Col7a1 (collagen type VII alpha 1 chain) - Rat Genome Database

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Gene: Col7a1 (collagen type VII alpha 1 chain) Rattus norvegicus
Analyze
Symbol: Col7a1
Name: collagen type VII alpha 1 chain
RGD ID: 1311417
Description: Predicted to have identical protein binding activity. Predicted to be involved in endodermal cell differentiation. Predicted to localize to basement membrane and extracellular space. Human ortholog(s) of this gene implicated in autosomal dominant dystrophic epidermolysis bullosa; epidermolysis bullosa dystrophica; epidermolysis bullosa with congenital localized absence of skin and deformity of nails; nonsyndromic congenital nail disorder 8; and transient bullous dermolysis of the newborn. Orthologous to human COL7A1 (collagen type VII alpha 1 chain); PARTICIPATES IN syndecan signaling pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: collagen alpha-1(VII) chain; collagen, type VII, alpha 1; LOC301012; procollagen, type VII, alpha 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
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 AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28109,604,877 - 109,637,252 (+)NCBI
Rnor_6.0 Ensembl8117,694,605 - 117,726,844 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.08117,694,441 - 117,726,844 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.08117,046,218 - 117,078,589 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48113,971,207 - 114,003,445 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.18113,990,661 - 114,022,897 (+)NCBI
Celera8108,898,754 - 108,930,986 (+)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-phenylprop-2-enal  (ISO)
4,4'-sulfonyldiphenol  (ISO)
6-propyl-2-thiouracil  (EXP)
8-Br-cAMP  (ISO)
acetylsalicylic acid  (ISO)
acrylamide  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
butan-1-ol  (ISO)
C60 fullerene  (EXP)
carbon nanotube  (ISO)
cefaloridine  (EXP)
chloropicrin  (ISO)
clothianidin  (ISO)
cobalt dichloride  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) sulfate  (ISO)
cortisol  (ISO)
cyclosporin A  (ISO)
D-glucose  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
diazepam  (ISO)
dichloroacetic acid  (ISO)
dimethylarsinic acid  (ISO)
dioxygen  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
ethanol  (ISO)
folic acid  (ISO)
fucoxanthin  (ISO)
furan  (EXP)
glucose  (ISO)
graphite  (EXP)
indometacin  (ISO)
irinotecan  (ISO)
lead diacetate  (EXP)
manganese(II) chloride  (EXP)
methylmercury chloride  (EXP)
nickel atom  (ISO)
paclitaxel  (ISO)
paracetamol  (ISO)
phenylmercury acetate  (ISO)
progesterone  (ISO)
quercetin  (ISO)
SB 431542  (ISO)
Se-methyl-L-selenocysteine  (ISO)
Se-methylselenocysteine  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (ISO)
sodium dichromate  (ISO)
sodium fluoride  (ISO)
Soman  (EXP)
streptozocin  (ISO)
succimer  (ISO)
sunitinib  (ISO)
tert-butyl hydroperoxide  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
tributylstannane  (ISO)
triptonide  (ISO)
troglitazone  (ISO)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:18757743   PMID:19651211   PMID:21570975   PMID:22664934   PMID:23154389   PMID:23717576  


Genomics

Comparative Map Data
Col7a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28109,604,877 - 109,637,252 (+)NCBI
Rnor_6.0 Ensembl8117,694,605 - 117,726,844 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.08117,694,441 - 117,726,844 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.08117,046,218 - 117,078,589 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48113,971,207 - 114,003,445 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.18113,990,661 - 114,022,897 (+)NCBI
Celera8108,898,754 - 108,930,986 (+)NCBICelera
Cytogenetic Map8q32NCBI
COL7A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl348,564,073 - 48,595,329 (-)EnsemblGRCh38hg38GRCh38
GRCh38348,564,073 - 48,595,329 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37348,601,506 - 48,632,762 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36348,576,510 - 48,607,597 (-)NCBINCBI36hg18NCBI36
Build 34348,576,509 - 48,607,689NCBI
Celera348,557,241 - 48,588,335 (-)NCBI
Cytogenetic Map3p21.31NCBI
HuRef348,659,828 - 48,690,843 (-)NCBIHuRef
CHM1_1348,553,813 - 48,584,903 (-)NCBICHM1_1
Col7a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399108,782,654 - 108,813,943 (+)NCBIGRCm39mm39
GRCm39 Ensembl9108,782,654 - 108,813,943 (+)Ensembl
GRCm389108,953,586 - 108,984,875 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9108,953,586 - 108,984,875 (+)EnsemblGRCm38mm10GRCm38
MGSCv379108,855,790 - 108,886,920 (+)NCBIGRCm37mm9NCBIm37
MGSCv369108,810,682 - 108,841,812 (+)NCBImm8
Celera9108,511,705 - 108,542,813 (+)NCBICelera
Cytogenetic Map9F2NCBI
cM Map959.63NCBI
Col7a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_004955532650,913 - 681,186 (-)NCBIChiLan1.0ChiLan1.0
COL7A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1349,567,831 - 49,599,027 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl349,568,163 - 49,598,919 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0348,485,922 - 48,518,036 (-)NCBIMhudiblu_PPA_v0panPan3
COL7A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12040,519,121 - 40,550,305 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2040,519,378 - 40,552,935 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2040,436,737 - 40,467,232 (+)NCBI
ROS_Cfam_1.02041,004,719 - 41,035,678 (+)NCBI
UMICH_Zoey_3.12040,242,306 - 40,272,806 (+)NCBI
UNSW_CanFamBas_1.02040,647,074 - 40,677,568 (+)NCBI
UU_Cfam_GSD_1.02040,928,007 - 40,958,502 (+)NCBI
Col7a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560263,588,441 - 63,621,451 (-)NCBI
SpeTri2.0NW_004936529348,938 - 381,701 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL7A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11331,262,750 - 31,295,112 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21334,507,211 - 34,539,557 (-)NCBISscrofa10.2Sscrofa10.2susScr3
COL7A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1229,964,652 - 9,996,785 (-)NCBI
ChlSab1.1 Ensembl229,964,651 - 9,996,626 (-)Ensembl
Vero_WHO_p1.0NW_023666041157,089,010 - 157,121,213 (+)NCBI
Col7a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247302,569,510 - 2,599,959 (-)NCBI

Position Markers
AW209154  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28109,637,111 - 109,637,204 (+)MAPPER
Rnor_6.08117,726,704 - 117,726,796NCBIRnor6.0
Rnor_5.08117,078,449 - 117,078,541UniSTSRnor5.0
RGSC_v3.48114,003,305 - 114,003,397UniSTSRGSC3.4
Celera8108,930,846 - 108,930,938UniSTS
Cytogenetic Map8q32UniSTS
BI277776  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28109,636,975 - 109,637,170 (+)MAPPER
Rnor_6.08117,726,568 - 117,726,762NCBIRnor6.0
Rnor_5.08117,078,313 - 117,078,507UniSTSRnor5.0
RGSC_v3.48114,003,169 - 114,003,363UniSTSRGSC3.4
Celera8108,930,710 - 108,930,904UniSTS
RH 3.4 Map81192.0UniSTS
Cytogenetic Map8q32UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)89531047119211942Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810938911120496129Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)844458129118087517Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)850529480128036471Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)850529480128036471Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)850529480128036471Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)850529480128036471Rat
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)865717449128033050Rat
631653Bp125Blood pressure QTL 1253.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)872849686117849686Rat
631210Bw3Body weight QTL35.9mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight as a percentage of body weight (CMO:0000654)874917593121080545Rat
1300171Bp184Blood pressure QTL 1843.66arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)876103982127182642Rat
9590292Uminl3Urine mineral level QTL 33.620.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)878805083123805083Rat
8694446Bw170Body weight QTL 17012.070.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)878805083123805083Rat
8694200Abfw4Abdominal fat weight QTL 49.070.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)878805083123805083Rat
8694392Bw161Body weight QTL 1618.060.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)878805083123805083Rat
1549909Stresp11Stress response QTL 116.830.0019stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)880697934125697934Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)883894304128894304Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)889058229132243842Rat
2313400Anxrr25Anxiety related response QTL 25aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)895963141122354314Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8100873811133307652Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8100873811133307652Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)8102051964133307652Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)8104682575133307652Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)8104682575133307652Rat
724539Cm19Cardiac mass QTL 192.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)8107769005129956433Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:201
Count of miRNA genes:124
Interacting mature miRNAs:148
Transcripts:ENSRNOT00000027994
Prediction methods: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
Medium 14
Low 2 21 18 2 19 2 8 11 72 33 20 11 8
Below cutoff 1 22 25 25 25 2 2 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000027994   ⟹   ENSRNOP00000027994
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl8117,694,605 - 117,726,844 (+)Ensembl
RefSeq Acc Id: NM_001106858   ⟹   NP_001100328
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28109,605,013 - 109,637,252 (+)NCBI
Rnor_6.08117,694,605 - 117,726,844 (+)NCBI
Rnor_5.08117,046,218 - 117,078,589 (+)NCBI
RGSC_v3.48113,971,207 - 114,003,445 (+)RGD
Celera8108,898,754 - 108,930,986 (+)RGD
Sequence:
RefSeq Acc Id: XM_006243759   ⟹   XP_006243821
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08117,694,441 - 117,726,840 (+)NCBI
Rnor_5.08117,046,218 - 117,078,589 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039081240   ⟹   XP_038937168
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28109,604,877 - 109,637,249 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001100328 (Get FASTA)   NCBI Sequence Viewer  
  XP_038937168 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL77130 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001100328   ⟸   NM_001106858
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: XP_006243821   ⟸   XM_006243759
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000027994   ⟸   ENSRNOT00000027994
RefSeq Acc Id: XP_038937168   ⟸   XM_039081240
- Peptide Label: isoform X1
Protein Domains
Fibronectin type-III   VWFA

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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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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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311417 AgrOrtholog
Ensembl Genes ENSRNOG00000020579 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000027994 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000027994 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
  3.40.50.410 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/TrEMBL
  FN3_sf UniProtKB/TrEMBL
  FN_III UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  VWF_A UniProtKB/TrEMBL
  vWFA_dom_sf UniProtKB/TrEMBL
KEGG Report rno:301012 UniProtKB/TrEMBL
NCBI Gene 301012 ENTREZGENE
Pfam Collagen UniProtKB/TrEMBL
  fn3 UniProtKB/TrEMBL
  VWA UniProtKB/TrEMBL
PhenoGen Col7a1 PhenoGen
PROSITE FN3 UniProtKB/TrEMBL
  VWFA UniProtKB/TrEMBL
SMART FN3 UniProtKB/TrEMBL
  VWA UniProtKB/TrEMBL
Superfamily-SCOP FN_III-like UniProtKB/TrEMBL
  SSF53300 UniProtKB/TrEMBL
UniProt D3ZE04_RAT UniProtKB/TrEMBL
  R9THZ8_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-27 Col7a1  collagen type VII alpha 1 chain  Col7a1  collagen, type VII, alpha 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-16 Col7a1  collagen, type VII, alpha 1  Col7a1  procollagen, type VII, alpha 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Col7a1  procollagen, type VII, alpha 1   Col7a1_predicted  procollagen, type VII, alpha 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Col7a1_predicted  procollagen, type VII, alpha 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED