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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

COL6A4P1 Gene

pseudogene   GIFtS: 27
GCID: GC03M015193

collagen, type VI, alpha 4 pseudogene 1

(Previous name: dual von Willebrand factor A domains )
(Previous symbol: DVWA)
 Explore 2 diseases affiliated with
COL6A4P1 via
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 Human Malady Compendium 
Biological research products
for COL6A4P1    

Aliases
for COL6A4P1 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Collagen, Type VI, Alpha 4 Pseudogene 11 2     COL6A4P1 2
DIVA1 2 5     VWA61 2
DVWA1 2 5     Dual Von Willebrand Factor A Domains1
COL6A41 2     LOC3448755

External Ids:    HGNC: 334841   Entrez Gene: 3448752   Ensembl: ENSG000002305247   OMIM: 6123975   
ORGUL members:         
NONCODE:n408071    

Export aliases for COL6A4P1 gene to outside databases

Previous GC identifers: GC03M015187 GC03M015142


Summaries
for COL6A4P1 gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
Entrez Gene summary for COL6A4P1:
This transcribed pseudogene represents the 5' end of a presumed ortholog to a mouse gene which encodes a collagen VI
alpha 4 chain protein (GeneID 68553). No complete ORF of comparable size to the mouse protein is found in this gene.
The predicted protein lacks a signal peptide; however, this truncated collagen polypeptide may have achieved a
different function as suggested by PubMed ID: 18622395. Evidence of in vivo translation is incomplete. A large
chromosome break separates this pseudogene from the 3' end of the presumed ortholog (COL6A4P2, GeneID 646300) which is
located downstream at chromosome 3q21.3. (provided by RefSeq, Jun 2009)




Genomic Views
for COL6A4P1 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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000003.11  NC_018914.1  NT_022517.18  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for COL6A4P1
         Other transcription factors

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Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat COL6A4P1


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

Entrez Gene cytogenetic band: 3p25.1   Ensembl cytogenetic band:  3p25.1   HGNC cytogenetic band: 3p25.1

COL6A4P1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
COL6A4P1 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03M015193:  view genomic region     (about GC identifiers)

Start:
 15,193,340 bp from pter      End:
 15,247,466 bp from pter
Size:
 54,127 bases      Orientation:
 minus strand

Proteins
for COL6A4P1 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB: --

Protein Domains /
Families
for COL6A4P1 gene

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
   --

Function
for COL6A4P1 gene

(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section
miRNA
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Inhib. RNA
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In Situ Assay
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Pathways & Interactions
for COL6A4P1 gene

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for COL6A4P1

Drugs & Compounds
for COL6A4P1 gene

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
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Browse Tocris compounds for COL6A4P1
Search CenterWatch for drugs/clinical trials and news about COL6A4P1 

Transcripts
for COL6A4P1 gene

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 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,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

Unigene Cluster for COL6A4P1:

Collagen, type VI, alpha 4 pseudogene 1
Hs.722756  [show with all ESTs]
Unigene Representative Sequence: NR_027927
5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000487147 ENST00000508169 ENST00000446690(uc010hel.1) ENST00000491915
ENST00000518859(uc011avo.1)

miRNA
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Inhib. RNA
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Clone
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Primer
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Additional cDNA sequence: 

FN394065.1 NR_027927.1 

2 DOTS entries:

DT.120911552  DT.120858702 

1 AceView cDNA sequence:

BF207674 

GeneLoc Exon Structure


Expression
for COL6A4P1 gene

(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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

COL6A4P1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: --

Microarray
RNAseq (Illumina Body Map)
(100×FPKM)½
SAGE (Serial Analysis of Gene Expression)
About this image

COL6A4P1 expression in embryonic tissues and stem cells
Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
6 LifeMap In Vivo Development Anatomical Compartments/Cells 
Tissue Anatomical Compartment CellCategory (developmental path)
Gut TubeHindgutHindgut Endoderm CellsEndoderm
Gut TubeMidgutMidgut Endoderm CellsEndoderm
OvaryPrimary FollicleGranulosa CellsOvary
OvaryPrimordial FolliclePre-Granulosa CellsOvary
Gut TubeHindgutGut Tube
Gut TubeMidgutGut Tube
Expression: Positive    Negative     Selective marker
Experimental details: Curated     Microarrays     In-situ hybridization

SOURCE GeneReport for Unigene cluster: Hs.722756
    SABiosciences Custom PCR Arrays for COL6A4P1
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In Situ
Assay Products: 
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Orthologs
for COL6A4P1 gene

(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)
About This Section
This gene was present in the common ancestor of human and mouse.

Orthologs for COL6A4P1 gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification		 Gene Description Human
Similarity		 Orthology
Type		 Details
mouse
(Mus musculus)		 Mammalia Col6a45 collagen, type VI, alpha 4   --   9 (57.39 cM) 105989454 


ENSEMBL Gene Tree for COL6A4P1 (if available)
TreeFam Gene Tree for COL6A4P1 (if available) 

Paralogs
for COL6A4P1 gene

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
  --

Genomic Variants
for COL6A4P1 gene

(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

10/623 NCBI SNPs in COL6A4P1 are shown (see all 623)     About this table
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance		Chr 3 posSequence#AA
Chg		TypeMore#Allele
freq		PopTotal
sample		More
----------
rs762161511,2
C,--15206393(+) AGCAAG/AATCCA 1 -- ds50012Minor allele frequency- A:0.04NA 122
rs1511510641,2
--15206408(+) TGGGGA/GAAAAA 1 -- ds50010--------
rs772501011,2
F,--15206417(+) AATGCG/ATAAAA 1 -- ds50011Minor allele frequency- A:0.06WA 118
rs1908134221,2
--15206435(+) GCTTAC/TTTAAA 1 -- ds50010--------
rs1834113921,2
--15206440(+) CTTAAA/GTAAAT 1 -- ds50010--------
rs117059261,2
C,F,A,H,--15206717(+) TATAAC/GATATC 1 -- ds500120Minor allele frequency- G:0.40NS EA NA WA CSA 1213
rs1402290441,2
--15206759(+) AACCTA/GAGTCA 1 -- ds50010--------
rs2011966391,2
C--15206867(+) GATAAA/GTTTAC 1 -- ds50010--------
rs1874573501,2
--15207032(+) CTTTTC/TGATGT 1 -- nc-transcript-variant0--------
rs1914600261,2
--15207033(+) TTTTCA/GATGTG 1 -- nc-transcript-variant0--------

HapMap Linkage Disequilibrium report for COL6A4P1 (15193340 - 15247466 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
      Database of Genomic Variants (DGV) variations for COL6A4P1: --

SABiosciences Cancer Mutation PCR Assays
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Disorders / Diseases
for COL6A4P1 gene

(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.)
About This Section
COL6A4P1 for disorders           About GeneDecksing

OMIM gene information: 612397    OMIM disorders: --

2 diseases for COL6A4P1:    About MalaCards
developmental dysplasia of hip    osteoarthritis

1 disease from the University of Copenhagen DISEASES database for COL6A4P1:
Osteoarthritis
Human Genome Epidemiology (HuGE) Navigator: COL6A4P1 (0 documents)

Export disorders for COL6A4P1 gene to outside databases

Publications
for COL6A4P1 gene

(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)
About This Section

PubMed articles for COL6A4P1 gene, integrated from 9 sources (see all 12):
(articles sorted by number of sources associating them with COL6A4P1)		    Utopia: connect your pdf to the dynamic
world of online information

  1. The knee osteoarthritis susceptibility locus DVWA on chromosome 3p24.3 is the 5' part of the split COL6A4 gene. (PubMed id 19486942)1, 3 Wagener R....Zaucke F. (2009)
  2. [Genomic study of susceptibility genes for common bon e and joint diseases] (PubMed id 19507504)1, 3 Ikegawa S. (2009)
  3. Cloning and characterization of the osteoarthritis-as sociated gene DVWA. (PubMed id 21057832)1 Nakajima M....Ikegawa S. (2011)
  4. [Association between polymorphism in DVWA and IL-1bet a and Kashin-Beck disease]. (PubMed id 20848793)1 Y U M....Tu Q.Q. (2010)
  5. Prediction model for knee osteoarthritis based on gen etic and clinical information. (PubMed id 20939878)1 Takahashi H....Ikegawa S. (2010)
  6. Lack of evidence for association between DVWA gene po lymorphisms and developmental dysplasia of the hip in Chinese Han population. (PubMed id 20238217)1 Zhu L....Jiang Q. (2010)
  7. Large replication study and meta-analyses of DVWA as an osteoarthritis susceptibility locus in European and Asian populations. (PubMed id 19181678)1 Meulenbelt I....Slagboom E.P. (2009)
  8. Three Novel Collagen VI Chains, {alpha}4(VI), {alpha}5(VI), and {alpha}6(VI). (PubMed id 18400749)1 Fitzgerald J....Hansen U. (2008)
  9. Association of the DVWA and GDF5 polymorphisms with osteoarthritis in UK populations. (PubMed id 19054821)1 Valdes A.M....Doherty M. (2008)
  10. Common variants in DVWA on chromosome 3p24.3 are associated with susceptibility to knee osteoarthritis. (PubMed id 18622395)1 Miyamoto Y.... Ikegawa S. (2008)

External Searches for COL6A4P1 gene

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 ANDOR
Aliases
Free Text  
  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

Genome Databases showing COL6A4P1 gene

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section
Entrez Gene: 344875 HGNC: 33484 AceView: LOC344875 Ensembl:ENSG00000230524 euGenes: HUgn344875
ECgene: COL6A4P1 H-InvDB: COL6A4P1

Other Databases showing COL6A4P1 gene

(According to HUGE)
About This Section
   --

Specialized Databases showing COL6A4P1 gene

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
   --

Intellectual Property
for COL6A4P1 gene

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
Patent Information for COL6A4P1 gene:
Search GeneIP for patents involving COL6A4P1

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



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