Aliases
for COL6A4P2 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 21 2 | | COL6A41 2 |
| External Ids: | HGNC: 385011 | Entrez Gene: 6463002 | Ensembl: ENSG000002282527 | | ORGUL members: | |
|---|
| NONCODE:n387286 | |
Export aliases for COL6A4P2 gene to outside databasesPrevious GC identifers: GC03P131446 GC03P129854
|---|
Summaries
for COL6A4P2 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 COL6A4P2:
This transcribed pseudogene represents the 3' end of a presumed ortholog to a mouse gene which encodes a collagen VIalpha 4 chain protein (GeneID 68553). The predicted ORF contains multiple premature stop codons. A large chromosomebreak separates this pseudogene from the 5' end of the presumed ortholog (DVWA, GeneID 344875) which is locatedupstream at chromosome 3p24.3. (provided by RefSeq, Jun 2009)
|
Genomic Views
for COL6A4P2 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_005612.16
Regulatory elements:
 Search SABiosciences Regulatory transcription factor binding sites for COL6A4P2
Other transcription factors
Search SABiosciences Chromatin IP Primers for COL6A4P2
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat COL6A4P2 |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 3q22.1 Ensembl cytogenetic band: 3q22.1 HGNC cytogenetic band: 3q22.1COL6A4P2 Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc information about chromosome 3 GeneLoc Exon Structure GeneLoc location for GC03P129931: view genomic region
(about GC identifiers)
Start:
|
129,931,663 bp from pter |
End:
|
129,992,649 bp from pter |
Size:
|
60,987 bases |
Orientation:
|
plus strand |
|
Proteins
for COL6A4P2 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 COL6A4P2 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
| -- |
Function
for COL6A4P2 gene
(According to 1UniProtKB,
Genatlas,
LifeMap Discovery™,
IUBMB, and/or
2DME,
Human phenotypes from GenomeRNAi,
Animal models from MGI Mar 06 2013,
inGenious Targeting Laboratory,
bound targets from SABiosciences,
miRNA Gene Targets from miRTarBase,
shRNA from
OriGene,
Sirion Biotech,
RNAi from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
microRNA from QIAGEN,
Gene Editing from DNA2.0,
Sirion Biotech,
Clones from EMD Millipore,
OriGene,
SwitchGear Genomics,
GenScript,
Sino Biological,
DNA2.0,
and Vector BioLabs,
Cell Lines from GenScript,
LifeMap BioReagents,
Sirion Biotech,
In Situ Hybridization Assays from Advanced Cell Diagnostics,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene.)
About This Section
|
Animal Models:
Cell Line
Products: |  | GenScript Custom overexpressing Cell Line Services for COL6A4P2 | |  | Search LifeMap BioReagents cell lines for COL6A4P2 | In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL6A4P2 |
Pathways & Interactions
for COL6A4P2 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 COL6A4P2
|
Drugs & Compounds
for COL6A4P2 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
|
 Browse Tocris compounds for COL6A4P2
Search CenterWatch for drugs/clinical trials and news about COL6A4P2 
|
Transcripts
for COL6A4P2 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,
Sirion Biotech,
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 COL6A4P2: Collagen, type VI, alpha 4 pseudogene 2 Hs.170475 [show with all ESTs]Unigene Representative Sequence: NR_0278986 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000504443(uc011blf.2) ENST00000507516 ENST00000542114 ENST00000509090
ENST00000430317 ENST00000509855
Additional cDNA sequence: NR_027898.1 2 DOTS entries: DT.102828928 DT.40234615
GeneLoc Exon Structure
|
Expression
for COL6A4P2 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
| COL6A4P2 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: --
About this image
SOURCE GeneReport for Unigene cluster: Hs.170475
SABiosciences Custom PCR Arrays for COL6A4P2
Primer
Products: |  | Browse OriGene genome-wide validated SYBR primer pairs
Browse OriGene validated miRNA SYBR primer pairs
| | | Search SABiosciences RT2 qPCR
Primer Assays in human, mouse, rat COL6A4P2 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat COL6A4P2 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat COL6A4P2 | In Situ
Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL6A4P2 |
Orthologs
for COL6A4P2 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
|
--
ENSEMBL Gene Tree for COL6A4P2 (if available)
TreeFam Gene Tree for COL6A4P2 (if available) |
Paralogs
for COL6A4P2 gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| -- |
Genomic Variants
for COL6A4P2 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
|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Clinical
significance | Chr 3 pos | Sequence | # | AA
Chg | Type | More | # | Allele
freq | Pop | Total
sample | More |
|---|
HapMap Linkage Disequilibrium report for COL6A4P2 (129931663 - 129992649 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 3 variations for COL6A4P2
3 CNVs: 2472 63588 3448 | SABiosciences Cancer Mutation PCR Assays |
|
Disorders
/ Diseases
for COL6A4P2 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
|
COL6A4P2 for disorders About GeneDecksing
1  disease for COL6A4P2: About MalaCardsosteoarthritis
Export disorders for COL6A4P2 gene to outside databases
|
Publications
for COL6A4P2 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 COL6A4P2 gene integrated from 9 sources:
(articles sorted by number of sources associating them with COL6A4P2) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- The knee osteoarthritis susceptibility locus DVWA on chromosome 3p24.3 is the 5' part of the split COL6A4 gene. (PubMed id 19486942)1 Wagener R....Zaucke F. (2009)
- Three Novel Collagen VI Chains, {alpha}4(VI), {alpha}5(VI), and {alpha}6(VI). (PubMed id 18400749)1 Fitzgerald J....Hansen U. (2008)
- Transcriptome characterization elucidates signaling networks that control human ES cell growth and differentiation. (PubMed id 15146197)1 Brandenberger R.... Stanton L.W. (2004)
|
External Searches for COL6A4P2 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing COL6A4P2 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing COL6A4P2 gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing COL6A4P2 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
|
|
About This Section
| Patent Information for COL6A4P2 gene:
Search GeneIP for patents involving COL6A4P2
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for COL6A4P2 gene(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, LifeMap BioReagents, and Sirion Biotech, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or
Enzo Life Sciences, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory)
About This Section
|
 | |
 |
| | | | |
 |
 |
|  | QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat COL6A4P2 | | | Search QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing COL6A4P2 | | | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat COL6A4P2 | | | QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat COL6A4P2 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat COL6A4P2 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat COL6A4P2 |
| |
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 |
 |
 | | | | | | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL6A4P2 |
|  |  |  |  | | | | Search ThermoFisher Antibodies for COL6A4P2 |
| | | Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat COL6A4P2 |
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|
|
|
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