esv1741401CNV Insertion17803354
esv1477203CNV Insertion17803354
nsv829726CNV Loss17160897

Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing CCDC163P
DNA2.0 Custom Variant and Variant Library Synthesis for CCDC163P

(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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2 diseases for CCDC163P:    
About MalaCards
retinitis    cerebritis


CCDC163P for disorders           About GeneDecksing


Export disorders for CCDC163P 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 CCDC163P gene integrated from 10 sources:
(articles sorted by number of sources associating them with CCDC163P)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Comparative analysis of an unusual gene arrangement in the human chromosome 1. (PubMed id 18672041)1, 3 MakaA8owska I. (Gene 2008)
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
  3. 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: 126661 HGNC: 27003 AceView: LOC126661 Ensembl:ENSG00000236624 euGenes: HUgn126661
ECgene: CCDC163P H-InvDB: CCDC163P

(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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(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for CCDC163P gene:
Search GeneIP for patents involving CCDC163P

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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