Human Gene COL6A1 (ENST00000498614.5) from GENCODE V44
  Description: collagen type VI alpha 1 chain (from HGNC COL6A1)
RefSeq Summary (NM_001848): The collagens are a superfamily of proteins that play a role in maintaining the integrity of various tissues. Collagens are extracellular matrix proteins and have a triple-helical domain as their common structural element. Collagen VI is a major structural component of microfibrils. The basic structural unit of collagen VI is a heterotrimer of the alpha1(VI), alpha2(VI), and alpha3(VI) chains. The alpha2(VI) and alpha3(VI) chains are encoded by the COL6A2 and COL6A3 genes, respectively. The protein encoded by this gene is the alpha 1 subunit of type VI collagen (alpha1(VI) chain). Mutations in the genes that code for the collagen VI subunits result in the autosomal dominant disorder, Bethlem myopathy. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000498614.5
Gencode Gene: ENSG00000142156.16
Transcript (Including UTRs)
   Position: hg38 chr21:46,001,197-46,005,050 Size: 3,854 Total Exon Count: 6 Strand: +


Page IndexSequence and LinksPrimersMalaCardsCTDRNA-Seq Expression
Microarray ExpressionOther SpeciesmRNA DescriptionsPathwaysOther NamesGeneReviews
Methods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr21:46,001,197-46,005,050)mRNA (may differ from genome)No protein
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
EnsemblExonPrimerGencodeHGNCLynxMalacards
myGene2PubMedWikipedia

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: COL6A1
Diseases sorted by gene-association score: bethlem myopathy 1* (1602), ullrich congenital muscular dystrophy 1* (1132), myopathy* (464), collagen type vi-related disorders* (115), diffuse idiopathic skeletal hyperostosis (16), ossification of the posterior longitudinal ligament of spine (10), proximal myopathy and ophthalmoplegia (10), muscular dystrophy (6), muscular dystrophy, congenital (6), muscle disorders (5), down syndrome (4)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 808.52 RPKM in Cells - Cultured fibroblasts
Total median expression: 10971.04 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Descriptions from all associated GenBank mRNAs
  LF208795 - JP 2014500723-A/16298: Polycomb-Associated Non-Coding RNAs.
MA444372 - JP 2018138019-A/16298: Polycomb-Associated Non-Coding RNAs.
BC052575 - Homo sapiens collagen, type VI, alpha 1, mRNA (cDNA clone MGC:59702 IMAGE:6598940), complete cds.
AK307989 - Homo sapiens cDNA, FLJ97937.
AK298968 - Homo sapiens cDNA FLJ58994 complete cds, highly similar to Collagen alpha-1(VI) chain precursor.
AK299396 - Homo sapiens cDNA FLJ61362 complete cds, highly similar to Collagen alpha-1(VI) chain precursor.
GQ891373 - Homo sapiens clone HEL-S-161m epididymis secretory sperm binding protein mRNA, complete cds.
BC005159 - Homo sapiens collagen, type VI, alpha 1, mRNA (cDNA clone IMAGE:3506644), partial cds.
X15880 - Human mRNA for collagen VI alpha-1 C-terminal globular domain.
BC022236 - Homo sapiens, clone IMAGE:4178997, mRNA, partial cds.
LF322923 - JP 2014500723-A/130426: Polycomb-Associated Non-Coding RNAs.
MA558500 - JP 2018138019-A/130426: Polycomb-Associated Non-Coding RNAs.
LF322921 - JP 2014500723-A/130424: Polycomb-Associated Non-Coding RNAs.
MA558498 - JP 2018138019-A/130424: Polycomb-Associated Non-Coding RNAs.
LF322918 - JP 2014500723-A/130421: Polycomb-Associated Non-Coding RNAs.
MA558495 - JP 2018138019-A/130421: Polycomb-Associated Non-Coding RNAs.
LF322916 - JP 2014500723-A/130419: Polycomb-Associated Non-Coding RNAs.
MA558493 - JP 2018138019-A/130419: Polycomb-Associated Non-Coding RNAs.
LF322914 - JP 2014500723-A/130417: Polycomb-Associated Non-Coding RNAs.
MA558491 - JP 2018138019-A/130417: Polycomb-Associated Non-Coding RNAs.
LF322912 - JP 2014500723-A/130415: Polycomb-Associated Non-Coding RNAs.
MA558489 - JP 2018138019-A/130415: Polycomb-Associated Non-Coding RNAs.
LF322911 - JP 2014500723-A/130414: Polycomb-Associated Non-Coding RNAs.
MA558488 - JP 2018138019-A/130414: Polycomb-Associated Non-Coding RNAs.
LF322909 - JP 2014500723-A/130412: Polycomb-Associated Non-Coding RNAs.
MA558486 - JP 2018138019-A/130412: Polycomb-Associated Non-Coding RNAs.
LF322908 - JP 2014500723-A/130411: Polycomb-Associated Non-Coding RNAs.
MA558485 - JP 2018138019-A/130411: Polycomb-Associated Non-Coding RNAs.
LF322907 - JP 2014500723-A/130410: Polycomb-Associated Non-Coding RNAs.
MA558484 - JP 2018138019-A/130410: Polycomb-Associated Non-Coding RNAs.
JD525201 - Sequence 506225 from Patent EP1572962.
LP886334 - Sequence 226 from Patent WO2017201352.
LP978091 - Sequence 226 from Patent WO2017120612.
JD395972 - Sequence 376996 from Patent EP1572962.
JD395973 - Sequence 376997 from Patent EP1572962.
JD426259 - Sequence 407283 from Patent EP1572962.
JD318392 - Sequence 299416 from Patent EP1572962.
JD421720 - Sequence 402744 from Patent EP1572962.
JD143024 - Sequence 124048 from Patent EP1572962.
JD426259 - Sequence 407283 from Patent EP1572962.
JD125889 - Sequence 106913 from Patent EP1572962.
JD465243 - Sequence 446267 from Patent EP1572962.
JD392775 - Sequence 373799 from Patent EP1572962.
JD192437 - Sequence 173461 from Patent EP1572962.
JD157395 - Sequence 138419 from Patent EP1572962.
JD157396 - Sequence 138420 from Patent EP1572962.
JD282390 - Sequence 263414 from Patent EP1572962.
JD231195 - Sequence 212219 from Patent EP1572962.
JD176670 - Sequence 157694 from Patent EP1572962.
JD450084 - Sequence 431108 from Patent EP1572962.
JD217219 - Sequence 198243 from Patent EP1572962.
JD307863 - Sequence 288887 from Patent EP1572962.
JD412183 - Sequence 393207 from Patent EP1572962.
JD310783 - Sequence 291807 from Patent EP1572962.
JD152132 - Sequence 133156 from Patent EP1572962.
JD487748 - Sequence 468772 from Patent EP1572962.
JD109005 - Sequence 90029 from Patent EP1572962.
JD391390 - Sequence 372414 from Patent EP1572962.
JD139620 - Sequence 120644 from Patent EP1572962.
JD245924 - Sequence 226948 from Patent EP1572962.
JD361040 - Sequence 342064 from Patent EP1572962.
MB419113 - JP 2019519516-A/75: MRNA COMBINATION THERAPIES FOR THE TREATMENT OF CANCER.
MB419978 - JP 2019519516-A/940: MRNA COMBINATION THERAPIES FOR THE TREATMENT OF CANCER.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04510 - Focal adhesion
hsa04512 - ECM-receptor interaction

-  Other Names for This Gene
  Alternate Gene Symbols: BC022236, ENST00000498614.1, ENST00000498614.2, ENST00000498614.3, ENST00000498614.4, uc002zhv.1, uc002zhv.2
UCSC ID: ENST00000498614.5
RefSeq Accession: NM_001848

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene COL6A1:
bethlem (Collagen VI-Related Dystrophies)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.