Human Gene COL6A1 (ENST00000361866.8_4) from GENCODE V47lift37
  Description: collagen type VI alpha 1 chain (from RefSeq NM_001848.3)
Gencode Transcript: ENST00000361866.8_4
Gencode Gene: ENSG00000142156.16_8
Transcript (Including UTRs)
   Position: hg19 chr21:47,401,684-47,424,962 Size: 23,279 Total Exon Count: 35 Strand: +
Coding Region
   Position: hg19 chr21:47,401,765-47,423,927 Size: 22,163 Coding Exon Count: 35 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr21:47,401,684-47,424,962)mRNA (may differ from genome)Protein (1028 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
Human Cortex Gene ExpressionMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CO6A1_HUMAN
DESCRIPTION: RecName: Full=Collagen alpha-1(VI) chain; Flags: Precursor;
FUNCTION: Collagen VI acts as a cell-binding protein.
SUBUNIT: Trimers composed of three different chains: alpha-1(VI), alpha-2(VI), and alpha-3(VI) or alpha-5(VI) or alpha-6(VI).
SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix (By similarity).
PTM: Prolines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the chains.
DISEASE: Defects in COL6A1 are a cause of Bethlem myopathy (BM) [MIM:158810]. BM is a rare autosomal dominant proximal myopathy characterized by early childhood onset (complete penetrance by the age of 5) and joint contractures most frequently affecting the elbows and ankles.
DISEASE: Defects in COL6A1 are a cause of Ullrich congenital muscular dystrophy (UCMD) [MIM:254090]; also known as Ullrich scleroatonic muscular dystrophy. UCMD is an autosomal recessive congenital myopathy characterized by muscle weakness and multiple joint contractures, generally noted at birth or early infancy. The clinical course is more severe than in Bethlem myopathy.
SIMILARITY: Belongs to the type VI collagen family.
SIMILARITY: Contains 3 VWFA domains.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/COL6A1";

-  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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  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.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -41.6081-0.514 Picture PostScript Text
3' UTR -356.001035-0.344 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR008160 - Collagen
IPR002035 - VWF_A

Pfam Domains:
PF00092 - von Willebrand factor type A domain
PF01391 - Collagen triple helix repeat (20 copies)
PF13519 - von Willebrand factor type A domain
PF13768 - von Willebrand factor type A domain

SCOP Domains:
53300 - vWA-like
53474 - alpha/beta-Hydrolases

ModBase Predicted Comparative 3D Structure on P12109
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0048407 platelet-derived growth factor binding

Biological Process:
GO:0001649 osteoblast differentiation
GO:0007155 cell adhesion
GO:0030198 extracellular matrix organization
GO:0035987 endodermal cell differentiation
GO:0070208 protein heterotrimerization
GO:0071230 cellular response to amino acid stimulus

Cellular Component:
GO:0005576 extracellular region
GO:0005581 collagen trimer
GO:0005589 collagen type VI trimer
GO:0005765 lysosomal membrane
GO:0005788 endoplasmic reticulum lumen
GO:0016020 membrane
GO:0031012 extracellular matrix
GO:0032991 macromolecular complex
GO:0042383 sarcolemma
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  LF208795 - JP 2014500723-A/16298: Polycomb-Associated Non-Coding RNAs.
JD152677 - Sequence 133701 from Patent EP1572962.
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.
BC032821 - Homo sapiens collagen, type VI, alpha 1, mRNA (cDNA clone IMAGE:5217429), partial cds.
LF322949 - JP 2014500723-A/130452: Polycomb-Associated Non-Coding RNAs.
X15879 - Human mRNA for collagen VI alpha-1 N-terminal globular domain.
JD438605 - Sequence 419629 from Patent EP1572962.
LF322948 - JP 2014500723-A/130451: Polycomb-Associated Non-Coding RNAs.
GQ891373 - Homo sapiens clone HEL-S-161m epididymis secretory sperm binding protein mRNA, complete cds.
LF322946 - JP 2014500723-A/130449: Polycomb-Associated Non-Coding RNAs.
LF322945 - JP 2014500723-A/130448: Polycomb-Associated Non-Coding RNAs.
LF322944 - JP 2014500723-A/130447: Polycomb-Associated Non-Coding RNAs.
LF322942 - JP 2014500723-A/130445: Polycomb-Associated Non-Coding RNAs.
LF322941 - JP 2014500723-A/130444: Polycomb-Associated Non-Coding RNAs.
LF322938 - JP 2014500723-A/130441: Polycomb-Associated Non-Coding RNAs.
M20776 - Homo sapiens, alpha-1 (VI) collagen.
LF322937 - JP 2014500723-A/130440: Polycomb-Associated Non-Coding RNAs.
LF322935 - JP 2014500723-A/130438: Polycomb-Associated Non-Coding RNAs.
LF322933 - JP 2014500723-A/130436: Polycomb-Associated Non-Coding RNAs.
LF322931 - JP 2014500723-A/130434: Polycomb-Associated Non-Coding RNAs.
LF322930 - JP 2014500723-A/130433: Polycomb-Associated Non-Coding RNAs.
LF322929 - JP 2014500723-A/130432: Polycomb-Associated Non-Coding RNAs.
M27447 - Human alpha-1 type VI collagen (COL6A1) mRNA, partial cds.
X06194 - Human mRNA for collagen alpha 1 (VI) chain 5' region.
LF322928 - JP 2014500723-A/130431: Polycomb-Associated Non-Coding RNAs.
LF322927 - JP 2014500723-A/130430: Polycomb-Associated Non-Coding RNAs.
LF322924 - JP 2014500723-A/130427: Polycomb-Associated Non-Coding RNAs.
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.
LF322921 - JP 2014500723-A/130424: Polycomb-Associated Non-Coding RNAs.
LF322918 - JP 2014500723-A/130421: Polycomb-Associated Non-Coding RNAs.
LF322916 - JP 2014500723-A/130419: Polycomb-Associated Non-Coding RNAs.
LF322914 - JP 2014500723-A/130417: Polycomb-Associated Non-Coding RNAs.
LF322912 - JP 2014500723-A/130415: Polycomb-Associated Non-Coding RNAs.
LF322911 - JP 2014500723-A/130414: Polycomb-Associated Non-Coding RNAs.
LF322909 - JP 2014500723-A/130412: Polycomb-Associated Non-Coding RNAs.
LF322908 - JP 2014500723-A/130411: Polycomb-Associated Non-Coding RNAs.
LF322907 - JP 2014500723-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.
MA558526 - JP 2018138019-A/130452: Polycomb-Associated Non-Coding RNAs.
MA558525 - JP 2018138019-A/130451: Polycomb-Associated Non-Coding RNAs.
MA558523 - JP 2018138019-A/130449: Polycomb-Associated Non-Coding RNAs.
MA558522 - JP 2018138019-A/130448: Polycomb-Associated Non-Coding RNAs.
MA558521 - JP 2018138019-A/130447: Polycomb-Associated Non-Coding RNAs.
MA558519 - JP 2018138019-A/130445: Polycomb-Associated Non-Coding RNAs.
MA558518 - JP 2018138019-A/130444: Polycomb-Associated Non-Coding RNAs.
MA558515 - JP 2018138019-A/130441: Polycomb-Associated Non-Coding RNAs.
MA558514 - JP 2018138019-A/130440: Polycomb-Associated Non-Coding RNAs.
MA558512 - JP 2018138019-A/130438: Polycomb-Associated Non-Coding RNAs.
MA558510 - JP 2018138019-A/130436: Polycomb-Associated Non-Coding RNAs.
MA558508 - JP 2018138019-A/130434: Polycomb-Associated Non-Coding RNAs.
MA558507 - JP 2018138019-A/130433: Polycomb-Associated Non-Coding RNAs.
MA558506 - JP 2018138019-A/130432: Polycomb-Associated Non-Coding RNAs.
MA558505 - JP 2018138019-A/130431: Polycomb-Associated Non-Coding RNAs.
MA558504 - JP 2018138019-A/130430: Polycomb-Associated Non-Coding RNAs.
MA558501 - JP 2018138019-A/130427: Polycomb-Associated Non-Coding RNAs.
MA558500 - JP 2018138019-A/130426: Polycomb-Associated Non-Coding RNAs.
MA558498 - JP 2018138019-A/130424: Polycomb-Associated Non-Coding RNAs.
MA558495 - JP 2018138019-A/130421: Polycomb-Associated Non-Coding RNAs.
MA558493 - JP 2018138019-A/130419: Polycomb-Associated Non-Coding RNAs.
MA558491 - JP 2018138019-A/130417: Polycomb-Associated Non-Coding RNAs.
MA558489 - JP 2018138019-A/130415: Polycomb-Associated Non-Coding RNAs.
MA558488 - JP 2018138019-A/130414: Polycomb-Associated Non-Coding RNAs.
MA558486 - JP 2018138019-A/130412: Polycomb-Associated Non-Coding RNAs.
MA558485 - JP 2018138019-A/130411: Polycomb-Associated Non-Coding RNAs.
MA558484 - JP 2018138019-A/130410: Polycomb-Associated Non-Coding RNAs.
MA444372 - JP 2018138019-A/16298: Polycomb-Associated Non-Coding RNAs.
MP015105 - Sequence 308 from Patent WO2019016252.
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
  Reactome (by CSHL, EBI, and GO)

Protein P12109 (Reactome details) participates in the following event(s):

R-HSA-8944247 Association of procollagen type VI
R-HSA-2002460 P4HB binds Collagen chains
R-HSA-8948230 P3HB binds 4-Hyp-collagen propeptides
R-HSA-1614460 Dimerization of procollagen type VI
R-HSA-1650808 Prolyl 4-hydroxylase converts collagen prolines to 4-hydroxyprolines
R-HSA-1980233 Collagen prolyl 3-hydroxylase converts 4-Hyp collagen to 3,4-Hyp collagen
R-HSA-8948219 PLOD3 binds Lysyl hydroxylated collagen propeptides
R-HSA-8948228 COLGALT1,COLGALT2 bind Lysyl hydroxylated collagen propeptides
R-HSA-2022073 Procollagen triple helix formation
R-HSA-1614461 Tetramerization of procollagen VI
R-HSA-1981104 Procollagen lysyl hydroxylases convert collagen lysines to 5-hydroxylysines
R-HSA-1981120 Galactosylation of collagen propeptide hydroxylysines by procollagen galactosyltransferases 1, 2.
R-HSA-1981128 Galactosylation of collagen propeptide hydroxylysines by PLOD3
R-HSA-1981157 Glucosylation of collagen propeptide hydroxylysines
R-HSA-375151 Interaction of NCAM1 with collagens
R-HSA-382054 PDGF binds to extracellular matrix proteins
R-HSA-2213207 Formation of collagen networks
R-HSA-8948216 Collagen chain trimerization
R-HSA-1650814 Collagen biosynthesis and modifying enzymes
R-HSA-1474290 Collagen formation
R-HSA-1474244 Extracellular matrix organization
R-HSA-419037 NCAM1 interactions
R-HSA-186797 Signaling by PDGF
R-HSA-375165 NCAM signaling for neurite out-growth
R-HSA-2022090 Assembly of collagen fibrils and other multimeric structures
R-HSA-9006934 Signaling by Receptor Tyrosine Kinases
R-HSA-422475 Axon guidance
R-HSA-162582 Signal Transduction
R-HSA-1266738 Developmental Biology

-  Other Names for This Gene
  Alternate Gene Symbols: CO6A1_HUMAN, ENST00000361866.1, ENST00000361866.2, ENST00000361866.3, ENST00000361866.4, ENST00000361866.5, ENST00000361866.6, ENST00000361866.7, NM_001848, O00117, O00118, P12109, Q14040, Q14041, Q16258, Q7Z645, Q9BSA8, uc318cjs.1, uc318cjs.2
UCSC ID: ENST00000361866.8_4
RefSeq Accession: NM_001848.3
Protein: P12109 (aka CO6A1_HUMAN or CA16_HUMAN)

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

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

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