Col6a2 (collagen type VI alpha 2 chain)

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Gene: Col6a2 (collagen type VI alpha 2 chain) Rattus norvegicus

Analyze

Symbol:

Col6a2

Name:

collagen type VI alpha 2 chain

RGD ID:

1305585

Description:

Predicted to have collagen binding activity. Involved in response to glucose. Predicted to localize to several cellular components, including extracellular matrix; extracellular region; and sarcolemma. Human ortholog(s) of this gene implicated in Ullrich congenital muscular dystrophy. Orthologous to human COL6A2 (collagen type VI alpha 2 chain); PARTICIPATES IN syndecan signaling pathway; cell-extracellular matrix signaling pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 2,2',4,4'-Tetrabromodiphenyl ether; 2,2,2-tetramine.

Type:

protein-coding

RefSeq Status:

VALIDATED

Also known as:

collagen alpha-2(VI) chain; collagen, type VI, alpha 2; LOC361821; procollagen, type VI, alpha 2

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	20	12,021,676 - 12,049,425 (+)	NCBI
Rnor_6.0 Ensembl	20	12,773,427 - 12,801,180 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	20	12,773,472 - 12,801,179 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	20	14,931,484 - 14,959,214 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	20	12,436,783 - 12,464,512 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	20	12,445,140 - 12,461,566 (+)	NCBI
Celera	20	13,520,111 - 13,547,903 (+)	NCBI		Celera
Cytogenetic Map	20	p12	NCBI

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)

Congenital Hip Dislocation (ISO)

COVID-19 (ISO)

dystonia 27 (ISO)

Experimental Liver Cirrhosis (IEP,ISO)

genetic disease (ISO)

glutamate formiminotransferase deficiency (ISO)

Mobility Limitation (ISO)

Muscle Weakness (ISO)

muscular dystrophy (ISO)

Mycoplasma pneumoniae pneumonia (ISO)

myopathy (ISO)

Myosclerosis, Autosomal Recessive (ISO)

osteoarthritis (ISO)

Ullrich congenital muscular dystrophy (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dichloroethane (ISO)

1,2-dimethylhydrazine (ISO)

1-naphthyl isothiocyanate (EXP)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (ISO)

2,2',4,4'-Tetrabromodiphenyl ether (EXP)

2,2,2-tetramine (EXP)

2,3,7,8-tetrachlorodibenzodioxine (ISO)

4,4'-diaminodiphenylmethane (EXP)

4,4'-sulfonyldiphenol (ISO)

4-hydroxyphenyl retinamide (ISO)

acetamide (EXP)

acrylamide (EXP)

aflatoxin B1 (ISO)

aflatoxin B2 (ISO)

aldehydo-D-glucose (ISO)

all-trans-retinoic acid (ISO)

Aroclor 1254 (ISO)

arsenite(3-) (ISO)

atrazine (ISO)

benzo[a]pyrene (ISO)

beta-naphthoflavone (EXP)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

bucladesine (ISO)

cadmium atom (ISO)

cadmium dichloride (ISO)

captan (ISO)

carbon nanotube (ISO)

cisplatin (ISO)

clothianidin (ISO)

copper atom (EXP,ISO)

copper(0) (EXP,ISO)

cytarabine (ISO)

D-glucose (ISO)

DDT (EXP)

decabromodiphenyl ether (EXP)

deoxynivalenol (ISO)

dexamethasone (ISO)

dextran sulfate (ISO)

dichromium trioxide (ISO)

disodium selenite (ISO)

diuron (EXP)

dorsomorphin (ISO)

doxorubicin (ISO)

elemental selenium (ISO)

endosulfan (EXP)

ethanol (ISO)

folic acid (ISO)

folpet (ISO)

furan (EXP)

genistein (ISO)

glucose (ISO)

isotretinoin (ISO)

lead diacetate (ISO)

lipopolysaccharide (ISO)

medroxyprogesterone acetate (ISO)

N-nitrosodiethylamine (EXP)

oxaliplatin (EXP)

paclitaxel (ISO)

paracetamol (ISO)

pentane-2,3-dione (EXP)

phenytoin (ISO)

pirinixic acid (ISO)

propanal (ISO)

Ptaquiloside (ISO)

resveratrol (ISO)

SB 431542 (ISO)

selenium atom (ISO)

simvastatin (ISO)

sodium arsenite (ISO)

sodium fluoride (EXP,ISO)

Soman (EXP)

streptozocin (EXP)

sulindac (ISO)

sunitinib (ISO)

tert-butyl hydroperoxide (ISO)

testosterone enanthate (ISO)

topotecan (EXP,ISO)

tris(2-butoxyethyl) phosphate (ISO)

urethane (ISO)

valproic acid (ISO)

vitamin E (ISO)

zinc atom (ISO)

zinc(0) (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

response to glucose (IEP)

Cellular Component

cellular_component (ND)

collagen trimer (IEA)

collagen-containing extracellular matrix (IBA)

extracellular matrix (ISO)

extracellular region (ISO,TAS)

extracellular space (IBA)

protein-containing complex (ISO)

sarcolemma (ISO)

Molecular Function

collagen binding (ISO)

molecular_function (ND)

protein binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

cell-extracellular matrix signaling pathway (IEA)

syndecan signaling pathway (ISO)

References

References - curated


1.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	GOA data from the GO Consortium
3.	Jobsis GJ, etal., Nat Genet. 1996 Sep;14(1):113-5.
4.	MGD data from the GO Consortium
5.	Muona P, etal., Am J Pathol. 1993 May;142(5):1586-97.
6.	OMIM Disease Annotation Pipeline
7.	Pipeline to import KEGG annotations from KEGG into RGD
8.	Pipeline to import Pathway Interaction Database annotations from NCI into RGD
9.	RGD automated data pipeline
10.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
11.	RGD automated import pipeline for gene-chemical interactions
12.	RGD comprehensive gene curation
13.	Takahara T, etal., Liver. 1995 Apr;15(2):78-86.

Additional References at PubMed

PMID:8806434	PMID:12477932	PMID:16810681	PMID:18400749	PMID:19199708	PMID:20551380	PMID:23658023	PMID:24006456	PMID:24769233	PMID:27068509	PMID:27559042

Genomics

Comparative Map Data

Col6a2
(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	12,021,676 - 12,049,425 (+)	NCBI
Rnor_6.0 Ensembl	20	12,773,427 - 12,801,180 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	20	12,773,472 - 12,801,179 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	20	14,931,484 - 14,959,214 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	20	12,436,783 - 12,464,512 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	20	12,445,140 - 12,461,566 (+)	NCBI
Celera	20	13,520,111 - 13,547,903 (+)	NCBI		Celera
Cytogenetic Map	20	p12	NCBI

COL6A2
(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	46,098,097 - 46,132,849 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38.p13 Ensembl	21	46,098,112 - 46,132,848 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	21	46,098,071 - 46,132,849 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	21	47,518,026 - 47,552,762 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	21	46,342,461 - 46,377,191 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	21	46,342,469 - 46,374,147	NCBI
Celera	21	32,629,797 - 32,665,343 (+)	NCBI
Cytogenetic Map	21	q22.3	NCBI
HuRef	21	32,899,133 - 32,933,853 (+)	NCBI		HuRef
CHM1_1	21	47,078,809 - 47,113,491 (+)	NCBI		CHM1_1

Col6a2
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	10	76,431,590 - 76,459,464 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	10	76,431,596 - 76,459,464 (-)	Ensembl
GRCm38	10	76,595,756 - 76,623,630 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	10	76,595,762 - 76,623,630 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	10	76,058,501 - 76,086,149 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	10	76,039,478 - 76,067,030 (-)	NCBI			mm8
Celera	10	77,640,875 - 77,668,353 (-)	NCBI		Celera
Cytogenetic Map	10	C1	NCBI
cM Map	10	39.32	NCBI

Col6a2
(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	42,575,170 - 42,600,495 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955407	42,575,677 - 42,600,967 (+)	NCBI	ChiLan1.0	ChiLan1.0

COL6A2
(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	45,696,865 - 45,731,192 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	21	45,710,491 - 45,730,895 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	21	32,442,859 - 32,478,076 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

Col6a2
(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	394,985 - 430,070 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

COL6A2
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa10.2	13	218,600,867 - 218,616,309 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

COL6A2
(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	89,724,355 - 89,758,389 (+)	NCBI
ChlSab1.1 Ensembl	2	89,737,003 - 89,758,425 (+)	Ensembl

Col6a2
(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	31,246,458 - 31,272,403 (+)	NCBI

Position Markers

BE115058

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	20	12,798,993 - 12,799,149	NCBI	Rnor6.0
Rnor_5.0	20	14,957,028 - 14,957,184	UniSTS	Rnor5.0
RGSC_v3.4	20	12,462,326 - 12,462,482	UniSTS	RGSC3.4
Celera	20	13,545,688 - 13,545,844	UniSTS
RH 3.4 Map	20	175.73	UniSTS
Cytogenetic Map	20	p12	UniSTS

RH127992

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	20	12,800,951 - 12,801,145	NCBI	Rnor6.0
Rnor_5.0	20	14,958,986 - 14,959,180	UniSTS	Rnor5.0
RGSC_v3.4	20	12,464,284 - 12,464,478	UniSTS	RGSC3.4
Celera	20	13,547,675 - 13,547,869	UniSTS
RH 3.4 Map	20	153.7	UniSTS
Cytogenetic Map	20	p12	UniSTS

RH140241

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	20	12,801,004 - 12,801,171	NCBI	Rnor6.0
Rnor_5.0	20	14,959,039 - 14,959,206	UniSTS	Rnor5.0
RGSC_v3.4	20	12,464,337 - 12,464,504	UniSTS	RGSC3.4
Celera	20	13,547,728 - 13,547,895	UniSTS
RH 3.4 Map	20	157.45	UniSTS
Cytogenetic Map	20	p12	UniSTS

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1354642	Despr15	Despair related QTL 15		0.0027	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	20	1	24652101	Rat
1600382	Edcs3	Endometrial carcinoma susceptibility QTL3	3.5	0.003	uterus morphology trait (VT:0001120)	percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)	20	1	25653396	Rat
1641893	Alcrsp7	Alcohol response QTL 7			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	20	1	26305996	Rat
2317851	Alcrsp22	Alcohol response QTL 22	3.2	0.05	response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	20	1	26305996	Rat
7387283	Uae44	Urinary albumin excretion QTL 44		0.1712	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	20	1	27357423	Rat
9590275	Scort15	Serum corticosterone level QTL 15	3.48	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	20	1	28375393	Rat
9589155	Insul32	Insulin level QTL 32	6.38	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	20	1	28375393	Rat
9590109	Sffal8	Serum free fatty acids level QTL 8	5.32	0.01	blood free fatty acid amount (VT:0001553)	plasma free fatty acids level (CMO:0000546)	20	1	28375393	Rat
7411650	Foco23	Food consumption QTL 23	20.7	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	20	1	28375393	Rat
8694189	Bw153	Body weight QTL 153	3.13	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	20	1	28375393	Rat
6893685	Bw111	Body weight QTL 111	2.7	0.004	body mass (VT:0001259)	body weight (CMO:0000012)	20	1	33300419	Rat
9590252	Scort12	Serum corticosterone level QTL 12	20.46	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	20	1	37550487	Rat
7411668	Foco32	Food consumption QTL 32	8	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	20	1	37550487	Rat
2305926	Iddm37	Insulin dependent diabetes mellitus QTL 37	6		blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	20	2018654	47018654	Rat
1641915	Colcr9	Colorectal carcinoma resistance QTL 9	2.97	0.0024	intestine integrity trait (VT:0010554)	benign colorectal tumor number (CMO:0001795)	20	2999707	47999707	Rat
2317057	Aia27	Adjuvant induced arthritis QTL 27	2.83		joint integrity trait (VT:0010548)	right rear ankle joint diameter (CMO:0002150)	20	3402111	27968216	Rat
1558640	Prcs2	Prostate cancer susceptibility QTL 2	3.3		prostate integrity trait (VT:0010571)	percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)	20	4039113	18872273	Rat
4889857	Pur27	Proteinuria QTL 27	12.2	0.001	total urine protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	20	4039113	18872273	Rat
1598816	Memor12	Memory QTL 12	2.4		exploratory behavior trait (VT:0010471)	average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)	20	4108956	49108956	Rat
61432	Cia1	Collagen induced arthritis QTL 1			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	20	4855475	15050565	Rat
70154	Insul2	Insulin level QTL 2	3.75		blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	20	5875448	18739210	Rat
1581577	Pur15	Proteinuria QTL 15	4.38	0.0002	total urine protein amount (VT:0000032)	urine protein excretion rate (CMO:0000759)	20	8654341	18872273	Rat
4889870	Pur30	Proteinuria QTL 30	19	0.005	total urine protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	20	8654341	30991290	Rat
631265	Iresp1	Immunoglobin response QTL1	8.3		blood anti-double stranded DNA antibody amount (VT:0004762)	serum anti-DNA antibody level (CMO:0001533)	20	9655642	14411641	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	282
Count of miRNA genes:	135
Interacting mature miRNAs:	159
Transcripts:	ENSRNOT00000001695
Prediction methods:	Microtar, Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High											4
Medium	3	41	52	36	19	36	8	11	58	35	35	11	8
Low		2	5	5		5			16		2
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001100741	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006256300	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC127868	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC089923	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CB616438	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473988	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CK365920	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	DN935075	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FM036514	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FM048712	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FM093132	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000324	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000001695 ⟹ ENSRNOP00000001695

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	20	12,773,427 - 12,801,180 (+)	Ensembl

RefSeq Acc Id:

NM_001100741 ⟹ NP_001094211

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	20	12,021,767 - 12,049,425 (+)	NCBI
Rnor_6.0	20	12,773,520 - 12,801,179 (+)	NCBI
Rnor_5.0	20	14,931,484 - 14,959,214 (+)	NCBI
RGSC_v3.4	20	12,436,783 - 12,464,512 (+)	RGD
Celera	20	13,520,111 - 13,547,903 (+)	RGD

Sequence:

show sequence

CCCGCACCTCGGGCCGTCAGGACCCGAGCTGTCCTCGGAAGTACCCAGACGTCCTCTCCAAGCC
AGGACATCAGGGCACATGACGACTACTACCAAGATGCTCCAGGGTTCTTTTTCTGTGCTCCTGC
TTGGGGGACTCTTGGGGGTCCTCCATGCCCAGCAGCAGGAAGCCATCTCACCTGATATCTCTAC
TACTGACAGGAACAACAACTGTCCAGAGAAGGCTGACTGCCCAGTCAACGTGTACTTCGTGTTG
GACACCTCGGAGAGCGTGGCCATGCAGTCCCCCACAGACAGCCTGCTTTATCACATGCAGCAGT
TCGTACCACAATTTATCAGCCAGCTGCAGAACGAGTTCTACCTGGAGCAGGTGGCCCTGAGCTG
GCGCTATGGTGGCCTACACTTCTCGGACCAGGTGGAGGTGTTCAGCCCCCCAGGCAGCGACCGG
GCCTCCTTCACTAAGAGCCTACAAGGCATCCGCTCCTTCCGCAGGGGCACCTTCACTGACTGTG
CCTTGGCCAACATGACCCAGCAGATCCGGCAGCACGTAGGCCGGGGTGTAGTCAACTTTGCCGT
GGTCATCACCGATGGCCACGTCACAGGCAATCCCTGTGGGGGCATCAAAATGCAGGCTGAGCGT
GCCCGCGAGGAGGGCATCCGGCTCTTTGCCGTGGCCCCCAATAGGAACCTAAATGAACAAGGCC
TGCGGGATATCGCCAACACCCCACATGAGCTATACCGAAACAACTATGCCACCATGCGACCTGA
CTCTACTGAGATTGACCAGGACACCATCAACCGCATCATCAAGGTCATGAAACATGAAGCCTAC
GGAGAGTGCTACAAGGTGAGCTGCCTGGAGATTCCGGGACCCCACGGACCCAAGGGTTACCGAG
GACAGAAGGGCGCCAAGGGCAACATGGGCGAGCCAGGAGAACCTGGACAGAAAGGACGACAGGG
AGACCCTGGCATTGAAGGCCCCATTGGATTCCCAGGACCCAAGGGTGTGCCTGGCTTCAAGGGA
GAGAAGGGTGAATTCGGATCAGATGGTCGGAAGGGAGCTCCGGGTCTAGCAGGCAAGAACGGAA
CAGATGGACAGAAGGGCAAACTGGGCCGTATTGGGCCTCCTGGTTGCAAGGGAGACCCGGGAAG
TCGGGGCCCCGATGGATACCCCGGAGAAGCTGGAAGCCCGGGAGAGCAAGGAGACCAAGGTGCC
AAGGGGGACTCTGGCCGCCCAGGACGCAGGGGACCACCAGGAAATCCTGGAGACAAAGGAAGCA
AGGGATATCGAGGCAACAGTGGAGCTCCCGGAAGTCCAGGAGTGAAAGGAGGCAAGGGAGGGCC
TGGCCCCCGTGGACCAAAAGGAGAGCCTGGACGCAGGGGAGATCCTGGGACCAAGGGCGGCCCG
GGCAGTGATGGTCCAAAGGGGGAGAAGGGAGACCCTGGTCCTGAGGGGCCACGAGGTCTGGCTG
GAGAAATCGGCAGTAAAGGAGCCAAGGGAGACAGAGGTTTGCCTGGACCCAGAGGCCCCCAGGG
AGCTCTTGGGGAGCCAGGGAAGCAGGGATCTCGGGGAGACCCTGGGGATGCTGGGCCTCGAGGA
GATTCAGGACAGCCAGGACCCAAGGGAGATCCTGGAAGGCCTGGATTCAGCTACCCAGGACCCC
GAGGGACACCCGGTGAAAAAGGCGAGCCCGGCCCACCAGGCCCTGAGGGAGGCCGAGGAGACTT
TGGTCTGAAAGGAGCACCCGGACGGAAGGGAGAAAAAGGAGAGCCAGCTGATCCTGGTCCCCCT
GGTGAACCTGGCCCTCGGGGGCCAAGAGGAATCCCAGGACCTGAGGGAGAACCCGGCCCTCCAG
GAGATCCTGGTCTCACGGAATGTGACGTCATGACCTATGTGAGGGAGACCTGTGGGTGCTGTGA
CTGTGAGAAGCGCTGCGGTGCCCTGGATGTGGTCTTCGTCATCGACAGCTCTGAGAGTATTGGC
TACACCAACTTCACCTTGGAGAAGAACTTTGTCATCAATGTGGTCAACAGGCTGGGCGCCATTG
CCAAGGACCCCAAGTCTGAAACGGGTACACGTGTGGGTGTGGTACAGTACAGCCATGAGGGCAC
CTTTGAGGCCATCCGGCTGGACGACGAGCGGGTCAACTCCCTGTCCAGTTTCAAGGAGGCCGTC
AAAAACCTTGAGTGGATTGCCGGCGGCACTTGGACGCCCTCTGCCCTCAAGTTCGCCTATAATC
AGCTCATCAAAGAGAGCCGGCGCCAGAAGACCCGGGTGTTCGCAGTGGTCATCACAGATGGGCG
CCATGACCCTCGAGATGATGACCTCAATCTTCGGGCACTGTGTGACCGAGACGTCACCGTGACA
GCCATCGGCATCGGTGACATGTTCCACGAGACCCACGAGAGCGAGAACCTCTACTCCATCGCCT
GTGACAAGCCCCAGCAGGTGCGCAACATGACGCTGTTCTCTGACCTGGTGGCCGAGAAATTCAT
CGATGACATGGAAGACGTCCTTTGTCCGGACCCCCAGATCGTGTGTCCAGAACTTCCCTGCCAA
ACAGAGCTCTATGTGGCCCAGTGCACACAACGGCCCGTGGACATTGTCTTCCTGCTGGATGGCT
CGGAGCGGCTGGGCGAGCAGAACTTCTACAAGGCACGGCGCTTCGTGGAGGAGGTGTCACGGCG
CCTGACTCTGGCACGAAGGGATGACGACCCACTCAATGCCCGCATGGCCCTGTTGCAGTATGGA
AGCCAGAACCAGCAACAGGTGGCCTTCCCGTTGACCTACAATGTGACCACCATCCACGAGGCCC
TGGAGAGAACCACCTACCTCAATTCTTTCTCGCACGTGGGCACAGGCATCGTGCACGCCATCAA
CAACGTGGTGCGGGGGGCACGGGGTGGGGCCCGGCGTCACGCGGAGCTGTCCTTCGTCTTCCTC
ACGGACGGCGTCACGGGCAACGACAGCCTGGAGGAGTCCGTACACTCCATGCGTAAGCAGAATG
TGGTGCCCACCGTGGTCGCTGTGGGTGGTGATGTGGACATGGATGTACTTACCAAGATCAGCCT
GGGTGACAGGGCGGCCATCTTCCGGGAGAAAGACTTCGACAGTCTAGCCCAGCCCAGCTTCTTC
GACAGGTTCATCCGCTGGATCTGTTAGCGCCGCCATGCTCTACCATCTCTTGACCATTTCCCAT
CTGTGGTGCTACTAGGACCCTAGCCAGTCCCAGCTAGACGGTACACTTGGGTCTTTCTAGAAAG
TGAAAGCCCTTCTCCCAAGGTCAGGACAGAAGGACTCTGAACCCAAAGCCCCTTCCCCACCTTC
GGCTCCCTTGGCTTCCCCTCCCCACATCTCCAGCCTACCTATACCTTGCTCTCAAACACTGGAG
GACCCCAGAGTCTTCCCACTGCCCATTTCCCACAGCCTCTGCCCTTCCACTTCCGTTTCTCCTT
CATGCATCCGCTAGTCCCTTCTGAAGGCCTGCACCAGTTGTGCCCAGGGCCCTGTCTTTCTCTA
CCCGTTATTTCCTATCTCAGGAGATCAACTCTGAGAGCACCATGTCACATGCCCAATGGCCCAA
TAAAGGTTTTGAGCCTCAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_006256300 ⟹ XP_006256362

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	20	12,021,676 - 12,047,478 (+)	NCBI
Rnor_6.0	20	12,773,472 - 12,799,233 (+)	NCBI
Rnor_5.0	20	14,931,484 - 14,959,214 (+)	NCBI

Sequence:

show sequence

TTCAGTCCCGGGCCGCGCCTGGGTCCCCTCCCTCCTGCCCACTCGGCGCCCGCACCTCGGGCCG
TCAGGACCCGAGCTGTCCTCGGAAGTACCCAGACGTCCTCTCCAAGCCAGGACATCAGGGCACA
TGACGACTACTACCAAGATGCTCCAGGGTTCTTTTTCTGTGCTCCTGCTTGGGGGACTCTTGGG
GGTCCTCCATGCCCAGCAGCAGGAAGCCATCTCACCTGATATCTCTACTACTGACAGGAACAAC
AACTGTCCAGAGAAGGCTGACTGCCCAGTCAACGTGTACTTCGTGTTGGACACCTCGGAGAGCG
TGGCCATGCAGTCCCCCACAGACAGCCTGCTTTATCACATGCAGCAGTTCGTACCACAATTTAT
CAGCCAGCTGCAGAACGAGTTCTACCTGGAGCAGGTGGCCCTGAGCTGGCGCTATGGTGGCCTA
CACTTCTCGGACCAGGTGGAGGTGTTCAGCCCCCCAGGCAGCGACCGGGCCTCCTTCACTAAGA
GCCTACAAGGCATCCGCTCCTTCCGCAGGGGCACCTTCACTGACTGTGCCTTGGCCAACATGAC
CCAGCAGATCCGGCAGCACGTAGGCCGGGGTGTAGTCAACTTTGCCGTGGTCATCACCGATGGC
CACGTCACAGGCAATCCCTGTGGGGGCATCAAAATGCAGGCTGAGCGTGCCCGCGAGGAGGGCA
TCCGGCTCTTTGCCGTGGCCCCCAATAGGAACCTAAATGAACAAGGCCTGCGGGATATCGCCAA
CACCCCACATGAGCTATACCGAAACAACTATGCCACCATGCGACCTGACTCTACTGAGATTGAC
CAGGACACCATCAACCGCATCATCAAGGTCATGAAACATGAAGCCTACGGAGAGTGCTACAAGG
TGAGCTGCCTGGAGATTCCGGGACCCCACGGACCCAAGGGTTACCGAGGACAGAAGGGCGCCAA
GGGCAACATGGGCGAGCCAGGAGAACCTGGACAGAAAGGACGACAGGGAGACCCTGGCATTGAA
GGCCCCATTGGATTCCCAGGACCCAAGGGTGTGCCTGGCTTCAAGGGAGAGAAGGGTGAATTCG
GATCAGATGGTCGGAAGGGAGCTCCGGGTCTAGCAGGCAAGAACGGAACAGATGGACAGAAGGG
CAAACTGGGCCGTATTGGGCCTCCTGGTTGCAAGGGAGACCCGGGAAGTCGGGGCCCCGATGGA
TACCCCGGAGAAGCTGGAAGCCCGGGAGAGCAAGGAGACCAAGGTGCCAAGGGGGACTCTGGCC
GCCCAGGACGCAGGGGACCACCAGGAAATCCTGGAGACAAAGGAAGCAAGGGATATCGAGGCAA
CAGTGGAGCTCCCGGAAGTCCAGGAGTGAAAGGAGGCAAGGGAGGGCCTGGCCCCCGTGGACCA
AAAGGAGAGCCTGGACGCAGGGGAGATCCTGGGACCAAGGGCGGCCCGGGCAGTGATGGTCCAA
AGGGGGAGAAGGGAGACCCTGGTCCTGAGGGGCCACGAGGTCTGGCTGGAGAAATCGGCAGTAA
AGGAGCCAAGGGAGACAGAGGTTTGCCTGGACCCAGAGGCCCCCAGGGAGCTCTTGGGGAGCCA
GGGAAGCAGGGATCTCGGGGAGACCCTGGGGATGCTGGGCCTCGAGGAGATTCAGGACAGCCAG
GACCCAAGGGAGATCCTGGAAGGCCTGGATTCAGCTACCCAGGACCCCGAGGGACACCCGGTGA
AAAAGGCGAGCCCGGCCCACCAGGCCCTGAGGGAGGCCGAGGAGACTTTGGTCTGAAAGGAGCA
CCCGGACGGAAGGGAGAAAAAGGAGAGCCAGCTGATCCTGGTCCCCCTGGTGAACCTGGCCCTC
GGGGGCCAAGAGGAATCCCAGGACCTGAGGGAGAACCCGGCCCTCCAGGAGATCCTGGTCTCAC
GGAATGTGACGTCATGACCTATGTGAGGGAGACCTGTGGGTGCTGTGACTGTGAGAAGCGCTGC
GGTGCCCTGGATGTGGTCTTCGTCATCGACAGCTCTGAGAGTATTGGCTACACCAACTTCACCT
TGGAGAAGAACTTTGTCATCAATGTGGTCAACAGGCTGGGCGCCATTGCCAAGGACCCCAAGTC
TGAAACGGGTACACGTGTGGGTGTGGTACAGTACAGCCATGAGGGCACCTTTGAGGCCATCCGG
CTGGACGACGAGCGGGTCAACTCCCTGTCCAGTTTCAAGGAGGCCGTCAAAAACCTTGAGTGGA
TTGCCGGCGGCACTTGGACGCCCTCTGCCCTCAAGTTCGCCTATAATCAGCTCATCAAAGAGAG
CCGGCGCCAGAAGACCCGGGTGTTCGCAGTGGTCATCACAGATGGGCGCCATGACCCTCGAGAT
GATGACCTCAATCTTCGGGCACTGTGTGACCGAGACGTCACCGTGACAGCCATCGGCATCGGTG
ACATGTTCCACGAGACCCACGAGAGCGAGAACCTCTACTCCATCGCCTGTGACAAGCCCCAGCA
GGTGCGCAACATGACGCTGTTCTCTGACCTGGTGGCCGAGAAATTCATCGATGACATGGAAGAC
GTCCTTTGTCCGGACCCCCAGATCGTGTGTCCAGAACTTCCCTGCCAAACAGATGAACCATGGC
CCGGGAACAAGCCCCCGGTCACCTTCCTCCGCACGGAAGAGGGTCCAGACCCCACCTTCCCCAA
GACCATCCCCCTGATCCAGCAGTTGCTAAACGCCACGGAGTTCACACAGAACCCAGCTGCCTAC
TCCCAACTGGTGGCTGTGATGGTCTACACCGCCGAGAGGGCCAAGTTCTCCACAGGGGTCGAGC
GGCAGGACTGGATGCAGCTGTTCATTGACACCTTTAAACTGGTGCACAGGGATATCACAGGGGA
CCCAGAGAGCGTGCTGGCACTCTGCTAAAGCTTCGGGCTCACTGCGGGCAGATAGCCAGATCTA
ACCCCTCATTTCTTTTAGATTCCCAGGGCTGAGGCCTTAGGCAGTAGGAACCTAGGAACTGGCC
CTCCCACTCCTGAGGCCAGAAGTATAGAACCTTGTGTCTTTAATATGACACTCTCTGAAGGGTC
CCTCCTAGTTCCTCCAGCCTCTGGTAGAAATTCCATCCTTGTGCTTGTGGGCACACCACTCCAG
TATCACTTCTATTTCCCCATAGGCTCTTTTCTTTGTATCCCCATGTCCCTCCTCCTTTTCCTCT
TCCTCTTCCTCCTCCTTCTCTCCCCTCTCCTCTTCCTCCTCCTTCTCTTCTTCCTCCTTCTCTC
TCTTCTTCCTCTTCCTCCTCCTCTTCCTCCTCCTCTCCCTTTTTCTCCCTCTTCCTCCTCCTCT
TCCTCTCATGTTTTACATTTTGTTTTGGGAGATGAGGTTTCTCTGTTTCACAGCCTTGACTGTT
CTGGAACTTGCTCTGTAGGCCTGAAACTCACAGAGCTCCCCCTGCTTCTGCCCCACGCCGCCAC
CCCCAGTGCTGGGATTAAAAAAAAAAAAAGGCATGCTCTCTCGTGCCCCTCTTTGCTCTGAGGA
CATCAGTGACCGAAGGCTCACCTTAAGCCCCAGAAGCTCACATGTGGCAAAGGGCTGTACTGCT
GGGATTAGGTTAAGGTTCATGAGATGTAAATTTCTGGGCATCTCTCAGCAGAGCACATCACCTC
AGTTCAGCTGAGTCCTGTGTTTGAGAGCACAGATGGGGGTGGTGCTATTTGAATGCTTGGGAAG
ATCCCCCTGTCCTGGTCCTTTCTGCGTTCTGATTGAGCTCAAGGGGTCTCATCAGGCTAGACGG
ATGTCCTCCACCCCATCTGTGCCCCTCTCTCCCAGGGTGAGGCTTACCCAGTCTCCTCCAGGCC
CTGGAGATGTTGATGTTGAGGGAAAGTGCTCAAGCCAGCAGCCCCCACTGTCTGTGTGCCTCTG
GGCTTGTGCTAATAACTGAGGGAGTGGGTGAGTTGTGAGGAGCCAGGAGATCCAGTAGTCCCTC
AAAATTTTCTGGAGCAGATTTCAGGGATTGCGGGTACTACATAAGGTTTTCGACTAATATGCTC
AGTAGGAAAGACCCTGCCCATTGAGGCACTACCCGACTCGGGGCTCAGACTCAGAGGTAGTGAG
CGATTGTAAACATTTTATAAAGAGATGAAACGTTTAACTGTG

hide sequence

Protein Sequences


Protein RefSeqs	NP_001094211	(Get FASTA)	NCBI Sequence Viewer
	XP_006256362	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH89923	(Get FASTA)	NCBI Sequence Viewer
	EDL97135	(Get FASTA)	NCBI Sequence Viewer
	EDL97136	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_001094211 ⟸ NM_001100741
- Peptide Label:	precursor
- UniProtKB:	F1LNH3 (UniProtKB/TrEMBL), Q5EB88 (UniProtKB/TrEMBL)
- Sequence:	show sequence MTTTTKMLQGSFSVLLLGGLLGVLHAQQQEAISPDISTTDRNNNCPEKADCPVNVYFVLDTSES VAMQSPTDSLLYHMQQFVPQFISQLQNEFYLEQVALSWRYGGLHFSDQVEVFSPPGSDRASFTK SLQGIRSFRRGTFTDCALANMTQQIRQHVGRGVVNFAVVITDGHVTGNPCGGIKMQAERAREEG IRLFAVAPNRNLNEQGLRDIANTPHELYRNNYATMRPDSTEIDQDTINRIIKVMKHEAYGECYK VSCLEIPGPHGPKGYRGQKGAKGNMGEPGEPGQKGRQGDPGIEGPIGFPGPKGVPGFKGEKGEF GSDGRKGAPGLAGKNGTDGQKGKLGRIGPPGCKGDPGSRGPDGYPGEAGSPGEQGDQGAKGDSG RPGRRGPPGNPGDKGSKGYRGNSGAPGSPGVKGGKGGPGPRGPKGEPGRRGDPGTKGGPGSDGP KGEKGDPGPEGPRGLAGEIGSKGAKGDRGLPGPRGPQGALGEPGKQGSRGDPGDAGPRGDSGQP GPKGDPGRPGFSYPGPRGTPGEKGEPGPPGPEGGRGDFGLKGAPGRKGEKGEPADPGPPGEPGP RGPRGIPGPEGEPGPPGDPGLTECDVMTYVRETCGCCDCEKRCGALDVVFVIDSSESIGYTNFT LEKNFVINVVNRLGAIAKDPKSETGTRVGVVQYSHEGTFEAIRLDDERVNSLSSFKEAVKNLEW IAGGTWTPSALKFAYNQLIKESRRQKTRVFAVVITDGRHDPRDDDLNLRALCDRDVTVTAIGIG DMFHETHESENLYSIACDKPQQVRNMTLFSDLVAEKFIDDMEDVLCPDPQIVCPELPCQTELYV AQCTQRPVDIVFLLDGSERLGEQNFYKARRFVEEVSRRLTLARRDDDPLNARMALLQYGSQNQQ QVAFPLTYNVTTIHEALERTTYLNSFSHVGTGIVHAINNVVRGARGGARRHAELSFVFLTDGVT GNDSLEESVHSMRKQNVVPTVVAVGGDVDMDVLTKISLGDRAAIFREKDFDSLAQPSFFDRFIR WIC hide sequence

RefSeq Acc Id:

XP_006256362 ⟸ XM_006256300

- Peptide Label:

isoform X1

- Sequence:

show sequence

MTTTTKMLQGSFSVLLLGGLLGVLHAQQQEAISPDISTTDRNNNCPEKADCPVNVYFVLDTSES
VAMQSPTDSLLYHMQQFVPQFISQLQNEFYLEQVALSWRYGGLHFSDQVEVFSPPGSDRASFTK
SLQGIRSFRRGTFTDCALANMTQQIRQHVGRGVVNFAVVITDGHVTGNPCGGIKMQAERAREEG
IRLFAVAPNRNLNEQGLRDIANTPHELYRNNYATMRPDSTEIDQDTINRIIKVMKHEAYGECYK
VSCLEIPGPHGPKGYRGQKGAKGNMGEPGEPGQKGRQGDPGIEGPIGFPGPKGVPGFKGEKGEF
GSDGRKGAPGLAGKNGTDGQKGKLGRIGPPGCKGDPGSRGPDGYPGEAGSPGEQGDQGAKGDSG
RPGRRGPPGNPGDKGSKGYRGNSGAPGSPGVKGGKGGPGPRGPKGEPGRRGDPGTKGGPGSDGP
KGEKGDPGPEGPRGLAGEIGSKGAKGDRGLPGPRGPQGALGEPGKQGSRGDPGDAGPRGDSGQP
GPKGDPGRPGFSYPGPRGTPGEKGEPGPPGPEGGRGDFGLKGAPGRKGEKGEPADPGPPGEPGP
RGPRGIPGPEGEPGPPGDPGLTECDVMTYVRETCGCCDCEKRCGALDVVFVIDSSESIGYTNFT
LEKNFVINVVNRLGAIAKDPKSETGTRVGVVQYSHEGTFEAIRLDDERVNSLSSFKEAVKNLEW
IAGGTWTPSALKFAYNQLIKESRRQKTRVFAVVITDGRHDPRDDDLNLRALCDRDVTVTAIGIG
DMFHETHESENLYSIACDKPQQVRNMTLFSDLVAEKFIDDMEDVLCPDPQIVCPELPCQTDEPW
PGNKPPVTFLRTEEGPDPTFPKTIPLIQQLLNATEFTQNPAAYSQLVAVMVYTAERAKFSTGVE
RQDWMQLFIDTFKLVHRDITGDPESVLALC

hide sequence

RefSeq Acc Id:

ENSRNOP00000001695 ⟸ ENSRNOT00000001695

Protein Domains

VWFA

Transcriptome

eQTL		View at Phenogen
WGCNA		View at Phenogen
Tissue/Strain Expression		View at Phenogen

Promoters

RGD ID:

13701513

Promoter ID:

EPDNEW_R12037

Type:

multiple initiation site

Name:

Col6a2_1

Description:

collagen type VI alpha 2 chain

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	20	12,773,512 - 12,773,572	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

ACI/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

ACI/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

BBDP/Wor (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

BN/SsN (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Buf/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

COP/CrCrl (MCW & UW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob) University of Wisconsin (Dr. James Shull)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Charles River Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)

F344/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

F344/NRrrc (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

FHH/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHH/EurMcwi (RGD)

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CSV

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

FHL/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHL/EurMcwi (RGD)

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CSV

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

GH/OmrMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

GK/Ox (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LE/Stm (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/Crl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/NCrlBR (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LH/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LL/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LN/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

M520/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

MHS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MNS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MR/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

SBH/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBH/Ygl sequenced by MCW

SBH/Ygl (RGD)

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CSV

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SBN/Ygl (MCW)

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CSV

TAB

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBN/Ygl sequenced by MCW

SBN/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHR/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHRSP/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SR/JrHsd (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Harlan Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SR/JrHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/Jr (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/JrHsdMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SS/JrHsdMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WAG/Rij (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

WKY/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WN/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Damaging Variants

Assembly: Rnor_5.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
20	14958559	14958560	C	T	snv	WKY/NCrl (KNAW), WKY/Gcrc (KNAW), WKY/NHsd (KNAW), GK/Ox (KNAW), WKY/N (KNAW)
20	14958739	14958740	C	A	snv	LL/MavRrrc (KNAW)

Assembly: Rnor_6.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
20	12800524	12800525	C	T	snv	GK/Ox (RGD), WKY/Gcrc (RGD), WKY/NHsd (RGD)
20	12800704	12800705	C	A	snv	LL/MavRrrc (RGD)

Assembly: RGSC_v3.4

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
20	12463857	12463858	C	T	snv	WKY/Gcrc (ICL), HCR/2Mco (UMich), HCR/1Mco (UMich), GK/Ox (ICL), LCR/2Mco (UMich), WKY/NHsd (ICL), WKY/NCrl (ICL), LCR/1Mco (UMich)
20	12464037	12464038	C	A	snv	LL/MavRrrc (ICL)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1305585	AgrOrtholog
Ensembl Genes	ENSRNOG00000001254	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000001695	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000001695	ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH	3.40.50.410	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7306918	IMAGE-MGC_LOAD
InterPro	Collagen	UniProtKB/TrEMBL
	VWF_A	UniProtKB/TrEMBL
	vWFA_dom_sf	UniProtKB/TrEMBL
KEGG Report	rno:361821	UniProtKB/TrEMBL
MGC_CLONE	MGC:109204	IMAGE-MGC_LOAD
NCBI Gene	361821	ENTREZGENE
Pfam	Collagen	UniProtKB/TrEMBL
	VWA	UniProtKB/TrEMBL
PhenoGen	Col6a2	PhenoGen
PROSITE	VWFA	UniProtKB/TrEMBL
SMART	VWA	UniProtKB/TrEMBL
Superfamily-SCOP	SSF53300	UniProtKB/TrEMBL
UniProt	F1LNH3	ENTREZGENE, UniProtKB/TrEMBL
	Q5EB88	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-07-27	Col6a2	collagen type VI alpha 2 chain	Col6a2	collagen, type VI, alpha 2	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-04-25	Col6a2	collagen, type VI, alpha 2	Col6a2	procollagen, type VI, alpha 2	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-12-06	Col6a2	procollagen, type VI, alpha 2	Col6a2_predicted	procollagen, type VI, alpha 2 (predicted)	Symbol and Name updated	1559027	APPROVED
2005-01-12	Col6a2_predicted	procollagen, type VI, alpha 2 (predicted)			Symbol and Name status set to approved	70820	APPROVED

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 - KEGG (archival)

Imported Annotations - PID (archival)