COL6A6 Gene
protein-coding GIFtS: 41
GCID: GC03P130280
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|
collagen, type VI, alpha 6
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Aliases
for COL6A6 gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
| Aliases |
|---|
| Collagen, Type VI, Alpha 61 2 | | Collagen Alpha-6(VI) Chain2 |
Export aliases for COL6A6 gene to outside databasesPrevious GC identifers: GC03P131715 GC03P127663 |
Summaries
for COL6A6 gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
PharmGKB,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
|
UniProtKB/Swiss-Prot: CO6A6_HUMAN, A6NMZ7Function: Collagen VI acts as a cell-binding protein (By similarity)
|
Genomic Views
for COL6A6 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:
 SABiosciences Regulatory transcription factor binding sites in the COL6A6 gene promoter:
AREB6 NF-AT4 NF-AT2 FOXJ2 (long isoform) NF-AT3 FOXJ2 Tal-1beta NF-AT1 NF-AT E47
Other transcription factors
Search SABiosciences Chromatin IP Primers for COL6A6
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat COL6A6 |
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: 3q22.1COL6A6 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 GC03P130280: view genomic region
(about GC identifiers)
Start:
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130,279,178 bp from pter |
End:
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130,396,999 bp from pter |
Size:
|
117,822 bases |
Orientation:
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plus strand |
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Proteins
for COL6A6 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/Swiss-Prot: CO6A6_HUMAN, A6NMZ7 (See
protein sequence)Recommended Name: Collagen alpha-6(VI) chain precursor Size: 2263 amino acids; 247173 Da
Subunit: Trimers composed of three different chains: alpha-1(VI), alpha-2(VI), and alpha-3(VI) or alpha-5(VI) oralpha-6(VI) (Probable)
Subcellular location: Secreted, extracellular space, extracellular matrix (By similarity). Note=Deposed in theextracellular matrix of skeletal muscle (By similarity)
Secondary accessions: A7DZQ0 A7DZQ1 A7DZQ2 Q69YT0Alternative splicing: 2 isoforms: A6NMZ7-1 A6NMZ7-2 (No experimental confirmation available)Explore the universe of human proteins at neXtProt for COL6A6: NX_A6NMZ7
Post-translational modifications:
Prolines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the chains(By similarity)1
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_A6NMZ7
COL6A6 Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins: NP_001096078.1
ENSEMBL proteins: ENSP00000351310 ENSP00000426006 ENSP00000422921 ENSP00000399236 Reactome Protein details: A6NMZ7
Human Recombinant Protein Products:
Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view): About this table
COL6A6 for ontologies About GeneDecksing
COL6A6 Antibody Products:
Assay Products for COL6A6: |
Protein
Domains /
Families
for COL6A6 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
COL6A6 for domains About GeneDecksing
2 InterPro domains/families:Graphical View of Domain Structure for InterPro Entry A6NMZ7ProtoNet protein and cluster: A6NMZ7 UniProtKB/Swiss-Prot: CO6A6_HUMAN, A6NMZ7Similarity: Belongs to the type VI collagen familySimilarity: Contains 9 VWFA domains |
Function
for COL6A6 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
|
Function Summary:
UniProtKB/Swiss-Prot: CO6A6_HUMAN, A6NMZ7Function: Collagen VI acts as a cell-binding protein (By similarity)
Clone
Products: |  | Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore | |  | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for COL6A6 (see all 3)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for COL6A6
OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling 
| |  | GenScript: all cDNA clones in your preferred vector: COL6A6 (NM_001102608) | |  | Browse Sino Biological Human cDNA Clones | |  | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for COL6A6 | |  | Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat COL6A6 |
In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL6A6 |
|
Pathways & Interactions
for COL6A6 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
|
Unified GeneCards pathways - 5/9 super-pathways (see all 9) About this table
See pathways by source
| Super-pathway | contained gene-specific pathways |
|---|
| 1 | Collagen formation | | | 2 | NCAM signaling for neurite out-growth | | | 3 | Degradation of the extracellular matrix | | | 4 | Axon guidance | | | 5 | Protein digestion and absorption | |
Pathway sources
See GeneCards unified pathways
Show all pathways
5/13 
Reactome Pathways for COL6A6 (see all 13)
3 
Kegg Pathways (Kegg details for COL6A6):
COL6A6 for pathways About GeneDecksing
Interactions:
Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for COL6A6
STRING Interaction
Network Preview (showing 5 interactants - click image to see 25)
5/26 Interacting proteins for COL6A6 (ENSP000003513104) via UniProtKB, MINT, STRING, and/or I2D (see all 26)About this table
Gene Ontology (GO): 1 biological process term (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0007155 | cell adhesion |
IEA | -- |
COL6A6 for ontologies About GeneDecksing
|
Drugs & Compounds
for COL6A6 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 COL6A6
Search CenterWatch for drugs/clinical trials and news about COL6A6 / CO6A6
|
Transcripts
for COL6A6 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
|
REFSEQ mRNAs for COL6A6 gene: NM_001102608.1 Unigene Cluster for COL6A6: Collagen, type VI, alpha 6 Hs.591282 [show with all ESTs]Unigene Representative Sequence: NM_0011026084 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000358511(uc010htl.3) ENST00000506143(uc003eni.4) ENST00000511332
ENST00000453409
Clone
Products: | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for COL6A6 (see all 3)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for COL6A6
OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling
| | | GenScript: all cDNA clones in your preferred vector: COL6A6 (NM_001102608) | | | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for COL6A6 | | | Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat COL6A6 |
Additional cDNA sequence: AL713792.1 AM774225.1 AM774226.1 AM774227.1 2 DOTS entries: DT.305267 DT.120887179 24/43 AceView cDNA sequences (see all 43): AA449944 N22964 AA772045 AA912545 BM725130 AA478634 BM725094 AL713792 H88506 BU741991 AF086237 N22966 BU742024 AI378321 AW274710 N32379 AA723595 BX486216 AI950049 AW043776 AA455862 AI761416 BF055159 BM091187
GeneLoc Exon Structure
|
Expression
for COL6A6 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
| COL6A6 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: --
About this image
See COL6A6 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for COL6A6
SOURCE GeneReport for Unigene cluster: Hs.591282
SABiosciences Custom PCR Arrays for COL6A6
Primer
Products: | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for COL6A6
Browse OriGene validated miRNA SYBR primer pairs
| | | SABiosciences RT2 qPCR Primer Assay in human, mouse, rat COL6A6 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat COL6A6 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat COL6A6 | In Situ
Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL6A6 |
Orthologs
for COL6A6 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 chordates.
Orthologs for COL6A6 gene from 3/14 species (see all 14) About this table
ENSEMBL Gene Tree for COL6A6 (if available)
TreeFam Gene Tree for COL6A6 (if available) |
Paralogs
for COL6A6 gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| Paralogs for COL6A6 gene
- COL28A12 COL6A12 COL6A22 COL6A52 COL6A32
17 SIMAP similar genes for COL6A6 using alignment to 4 protein entries: CO6A6_HUMAN (see all proteins):COL6A5 COCH VIT MSR1 DKFZp686K04147 ITGA2
COL6A3 COL21A1 COLQ COLEC11 COL13A1 C1QTNF9
C1QTNF9B SCARA5 COL6A2 MARCO SFTPD
COL6A6 for paralogs About GeneDecksing
2 Pseudogenes.org Pseudogenes for COL6A6
PGOHUM00000237544 PGOHUM00000238185
|
Genomic Variants
for COL6A6 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 COL6A6 (130279178 - 130396999 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 19 variations for COL6A6
15/19 CNVs (see all 19): 23145 91547 50927 98446 79900 79898 44082 62100 91546 22630 47867 91545 43590 79903 79902 | SABiosciences Cancer Mutation PCR Assays |
| | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing COL6A6 |
|
Disorders
/ Diseases
for COL6A6 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
|
COL6A6 for disorders About GeneDecksing
1  disease for COL6A6: About MalaCardsmyopathy
Export disorders for COL6A6 gene to outside databases
|
Publications
for COL6A6 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 COL6A6 gene integrated from 9 sources:
(articles sorted by number of sources associating them with COL6A6) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- Three novel collagen VI chains with high homology to the alpha 3 chain. (PubMed id 18276594)1, 2 Gara S.K.... Wagener R. (2008)
- The DNA sequence, annotation and analysis of human chromosome 3. (PubMed id 16641997)1, 2 Muzny D.M....Gibbs R.A. (2006)
- Expression of collagen VI a5 and a6 chains in human mu scle and in Duchenne muscular dystrophy-related muscle fibrosis. (PubMed id 22226732)1 Sabatelli P....Wagener R. (2012)
- Expression of the collagen VI I+5 and I+6 chains in nor mal human skin and in skin of patients with collagen VI-related myopathies. (PubMed id 20882040)1 Sabatelli P....Wagener R. (2011)
- Collagen VI is a basement membrane component that reg ulates epithelial cell-fibronectin interactions. (PubMed id 21406227)1 Groulx J.F....Beaulieu J.F. (2011)
- Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry. (PubMed id 19159218)2 Chen R.... Zou H. (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)
- The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (2007)
|
External Searches for COL6A6 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing COL6A6 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing COL6A6 gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing COL6A6 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
|
| Name | Description |
| PharmGKB entry for COL6A6 | Pharmacogenomics, SNPs, Pathways |
|
| | |
About This Section
| Patent Information for COL6A6 gene:
Search GeneIP for patents involving COL6A6
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for COL6A6 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, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, 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
About This Section
|
 | |
 | |
 |
| | |  | Browse OriGene Antibodies | | OriGene shRNA RFP for COL6A6 | | | OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for COL6A6 | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for COL6A6 | | | Browse OriGene Protein Over-expression Lysates | | Browse OriGene Fluorogenic Cell Assay Kits | | | OriGene siRNA for COL6A6 | | Browse 3'-UTR reporter clones for miRNA target validation | | | OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for COL6A6 | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for COL6A6 | | | Browse OriGene GFP tagged cDNA clones in CMV expression vector | | Browse OriGene MicroRNA Expression Plasmids | | | Browse OriGene basic RS shRNAs | | Browse OriGene validated miRNA SYBR primer pairs | | | Browse OriGene full length recombinant human proteins expressed in human HEK293 cells | | OriGene custom cloning services - gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling | | | OriGene Custom Antibody Services for COL6A6 | | OriGene Custom Protein Services for COL6A6 | | | OriGene Custom Immunoassay Development | | |
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 |
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| | | QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat COL6A6 | | | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing COL6A6 | | | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat COL6A6 | | | QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat COL6A6 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat COL6A6 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat COL6A6 |
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 |  |  |  | |
| | | | Search Tocris compounds for COL6A6 |
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 | | | | | | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL6A6 |
|  |  |  | | | | Search ThermoFisher Antibodies for COL6A6 |
| | | Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat COL6A6 |
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