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P12109 (CO6A1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 153. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Collagen alpha-1(VI) chain
Gene names
Name:COL6A1
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length1028 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Collagen VI acts as a cell-binding protein.

Subunit 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).

Subcellular location

Secretedextracellular spaceextracellular matrix By similarity.

Post-translational modification

Prolines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the chains.

Involvement in disease

Bethlem myopathy (BM) [MIM:158810]: A benign autosomal dominant proximal myopathy characterized by early childhood onset and joint contractures most frequently affecting the elbows and ankles.
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.13 Ref.14 Ref.16 Ref.17

Ullrich congenital muscular dystrophy (UCMD) [MIM:254090]: UCMD is a 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.
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.15 Ref.16 Ref.18

Sequence similarities

Belongs to the type VI collagen family.

Contains 3 VWFA domains.

Ontologies

Keywords
   Biological processCell adhesion
   Cellular componentExtracellular matrix
Secreted
   Coding sequence diversityPolymorphism
   DiseaseDisease mutation
   DomainCollagen
Repeat
Signal
   PTMGlycoprotein
Hydroxylation
   Technical termComplete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processaxon guidance

Traceable author statement. Source: Reactome

cell adhesion

Inferred from electronic annotation. Source: UniProtKB-KW

cellular response to amino acid stimulus

Inferred from electronic annotation. Source: Ensembl

collagen catabolic process

Traceable author statement. Source: Reactome

extracellular matrix disassembly

Traceable author statement. Source: Reactome

extracellular matrix organization

Traceable author statement. Source: Reactome

protein heterotrimerization

Inferred from physical interaction PubMed 18400749. Source: MGI

   Cellular_componentcollagen type VI

Non-traceable author statement Ref.1. Source: UniProtKB

endoplasmic reticulum lumen

Traceable author statement. Source: Reactome

extracellular region

Inferred from direct assay PubMed 18400749. Source: MGI

extracellular vesicular exosome

Inferred from direct assay PubMed 19056867PubMed 19199708. Source: UniProt

lysosomal membrane

Inferred from direct assay PubMed 17897319. Source: UniProtKB

protein complex

Inferred from physical interaction PubMed 18400749. Source: MGI

sarcolemma

Inferred from electronic annotation. Source: Ensembl

   Molecular_functionplatelet-derived growth factor binding

Inferred from direct assay PubMed 8900172. Source: MGI

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 1919
Chain20 – 10281009Collagen alpha-1(VI) chain
PRO_0000005758

Regions

Domain37 – 235199VWFA 1
Domain615 – 805191VWFA 2
Domain829 – 1021193VWFA 3
Region20 – 256237N-terminal globular domain
Region257 – 592336Triple-helical region
Region593 – 1028436C-terminal globular domain
Motif262 – 2643Cell attachment site
Motif442 – 4443Cell attachment site
Motif478 – 4803Cell attachment site

Amino acid modifications

Glycosylation2121N-linked (GlcNAc...) Ref.11
Glycosylation5161N-linked (GlcNAc...) Ref.11
Glycosylation5371N-linked (GlcNAc...) Potential
Glycosylation8041N-linked (GlcNAc...) Ref.11
Glycosylation8961N-linked (GlcNAc...) Ref.11

Natural variations

Natural variant1161S → N in BM. Ref.15 Ref.16
Corresponds to variant rs11553519 [ dbSNP | Ensembl ].
VAR_058213
Natural variant1211K → R in BM. Ref.14
VAR_013580
Natural variant2721G → D in BM. Ref.17
VAR_058214
Natural variant2741P → L in BM. Ref.16
VAR_058215
Natural variant2751G → R in BM. Ref.17
VAR_058216
Natural variant2811G → R in UCMD. Ref.16
VAR_058217
Natural variant2841G → R in UCMD; fibroblasts with the mutation assembled and secreted normal collagen VI microfibrils; cell adhesion of heterozygous Arg-284 fibroblasts is markedly decreased but can be rescued by the addition of normal collagen VI. Ref.15 Ref.16 Ref.18
VAR_058218
Natural variant2901G → R in BM and UCMD. Ref.15 Ref.16 Ref.17
VAR_058219
Natural variant3051G → V in BM. Ref.13
VAR_013581
Natural variant3321G → S.
Corresponds to variant rs11701912 [ dbSNP | Ensembl ].
VAR_058220
Natural variant3411G → D in BM. Ref.14
VAR_013582
Natural variant3411G → V in BM. Ref.16 Ref.17
VAR_058221
Natural variant4391R → Q.
Corresponds to variant rs35059000 [ dbSNP | Ensembl ].
VAR_048763
Natural variant5711K → T in BM. Ref.16
VAR_058222
Natural variant8501R → H. Ref.16
Corresponds to variant rs1053312 [ dbSNP | Ensembl ].
VAR_048764
Natural variant8811T → M. Ref.16
Corresponds to variant rs150432347 [ dbSNP | Ensembl ].
VAR_058223
Natural variant8901S → L. Ref.15 Ref.16
Corresponds to variant rs13051496 [ dbSNP | Ensembl ].
VAR_058224

Experimental info

Sequence conflict387 – 3882SS → AR in M20776. Ref.6
Sequence conflict387 – 3882SS → AR in AAB20835. Ref.7
Sequence conflict396 – 3972QP → PA in M20776. Ref.6
Sequence conflict396 – 3972QP → PA in AAB20835. Ref.7
Sequence conflict4381T → P in M20776. Ref.6
Sequence conflict835 – 8395DGSAS → EPPPD in CAA33889. Ref.1
Sequence conflict9971A → P in CAA67576. Ref.4

Sequences

Sequence LengthMass (Da)Tools
P12109 [UniParc].

Last modified February 6, 2007. Version 3.
Checksum: 04AFF538002A01CD

FASTA1,028108,529
        10         20         30         40         50         60 
MRAARALLPL LLQACWTAAQ DEPETPRAVA FQDCPVDLFF VLDTSESVAL RLKPYGALVD 

        70         80         90        100        110        120 
KVKSFTKRFI DNLRDRYYRC DRNLVWNAGA LHYSDEVEII QGLTRMPGGR DALKSSVDAV 

       130        140        150        160        170        180 
KYFGKGTYTD CAIKKGLEQL LVGGSHLKEN KYLIVVTDGH PLEGYKEPCG GLEDAVNEAK 

       190        200        210        220        230        240 
HLGVKVFSVA ITPDHLEPRL SIIATDHTYR RNFTAADWGQ SRDAEEAISQ TIDTIVDMIK 

       250        260        270        280        290        300 
NNVEQVCCSF ECQPARGPPG LRGDPGFEGE RGKPGLPGEK GEAGDPGRPG DLGPVGYQGM 

       310        320        330        340        350        360 
KGEKGSRGEK GSRGPKGYKG EKGKRGIDGV DGVKGEMGYP GLPGCKGSPG FDGIQGPPGP 

       370        380        390        400        410        420 
KGDPGAFGLK GEKGEPGADG EAGRPGSSGP SGDEGQPGEP GPPGEKGEAG DEGNPGPDGA 

       430        440        450        460        470        480 
PGERGGPGER GPRGTPGTRG PRGDPGEAGP QGDQGREGPV GVPGDPGEAG PIGPKGYRGD 

       490        500        510        520        530        540 
EGPPGSEGAR GAPGPAGPPG DPGLMGERGE DGPAGNGTEG FPGFPGYPGN RGAPGINGTK 

       550        560        570        580        590        600 
GYPGLKGDEG EAGDPGDDNN DIAPRGVKGA KGYRGPEGPQ GPPGHQGPPG PDECEILDII 

       610        620        630        640        650        660 
MKMCSCCECK CGPIDLLFVL DSSESIGLQN FEIAKDFVVK VIDRLSRDEL VKFEPGQSYA 

       670        680        690        700        710        720 
GVVQYSHSQM QEHVSLRSPS IRNVQELKEA IKSLQWMAGG TFTGEALQYT RDQLLPPSPN 

       730        740        750        760        770        780 
NRIALVITDG RSDTQRDTTP LNVLCSPGIQ VVSVGIKDVF DFIPGSDQLN VISCQGLAPS 

       790        800        810        820        830        840 
QGRPGLSLVK ENYAELLEDA FLKNVTAQIC IDKKCPDYTC PITFSSPADI TILLDGSASV 

       850        860        870        880        890        900 
GSHNFDTTKR FAKRLAERFL TAGRTDPAHD VRVAVVQYSG TGQQRPERAS LQFLQNYTAL 

       910        920        930        940        950        960 
ASAVDAMDFI NDATDVNDAL GYVTRFYREA SSGAAKKRLL LFSDGNSQGA TPAAIEKAVQ 

       970        980        990       1000       1010       1020 
EAQRAGIEIF VVVVGRQVNE PHIRVLVTGK TAEYDVAYGE SHLFRVPSYQ ALLRGVFHQT 


VSRKVALG 

« Hide

References

« Hide 'large scale' references
[1]"Sequence analysis of alpha 1(VI) and alpha 2(VI) chains of human type VI collagen reveals internal triplication of globular domains similar to the A domains of von Willebrand factor and two alpha 2(VI) chain variants that differ in the carboxy terminus."
Chu M.-L., Pan T.-C., Conway D., Kuo H.J., Glanville R.W., Timpl R., Mann K., Deutzmann R.
EMBO J. 8:1939-1946(1989) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], PARTIAL PROTEIN SEQUENCE.
Tissue: Fibroblast.
[2]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Kidney and Ovary.
[3]"Recombinant expression and structural and binding properties of alpha 1(VI) and alpha 2(VI) chains of human collagen type VI."
Tillet E., Wiedemann H., Golbik R., Pan T.-C., Zhang R.Z., Mann K., Chu M.-L., Timpl R.
Eur. J. Biochem. 221:177-185(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1-380 AND 383-1028.
[4]"Human COL6A1: genomic characterization of the globular domains, structural and evolutionary comparison with COL6A2."
Trikka D., Davis T., Lapenta V., Brahe C., Kessling A.M.
Mamm. Genome 8:342-345(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 144-268 AND 593-1028.
[5]"Further characterization of the three polypeptide chains of bovine and human short-chain collagen (intima collagen)."
Jander R., Rauterberg J., Glanville R.W.
Eur. J. Biochem. 133:39-46(1983) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 246-258.
[6]"Amino acid sequence of the triple-helical domain of human collagen type VI."
Chu M.-L., Conway D., Pan T.-C., Baldwin C., Mann K., Deutzmann R., Timpl R.
J. Biol. Chem. 263:18601-18606(1988) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 257-592.
[7]"The exon organization of the triple-helical coding regions of the human alpha 1(VI) and alpha 2(VI) collagen genes is highly similar."
Saitta B., Wang Y.-M., Renkart L., Zhang R.-Z., Pan T.-C., Timpl R., Chu M.-L.
Genomics 11:145-153(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 287-592.
[8]"Characterization of three constituent chains of collagen type VI by peptide sequences and cDNA clones."
Chu M.-L., Mann K., Deutzmann R., Pribula-Conway D., Hsu-Chen C.-C., Bernard M.P., Timpl R.
Eur. J. Biochem. 168:309-317(1987) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 422-482.
[9]"Cloning and chromosomal localization of human genes encoding the three chains of type VI collagen."
Weil D., Mattei M.-G., Passage E., N'Guyen V.C., Pribula-Conway D., Mann K., Deutzmann R., Timpl R., Chu M.-L.
Am. J. Hum. Genet. 42:435-445(1988) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 422-481.
Tissue: Placenta.
[10]Lubec G., Chen W.-Q., Sun Y.
Submitted (DEC-2008) to UniProtKB
Cited for: PROTEIN SEQUENCE OF 693-711; 737-757; 939-957 AND 991-1005, IDENTIFICATION BY MASS SPECTROMETRY.
Tissue: Fetal brain cortex.
[11]"Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry."
Chen R., Jiang X., Sun D., Han G., Wang F., Ye M., Wang L., Zou H.
J. Proteome Res. 8:651-661(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-212; ASN-516; ASN-804 AND ASN-896.
Tissue: Liver.
[12]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[13]"Type VI collagen mutations in Bethlem myopathy, an autosomal dominant myopathy with contractures."
Joebsis G.J., Keizers H., Vreijling J.P., de Visser M., Speer M.C., Wolterman R.A., Baas F., Bohlhuis P.A.
Nat. Genet. 14:113-115(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANT BM VAL-305.
[14]"Novel mutations in collagen VI genes: expansion of the Bethlem myopathy phenotype."
Scacheri P.C., Gillanders E.M., Subramony S.H., Vedanarayanan V., Crowe C.A., Thakore N., Bingler M., Hoffman E.P.
Neurology 58:593-602(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANTS BM ARG-121 AND ASP-341.
[15]"Dominant and recessive COL6A1 mutations in Ullrich scleroatonic muscular dystrophy."
Giusti B., Lucarini L., Pietroni V., Lucioli S., Bandinelli B., Sabatelli P., Squarzoni S., Petrini S., Gartioux C., Talim B., Roelens F., Merlini L., Topaloglu H., Bertini E., Guicheney P., Pepe G.
Ann. Neurol. 58:400-410(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANTS UCMD ARG-284 AND ARG-290, VARIANTS ASN-116 AND LEU-890.
[16]"Automated genomic sequence analysis of the three collagen VI genes: applications to Ullrich congenital muscular dystrophy and Bethlem myopathy."
Lampe A.K., Dunn D.M., von Niederhausern A.C., Hamil C., Aoyagi A., Laval S.H., Marie S.K., Chu M.-L., Swoboda K., Muntoni F., Bonnemann C.G., Flanigan K.M., Bushby K.M.D., Weiss R.B.
J. Med. Genet. 42:108-120(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANTS BM ASN-116; LEU-274; ARG-290; VAL-341 AND THR-571, VARIANTS UCMD ARG-281 AND ARG-284, VARIANTS HIS-850; MET-881 AND LEU-890.
[17]"Detection of common and private mutations in the COL6A1 gene of patients with Bethlem myopathy."
Lucioli S., Giusti B., Mercuri E., Vanegas O.C., Lucarini L., Pietroni V., Urtizberea A., Ben Yaou R., de Visser M., van der Kooi A.J., Boennemann C., Iannaccone S.T., Merlini L., Bushby K., Muntoni F., Bertini E., Chu M.-L., Pepe G.
Neurology 64:1931-1937(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANTS BM ASP-272; ARG-275; ARG-290 AND VAL-341.
[18]"Reduced cell anchorage may cause sarcolemma-specific collagen VI deficiency in Ullrich disease."
Kawahara G., Okada M., Morone N., Ibarra C.A., Nonaka I., Noguchi S., Hayashi Y.K., Nishino I.
Neurology 69:1043-1049(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: CHARACTERIZATION OF VARIANT UCMD ARG-284.
+Additional computationally mapped references.

Web resources

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X15879 mRNA. Translation: CAA33888.1.
X15880 mRNA. Translation: CAA33889.1.
BC005159 mRNA. Translation: AAH05159.2.
BC052575 mRNA. Translation: AAH52575.1.
X99109 Genomic DNA. Translation: CAA67559.1.
X99135, X99136 Genomic DNA. Translation: CAA67576.1.
M20776 mRNA. No translation available.
S75420 expand/collapse EMBL AC list , S75385, S75388, S75390, S75392, S75394, S75396, S75398, S75400, S75402, S75404, S75406, S75408, S75410, S75412, S75414, S75416, S75418 Genomic DNA. Translation: AAB20835.2.
X06194 mRNA. Translation: CAA29555.1.
M27447 mRNA. Translation: AAA52055.1.
PIRCGHU1A. S05377.
RefSeqNP_001839.2. NM_001848.2.
UniGeneHs.474053.

3D structure databases

ProteinModelPortalP12109.
SMRP12109. Positions 35-236, 252-277, 608-797, 825-1014.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid107688. 9 interactions.
IntActP12109. 5 interactions.
STRING9606.ENSP00000355180.

Chemistry

ChEMBLCHEMBL2364188.
DrugBankDB00039. Palifermin.

PTM databases

PhosphoSiteP12109.

Polymorphism databases

DMDM125987811.

2D gel databases

REPRODUCTION-2DPAGEIPI00291136.
P12109.

Proteomic databases

PaxDbP12109.
PeptideAtlasP12109.
PRIDEP12109.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000361866; ENSP00000355180; ENSG00000142156.
GeneID1291.
KEGGhsa:1291.
UCSCuc002zhu.1. human.

Organism-specific databases

CTD1291.
GeneCardsGC21P047401.
HGNCHGNC:2211. COL6A1.
HPAHPA019142.
HPA029401.
MIM120220. gene.
158810. phenotype.
254090. phenotype.
neXtProtNX_P12109.
Orphanet610. Bethlem myopathy.
75840. Congenital muscular dystrophy, Ullrich type.
PharmGKBPA26727.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG256042.
HOVERGENHBG095954.
InParanoidP12109.
KOK06238.
OMAVKENYAE.
OrthoDBEOG71K628.
PhylomeDBP12109.
TreeFamTF331207.

Enzyme and pathway databases

ReactomeREACT_111045. Developmental Biology.
REACT_111102. Signal Transduction.
REACT_118779. Extracellular matrix organization.

Gene expression databases

ArrayExpressP12109.
BgeeP12109.
CleanExHS_COL6A1.
GenevestigatorP12109.

Family and domain databases

Gene3D3.40.50.410. 3 hits.
InterProIPR008160. Collagen.
IPR002035. VWF_A.
[Graphical view]
PfamPF01391. Collagen. 6 hits.
PF00092. VWA. 3 hits.
[Graphical view]
SMARTSM00327. VWA. 3 hits.
[Graphical view]
SUPFAMSSF53300. SSF53300. 3 hits.
PROSITEPS50234. VWFA. 3 hits.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSCOL6A1. human.
GeneWikiCollagen,_type_VI,_alpha_1.
GenomeRNAi1291.
NextBio5227.
PMAP-CutDBP12109.
PROP12109.
SOURCESearch...

Entry information

Entry nameCO6A1_HUMAN
AccessionPrimary (citable) accession number: P12109
Secondary accession number(s): O00117 expand/collapse secondary AC list , O00118, Q14040, Q14041, Q16258, Q7Z645, Q9BSA8
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1989
Last sequence update: February 6, 2007
Last modified: April 16, 2014
This is version 153 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Relevant documents

SIMILARITY comments

Index of protein domains and families

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 21

Human chromosome 21: entries, gene names and cross-references to MIM