Aliases for COL6A6 Gene
External Ids for COL6A6 Gene
- HGNC: 27023
- Entrez Gene: 131873
- Ensembl: ENSG00000206384
- OMIM: 616613
- UniProtKB: A6NMZ7
Previous GeneCards Identifiers for COL6A6 Gene
- GC03P131715
- GC03P130280
- GC03P127663
Summaries for COL6A6 Gene
GeneCards Summary for COL6A6 Gene
COL6A6 (Collagen Type VI Alpha 6 Chain) is a Protein Coding gene. Among its related pathways are Collagen chain trimerization and Developmental Biology. An important paralog of this gene is COL6A5.
UniProtKB/Swiss-Prot for COL6A6 Gene
-
Collagen VI acts as a cell-binding protein.
No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COL6A6 Gene
Genomics for COL6A6 Gene
Regulatory Elements for COL6A6 Gene
Enhancers for COL6A6 Gene
| GeneHancer Identifier | Enhancer Score | Enhancer Sources | Gene-Enhancer Score | TSS distance (kb) | Number of Genes Away | Size (kb) | Transcription Factor Binding Sites within enhancer | Gene Targets for Enhancer |
|---|---|---|---|---|---|---|---|---|
| GH03G130508 | 0.6 | ENCODE | 9.5 | -8.1 | -8061 | 0.8 | MAFF ZNF316 MAFG MAX EMSY MAFK NR2F2 | COL6A6 GC03M130467 |
| GH03G130582 | 0.4 | ENCODE | 11.8 | +65.3 | 65331 | 0.9 | JUNB | COL6A6 GC03P130592 |
| GH03G130576 | 0.2 | ENCODE | 11.8 | +59.6 | 59615 | 0.2 | COL6A6 GC03P130592 | |
| GH03G130516 | 0.8 | ENCODE | 0.7 | +0.2 | 245 | 1.3 | ZSCAN18 HDAC6 SUZ12 YBX1 ZIC2 ZFHX2 ZNF23 GLIS2 ZNF157 PRDM10 | COL6A6 GC03P130592 |
| GH03G130537 | 0.4 | ENCODE | 0.3 | +20.8 | 20795 | 0.2 | EZH2 | COL6A6 GC03P130592 |
- Elite enhancer and/or Elite enhancer-gene association
Download GeneHancer data dump
Enhancers around COL6A6 on UCSC Golden Path with GeneCards custom track
- Transcription factor binding sites by QIAGEN in the COL6A6 gene promoter:
Regulatory Element Products
Genomic Location for COL6A6 Gene
- Chromosome:
- 3
- Start:
- 130,517,177 bp from pter
- End:
- 130,678,155 bp from pter
- Size:
- 160,979 bases
- Orientation:
- Plus strand
Genomic View for COL6A6 Gene
Genes around COL6A6 on UCSC Golden Path with GeneCards custom track
- Cytogenetic band:
-
- 3q22.1 by Ensembl
- 3q22.1 by Entrez Gene
- 3q22.1 by HGNC
COL6A6 Gene in genomic location: bands according to
Ensembl, locations according to GeneLoc
(and/or Entrez Gene and/or Ensembl if different)
Genomic Neighborhood
• Exon Structure
• Gene Density
RefSeq DNA sequence for COL6A6 Gene
Proteins for COL6A6 Gene
-
Protein details for COL6A6 Gene (UniProtKB/Swiss-Prot)
- Protein Symbol:
- A6NMZ7-CO6A6_HUMAN
- Recommended name:
- Collagen alpha-6(VI) chain
- Protein Accession:
- A6NMZ7
- A7DZQ0
- A7DZQ1
- A7DZQ2
- Q69YT0
Protein attributes for COL6A6 Gene
- Size:
- 2263 amino acids
- Molecular mass:
- 247173 Da
- Quaternary structure:
-
- Trimers composed of three different chains: alpha-1(VI), alpha-2(VI), and alpha-3(VI) or alpha-5(VI) or alpha-6(VI).
Protein Expression for COL6A6 Gene
Post-translational modifications for COL6A6 Gene
- Prolines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the chains.
- Glycosylation at Asn198, posLast=275275, posLast=288288, posLast=298298, posLast=347347, Asn520, Asn930, posLast=988988, Asn1290, and Asn2034
- Modification sites at PhosphoSitePlus
Other Protein References for COL6A6 Gene
- ENSEMBL proteins:
- REFSEQ proteins:
Antibody Products
- Novus Biologicals Antibodies for COL6A6
- Invitrogen Antibodies for COL6A6
- Search GeneTex for Antibodies for COL6A6
Protein Products
- Search Origene for Purified Proteins, MassSpec and Protein Over-expression Lysates for COL6A6
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- Novus Biologicals proteins for COL6A6
- Search GeneTex for Proteins for COL6A6
Assay Products
No data available for DME Specific Peptides for COL6A6 Gene
Domains & Families for COL6A6 Gene
Gene Families for COL6A6 Gene
- HGNC:
Protein Domains for COL6A6 Gene
- InterPro:
- ProtoNet:
Suggested Antigen Peptide Sequences for COL6A6 Gene
- GenScript: Design optimal peptide antigens:
Graphical View of Domain Structure for InterPro Entry
A6NMZ7- Family:
-
- Belongs to the type VI collagen family.
Function for COL6A6 Gene
Molecular function for COL6A6 Gene
- UniProtKB/Swiss-Prot Function:
- Collagen VI acts as a cell-binding protein.
Phenotypes for COL6A6 Gene
- GenomeRNAi human phenotypes for COL6A6:
Animal Model Products
- Taconic Biosciences: Generate A Custom CRISPR Mouse Model For Your Study
- Cyagen custom Knockout/knockin (KOKI) mouse models for COL6A6
-
-
ViGene Biosciences lentiviral particle packaged cDNA for COL6A6 gene
-
ViGene Biosciences ready-to-package AAV shRNAs for COL6A6 gene
- Search ViGene Biosciences for COL6A6
CRISPR Products
-
OriGene CRISPR knockouts for COL6A6
-
Santa Cruz Biotechnology (SCBT) CRISPR for COL6A6
- GenScript: Design CRISPR guide RNA sequences for COL6A6
miRNA for COL6A6 Gene
- miRTarBase miRNAs that target COL6A6
miRNA Products
- Search ViGene Biosciences for COL6A6
Inhibitory RNA Products
- Origene shRNA, siRNA, and RNAi products in human, mouse, rat for COL6A6
- Browse OriGene Inhibitory RNA Products For COL6A6
-
ViGene Biosciences ready-to-package AAV shRNAs for COL6A6 gene
Clone Products
- VectorBuilder custom plasmid, inducible vectors for COL6A6
- VectorBuilder custom lentivirus, adenovirus, AAV vector/virus packaging for COL6A6
-
VectorBuilder Other custom vectors
- Mammalian expression: PiggyBac
- Mammalian Tet-on expression: plasmid
- Mammalian conditional (Cre-Lox): plasmid and PiggyBac
- Mammalian shRNA knockdown: lentiviral, adenoviral, AAV, and PiggyBac
- CRISPR: plasmid gRNA, lentiviral gRNA, and donor plasmid
- Bacterial expression: pET, pBAD, and pCS
- Yeast expression
Cell Line Products
-
Horizon Cell Lines for COL6A6
-
ViGene Biosciences adenoviral particle packaged cDNA for COL6A6 gene
-
ViGene Biosciences lentiviral particle packaged cDNA for COL6A6 gene
-
ViGene Biosciences ready-to-package AAV shRNAs for COL6A6 gene
Flow Cytometry Products
No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for COL6A6 Gene
Localization for COL6A6 Gene
Subcellular locations from UniProtKB/Swiss-Prot for COL6A6 Gene
- Secreted, extracellular space, extracellular matrix. Note=Deposed in the extracellular matrix of skeletal muscle. {ECO:0000250}.
| Compartment | Confidence |
|---|---|
| extracellular | 5 |
| endoplasmic reticulum | 3 |
| plasma membrane | 1 |
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0005576 | extracellular region | TAS | -- |
| GO:0005578 | proteinaceous extracellular matrix | IDA,IEA | 18400749 |
| GO:0005581 | collagen trimer | IEA | -- |
Pathways & Interactions for COL6A6 Gene
| SuperPathway | Contained pathways | ||
|---|---|---|---|
| 1 | Collagen chain trimerization | ||
| 2 | Developmental Biology |
.51
|
|
| 3 | RET signaling | ||
| 4 | ECM-receptor interaction | ||
| 5 | Focal Adhesion |
.62
|
|
Pathways by source for COL6A6 Gene
11 Reactome pathways for COL6A6 Gene
4 KEGG pathways for COL6A6 Gene
Interacting Proteins for COL6A6 Gene
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0007155 | cell adhesion | IEA | -- |
| GO:0030574 | collagen catabolic process | TAS | -- |
No data available for SIGNOR curated interactions for COL6A6 Gene
Transcripts for COL6A6 Gene
mRNA/cDNA for COL6A6 Gene
- (15) REFSEQ mRNAs :
- (4) Additional mRNA sequences :
- (43) Selected AceView cDNA sequences:
- (3) Ensembl transcripts including schematic representations, and UCSC links where relevant :
Unigene Clusters for COL6A6 Gene
- Collagen, type VI, alpha 6:
- Representative Sequences:
CRISPR Products
-
OriGene CRISPR knockouts for COL6A6
-
Santa Cruz Biotechnology (SCBT) CRISPR for COL6A6
- GenScript: Design CRISPR guide RNA sequences for COL6A6
miRNA Products
- Search ViGene Biosciences for COL6A6
Inhibitory RNA Products
- Origene shRNA, siRNA, and RNAi products in human, mouse, rat for COL6A6
- Browse OriGene Inhibitory RNA Products For COL6A6
-
ViGene Biosciences ready-to-package AAV shRNAs for COL6A6 gene
Clone Products
- VectorBuilder custom plasmid, inducible vectors for COL6A6
- VectorBuilder custom lentivirus, adenovirus, AAV vector/virus packaging for COL6A6
-
VectorBuilder Other custom vectors
- Mammalian expression: PiggyBac
- Mammalian Tet-on expression: plasmid
- Mammalian conditional (Cre-Lox): plasmid and PiggyBac
- Mammalian shRNA knockdown: lentiviral, adenoviral, AAV, and PiggyBac
- CRISPR: plasmid gRNA, lentiviral gRNA, and donor plasmid
- Bacterial expression: pET, pBAD, and pCS
- Yeast expression
Flow Cytometry Products
Expression for COL6A6 Gene
mRNA differential expression in normal tissues according to GTEx for COL6A6 Gene
This gene is overexpressed in Pituitary (x18.0), Lung (x11.1), and Heart - Atrial Appendage (x7.5).
This gene is overexpressed in Fetal ovary (10.2), Fetal heart (8.5), Lung (8.2), and Urine (7.9).
Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for COL6A6 Gene
NURSA nuclear receptor signaling pathways regulating expression of COL6A6 Gene:
COL6A6SOURCE GeneReport for Unigene cluster for COL6A6 Gene:
Hs.591282Evidence on tissue expression from TISSUES for COL6A6 Gene
- Liver(4.2)
- Lymph node(4)
Primer Products
-
OriGene qPCR primer pairs for COL6A6
No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for COL6A6 Gene
Orthologs for COL6A6 Gene
This gene was present in the common ancestor of chordates.
| Organism | Taxonomy | Gene | Similarity | Type | Details |
|---|---|---|---|---|---|
| chimpanzee (Pan troglodytes) |
Mammalia | COL6A6 34 35 |
|
||
| dog (Canis familiaris) |
Mammalia | COL6A6 34 35 |
|
||
| cow (Bos Taurus) |
Mammalia | COL6A6 34 35 |
|
||
| mouse (Mus musculus) |
Mammalia | Col6a6 34 16 35 |
|
||
| rat (Rattus norvegicus) |
Mammalia | Col6a6 34 |
|
||
| platypus (Ornithorhynchus anatinus) |
Mammalia | -- 35 |
|
ManyToMany | |
| oppossum (Monodelphis domestica) |
Mammalia | -- 35 |
|
ManyToMany | |
| chicken (Gallus gallus) |
Aves | COL6A6 34 |
|
||
| -- 35 |
|
ManyToMany | |||
| lizard (Anolis carolinensis) |
Reptilia | -- 35 |
|
ManyToMany | |
| tropical clawed frog (Silurana tropicalis) |
Amphibia | LOC100486063 34 |
|
||
| zebrafish (Danio rerio) |
Actinopterygii | col6a6 34 |
|
||
| zmp:0000000759 35 |
|
ManyToMany |
- Species where no ortholog for COL6A6 was found in the sources mined by GeneCards:
-
- A. gosspyii yeast (Ashbya gossypii)
- Actinobacteria (Mycobacterium tuberculosis)
- African clawed frog (Xenopus laevis)
- African malaria mosquito (Anopheles gambiae)
- Alicante grape (Vitis vinifera)
- alpha proteobacteria (Wolbachia pipientis)
- amoeba (Dictyostelium discoideum)
- Archea (Pyrococcus horikoshii)
- baker's yeast (Saccharomyces cerevisiae)
- barley (Hordeum vulgare)
- beta proteobacteria (Neisseria meningitidis)
- bread mold (Neurospora crassa)
- Chromalveolata (Phytophthora infestans)
- common water flea (Daphnia pulex)
- corn (Zea mays)
- E. coli (Escherichia coli)
- filamentous fungi (Aspergillus nidulans)
- Firmicute bacteria (Streptococcus pneumoniae)
- fission yeast (Schizosaccharomyces pombe)
- fruit fly (Drosophila melanogaster)
- green algae (Chlamydomonas reinhardtii)
- honey bee (Apis mellifera)
- K. lactis yeast (Kluyveromyces lactis)
- loblloly pine (Pinus taeda)
- malaria parasite (Plasmodium falciparum)
- medicago trunc (Medicago Truncatula)
- moss (Physcomitrella patens)
- orangutan (Pongo pygmaeus)
- pig (Sus scrofa)
- rainbow trout (Oncorhynchus mykiss)
- rice (Oryza sativa)
- rice blast fungus (Magnaporthe grisea)
- schistosome parasite (Schistosoma mansoni)
- sea anemone (Nematostella vectensis)
- sea squirt (Ciona intestinalis)
- sea squirt (Ciona savignyi)
- sea urchin (Strongylocentrotus purpuratus)
- sorghum (Sorghum bicolor)
- soybean (Glycine max)
- stem rust fungus (Puccinia graminis)
- sugarcane (Saccharum officinarum)
- thale cress (Arabidopsis thaliana)
- tomato (Lycopersicon esculentum)
- toxoplasmosis (Toxoplasma gondii)
- Trichoplax (Trichoplax adhaerens)
- wheat (Triticum aestivum)
- worm (Caenorhabditis elegans)
Paralogs for COL6A6 Gene
Paralogs for COL6A6 Gene
(14) SIMAP similar genes for COL6A6 Gene using alignment to 4 proteins:
Pseudogenes.org Pseudogenes for COL6A6 Gene
Variants for COL6A6 Gene
| SNP ID | Clin | Chr 03 pos | Sequence Context | AA Info | Type |
|---|---|---|---|---|---|
| rs140872639 | Uncertain significance | 130,592,568(+) | CAGTG(G/T)GAGAG | nc-transcript-variant, reference, stop-gained | |
| rs200960657 | Uncertain significance | 130,581,896(+) | CTGCT(C/T)GAGGA | nc-transcript-variant, reference, stop-gained | |
| rs1000032636 | -- | 130,548,094(+) | GGCCA(A/G)TCCTA | intron-variant | |
| rs1000100593 | -- | 130,515,376(+) | ATAGA(A/G)TGTAT | upstream-variant-2KB | |
| rs1000128798 | -- | 130,657,127(+) | ATGGC(C/T)GCAGC | intron-variant |
| Variant ID | Type | Subtype | PubMed ID |
|---|---|---|---|
| dgv2597n106 | CNV | deletion | 24896259 |
| dgv2598n106 | CNV | deletion | 24896259 |
| dgv83n16 | CNV | deletion | 17901297 |
| esv2271871 | CNV | deletion | 18987734 |
| esv2450346 | CNV | deletion | 19546169 |
| esv2639906 | CNV | loss | 19546169 |
| esv2725914 | CNV | deletion | 23290073 |
| esv2725915 | CNV | deletion | 23290073 |
| esv34166 | CNV | loss | 18971310 |
| esv3562539 | CNV | deletion | 23714750 |
| esv3575605 | CNV | gain | 25503493 |
| esv4329 | CNV | loss | 18987735 |
| esv5883 | CNV | loss | 19470904 |
| nsv1073679 | CNV | deletion | 25765185 |
| nsv4003 | CNV | insertion | 18451855 |
| nsv4004 | CNV | deletion | 18451855 |
| nsv4005 | CNV | insertion | 18451855 |
| nsv460855 | CNV | loss | 19166990 |
| nsv508243 | CNV | deletion | 20534489 |
| nsv521211 | CNV | loss | 19592680 |
| nsv956800 | CNV | deletion | 24416366 |
Residual Variation Intolerance Score:
98.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score:
14.65;
96.57% of all genes are more intolerant (likely to be disease-causing)
Relevant External Links for COL6A6 Gene
No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COL6A6 Gene
Disorders for COL6A6 Gene
Relevant External Links for COL6A6
- Atlas of Genetics and Cytogenetics in Oncology and Haematology:
- COL6A6
No disorders were found for COL6A6 Gene.
No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for COL6A6 Gene
Publications for COL6A6 Gene
- The expanded collagen VI family: new chains and new questions. (PMID: 23869615) Fitzgerald J. … Hansen U. (Connect. Tissue Res. 2013) 2 3 64
- Three novel collagen VI chains with high homology to the alpha 3 chain. (PMID: 18276594) Gara S.K. … Wagener R. (J. Biol. Chem. 2008) 3 4 64
- The DNA sequence, annotation and analysis of human chromosome 3. (PMID: 16641997) Muzny D.M. … Gibbs R.A. (Nature 2006) 3 4 64
- New COL6A6 variant detected by whole-exome sequencing is linked to break points in intron 4 and 3'-UTR, deleting exon 5 of RHO, and causing adRP. (PMID: 26321861) de Sousa Dias M. … Carballo M. (Mol. Vis. 2015) 3 64
- An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome. (PMID: 24275569) Bian Y. … Zou H. (J. Proteomics 2014) 4 64
Products for COL6A6 Gene
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- Browse Primary Antibodies
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- Search Origene for Purified Proteins, MassSpec and Protein Over-expression Lysates for COL6A6
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- OriGene qPCR primer pairs for COL6A6
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- Novus Biologicals Antibodies for COL6A6
- Novus Biologicals proteins for COL6A6
- Novus Biologicals
- Novus Biologicals Tissue Microarrays
- Invitrogen Antibodies for COL6A6
- ViGene Biosciences adenoviral particle packaged cDNA for COL6A6 gene
- ViGene Biosciences lentiviral particle packaged cDNA for COL6A6 gene
- ViGene Biosciences ready-to-package AAV shRNAs for COL6A6 gene
- Search ViGene Biosciences for COL6A6
- Horizon Cell Lines for COL6A6
- Cyagen custom Knockout/knockin (KOKI) mouse models for COL6A6
- VectorBuilder custom plasmid, inducible vectors for COL6A6
- VectorBuilder custom lentivirus, adenovirus, AAV vector/virus packaging for COL6A6
- VectorBuilder Other custom vectors
- Mammalian expression: PiggyBac
- Mammalian Tet-on expression: plasmid
- Mammalian conditional (Cre-Lox): plasmid and PiggyBac
- Mammalian shRNA knockdown: lentiviral, adenoviral, AAV, and PiggyBac
- CRISPR: plasmid gRNA, lentiviral gRNA, and donor plasmid
- Bacterial expression: pET, pBAD, and pCS
- Yeast expression
Sources for COL6A6 Gene
- (1) GeneCards
- (2) HGNC
- (3) EntrezGene
- (4) Swiss-Prot
- (5) Ensembl
- (6) OMIM
- (7) GeneLoc
- (8) Gene Wiki
- (9) UCSC
- (10) PhosphoSitePlus
- (11) GO
- (12) TrEMBL
- (13) InterPro
- (14) ProtoNet
- (15) Blocks
- (16) MGI
- (17) IUBMB
- (18) KEGG
- (19) MINT
- (20) STRING
- (21) IntAct
- (22) Novoseek
- (23) PharmGKB
- (24) DrugBank
- (25) HMDB
- (26) UniGene
- (27) AceView
- (28) RNAdb
- (29) ASD
- (30) ECgene
- (31) GeneAnnot
- (32) CGAP SAGE
- (33) SOURCE
- (34) HomoloGene
- (35) PanEnsembl
- (36) euGenes
- (37) SGD
- (38) FlyBase
- (39) WormBase
- (40) Pseudogene
- (41) DGV
- (42) dbSNP
- (43) GenAtlas
- (44) GeneTests
- (45) HGMD
- (46) GAD
- (47) LSDB
- (48) BGMUT
- (49) HuGE
- (50) eBioscience
- (51) Atlas
- (52) Cell Signaling Technology
- (53) GenBank
- (54) H-invDB
- (55) HORDE
- (56) HUGE
- (57) IMGT
- (58) Leiden
- (59) MILLIPORE
- (60) miRBase
- (61) DME
- (62) NCBI
- (63) OriGene
- (64) PubMed
- (65) R&D Systems
- (66) TGDB
- (67) Tocris
- (68) Abcam
- (69) Novus
- (70) ProSpec
- (71) Sino Biological
- (72) GenScript
- (73) Qiagen
- (74) Cloud-Clone Corp.
- (75) Enzo Life Sciences
- (76) OCA
- (77) Proteopedia
- (78) MOPED
- (79) SPIRE
- (80) neXtProt
- (81) Reactome
- (82) GeneGo (Thomson Reuters)
- (83) fRNAdb
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- (100) COMPARTMENTS
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