COL6A1 (collagen type VI alpha 1 chain)

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Gene: COL6A1 (collagen type VI alpha 1 chain) Pan paniscus

Analyze

Symbol:

COL6A1

Name:

collagen type VI alpha 1 chain

RGD ID:

11757685

Description:

ENCODES a protein that exhibits collagen binding (ortholog); platelet-derived growth factor binding (ortholog); INVOLVED IN cellular response to amino acid stimulus (ortholog); endodermal cell differentiation (ortholog); PARTICIPATES IN syndecan signaling pathway; ASSOCIATED WITH autistic disorder (ortholog); Axenfeld-Rieger syndrome type 3 (ortholog); Bethlem myopathy (ortholog); FOUND IN extracellular matrix (ortholog); extracellular region (ortholog); protein-containing complex (ortholog)

Type:

protein-coding

RefSeq Status:

MODEL

Also known as:

collagen alpha-1(VI) chain; LOC103783489; uncharacterized LOC103783489

RGD Orthologs

Human

Mouse

Rat

Chinchilla

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

Latest Assembly:

Mhudiblu_PPA_v0 - Bonobo Mhudiblu_PPA_v0 Assembly

Position:

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	21	45,583,978 - 45,608,233 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	21	45,584,096 - 45,607,240 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	21	32,322,185 - 32,346,850 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autistic disorder (ISO)

Axenfeld-Rieger syndrome type 3 (ISO)

Bethlem myopathy (ISO)

Bethlem Myopathy 1 (ISO)

diastolic heart failure (ISO)

dystonia 27 (ISO)

Experimental Liver Cirrhosis (ISO)

genetic disease (ISO)

Lung Neoplasms (ISO)

muscular dystrophy (ISO)

Mycoplasma pneumoniae pneumonia (ISO)

myopathy (ISO)

primary cerebellar degeneration (ISO)

Spontaneous Abortions (ISO)

Ullrich congenital muscular dystrophy (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cellular response to amino acid stimulus (ISO)

endodermal cell differentiation (ISO)

Cellular Component

extracellular matrix (ISO)

extracellular region (ISO)

protein-containing complex (ISO)

sarcolemma (ISO)

Molecular Function

collagen binding (ISO)

platelet-derived growth factor binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

syndecan signaling pathway (ISO)

References

Genomics

Comparative Map Data

COL6A1
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	21	45,583,978 - 45,608,233 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	21	45,584,096 - 45,607,240 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	21	32,322,185 - 32,346,850 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

COL6A1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	21	45,981,737 - 46,005,050 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38.p13 Ensembl	21	45,981,769 - 46,005,050 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	21	45,981,770 - 46,005,048 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	21	47,401,684 - 47,424,962 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	21	46,226,091 - 46,249,391 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	21	46,226,095 - 46,249,390	NCBI
Celera	21	32,514,265 - 32,537,566 (+)	NCBI
Cytogenetic Map	21	q22.3	NCBI
HuRef	21	32,782,505 - 32,806,491 (+)	NCBI		HuRef
CHM1_1	21	46,962,501 - 46,985,646 (+)	NCBI		CHM1_1

Col6a1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	10	76,544,626 - 76,561,878 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	10	76,544,626 - 76,562,002 (-)	Ensembl
GRCm38	10	76,708,792 - 76,726,044 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	10	76,708,792 - 76,726,168 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	10	76,171,537 - 76,188,789 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	10	76,152,508 - 76,169,760 (-)	NCBI			mm8
Celera	10	77,753,031 - 77,770,283 (-)	NCBI		Celera
Cytogenetic Map	10	C1	NCBI
cM Map	10	39.71	NCBI

Col6a1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	20	11,906,105 - 11,924,599 (+)	NCBI
Rnor_6.0 Ensembl	20	12,658,065 - 12,675,561 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	20	12,657,913 - 12,676,370 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	20	14,817,411 - 14,835,868 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	20	12,320,102 - 12,338,500 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	20	13,404,454 - 13,422,911 (+)	NCBI		Celera
Cytogenetic Map	20	p12	NCBI

Col6a1
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955407	42,461,952 - 42,478,261 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955407	42,461,837 - 42,479,048 (+)	NCBI	ChiLan1.0	ChiLan1.0

COL6A1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1 Ensembl	31	39,301,748 - 39,448,062 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	31	39,301,718 - 39,319,895 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Col6a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
SpeTri2.0	NW_004936778	515,600 - 530,828 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

LOC100623720
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	13	208,295,240 - 208,313,127 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	13	208,295,245 - 208,321,789 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

COL6A1
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	2	89,608,525 - 89,649,823 (+)	NCBI

Col6a1
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624745	31,125,136 - 31,140,126 (+)	NCBI

Expression

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_034947880	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	SSBP01000389	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSPPAT00000031842 ⟹ ENSPPAP00000009202

RefSeq Status:

Type:

CODING

Position:

Bonobo Assembly	Chr	Position (strand)	Source
PanPan1.1 Ensembl	21	45,584,096 - 45,607,240 (+)	Ensembl

RefSeq Acc Id:

ENSPPAT00000031848 ⟹ ENSPPAP00000009208

RefSeq Status:

Type:

CODING

Position:

Bonobo Assembly	Chr	Position (strand)	Source
PanPan1.1 Ensembl	21	45,584,096 - 45,607,240 (+)	Ensembl

RefSeq Acc Id:

XM_034947880 ⟹ XP_034803771

RefSeq Status:

Type:

CODING

Position:

Bonobo Assembly	Chr	Position (strand)	Source
Mhudiblu_PPA_v0	21	32,322,185 - 32,346,850 (+)	NCBI

Protein Sequences


Protein RefSeqs	XP_034803771	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

XP_034803771 ⟸ XM_034947880

RefSeq Acc Id:

ENSPPAP00000009202 ⟸ ENSPPAT00000031842

RefSeq Acc Id:

ENSPPAP00000009208 ⟸ ENSPPAT00000031848

Protein Domains

VWFA

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSPPAG00000027819	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSPPAP00000009202	UniProtKB/TrEMBL
	ENSPPAP00000009208	UniProtKB/TrEMBL
Ensembl Transcript	ENSPPAT00000031842	UniProtKB/TrEMBL
	ENSPPAT00000031848	UniProtKB/TrEMBL
Gene3D-CATH	3.40.50.410	UniProtKB/TrEMBL
InterPro	Collagen	UniProtKB/TrEMBL
	VWF_A	UniProtKB/TrEMBL
	vWFA_dom_sf	UniProtKB/TrEMBL
NCBI Gene	COL6A1	ENTREZGENE
Pfam	Collagen	UniProtKB/TrEMBL
	VWA	UniProtKB/TrEMBL
PROSITE	VWFA	UniProtKB/TrEMBL
SMART	VWA	UniProtKB/TrEMBL
Superfamily-SCOP	SSF53300	UniProtKB/TrEMBL
UniProt	A0A2R8ZZU7_PANPA	UniProtKB/TrEMBL
	A0A2R9A1S9_PANPA	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2020-06-11	COL6A1	collagen type VI alpha 1 chain	LOC103783489	uncharacterized LOC103783489	Data Merged	737654	PROVISIONAL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

Imported Annotations - PID (archival)