Vwa5b2 (von Willebrand factor A domain containing 5B2) - Rat Genome Database

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Gene: Vwa5b2 (von Willebrand factor A domain containing 5B2) Rattus norvegicus
Analyze
Symbol: Vwa5b2
Name: von Willebrand factor A domain containing 5B2
RGD ID: 1564491
Description: Orthologous to human VWA5B2 (von Willebrand factor A domain containing 5B2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; amphetamine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: hypothetical LOC303812; LOC303812; RGD1564491; von Willebrand factor A domain-containing protein 5B2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
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
mRatBN7.21180,306,067 - 80,323,220 (-)NCBI
Rnor_6.0 Ensembl1183,992,076 - 84,008,946 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01183,991,793 - 84,008,946 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01187,064,115 - 87,081,268 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41182,535,711 - 82,552,800 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1179,146,019 - 79,162,890 (-)NCBICelera
Cytogenetic Map11q23NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:25002582  


Genomics

Comparative Map Data
Vwa5b2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21180,306,067 - 80,323,220 (-)NCBI
Rnor_6.0 Ensembl1183,992,076 - 84,008,946 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01183,991,793 - 84,008,946 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01187,064,115 - 87,081,268 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41182,535,711 - 82,552,800 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1179,146,019 - 79,162,890 (-)NCBICelera
Cytogenetic Map11q23NCBI
VWA5B2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl3184,230,429 - 184,242,329 (+)EnsemblGRCh38hg38GRCh38
GRCh383184,229,585 - 184,242,329 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh373183,948,141 - 183,960,117 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363185,431,011 - 185,442,814 (+)NCBINCBI36hg18NCBI36
Celera3182,389,082 - 182,400,881 (+)NCBI
Cytogenetic Map3q27.1NCBI
HuRef3181,354,091 - 181,367,086 (+)NCBIHuRef
CHM1_13183,912,639 - 183,924,539 (+)NCBICHM1_1
Vwa5b2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391620,408,174 - 20,424,128 (+)NCBIGRCm39mm39
GRCm39 Ensembl1620,408,221 - 20,424,127 (+)Ensembl
GRCm381620,589,428 - 20,605,378 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1620,589,471 - 20,605,377 (+)EnsemblGRCm38mm10GRCm38
MGSCv371620,589,655 - 20,605,450 (+)NCBIGRCm37mm9NCBIm37
MGSCv361620,503,689 - 20,511,991 (+)NCBImm8
Celera1621,153,658 - 21,169,453 (+)NCBICelera
Cytogenetic Map16A3NCBI
Vwa5b2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542023,242,396 - 23,251,352 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542023,243,197 - 23,253,202 (-)NCBIChiLan1.0ChiLan1.0
VWA5B2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.13189,747,074 - 189,759,699 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3189,747,903 - 189,764,378 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v03181,263,976 - 181,276,843 (+)NCBIMhudiblu_PPA_v0panPan3
VWA5B2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13417,125,012 - 17,135,285 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3417,123,642 - 17,135,287 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3421,210,104 - 21,221,672 (+)NCBI
ROS_Cfam_1.03417,031,429 - 17,042,994 (+)NCBI
UMICH_Zoey_3.13417,068,759 - 17,080,330 (+)NCBI
UNSW_CanFamBas_1.03417,064,626 - 17,076,186 (+)NCBI
UU_Cfam_GSD_1.03417,294,854 - 17,306,415 (+)NCBI
Vwa5b2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602119,530,349 - 119,543,840 (-)NCBI
SpeTri2.0NW_0049365785,622,201 - 5,634,807 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VWA5B2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1155,182,536 - 5,194,820 (-)NCBI
ChlSab1.1 Ensembl155,182,830 - 5,193,998 (-)Ensembl
Vwa5b2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473072,343,400 - 72,354,625 (-)NCBI

Position Markers
RH118405  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21180,305,753 - 80,305,906 (+)MAPPER
Rnor_6.01183,991,480 - 83,991,632NCBIRnor6.0
Rnor_5.01187,063,802 - 87,063,954UniSTSRnor5.0
RGSC_v3.41182,535,115 - 82,535,267UniSTSRGSC3.4
Celera1179,145,423 - 79,145,575UniSTS
Cytogenetic Map11q23UniSTS
RH130739  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21180,306,086 - 80,306,274 (+)MAPPER
Rnor_6.01183,991,813 - 83,992,000NCBIRnor6.0
Rnor_5.01187,064,135 - 87,064,322UniSTSRnor5.0
RGSC_v3.41182,535,448 - 82,535,635UniSTSRGSC3.4
Celera1179,145,756 - 79,145,943UniSTS
RH 3.4 Map11658.0UniSTS
Cytogenetic Map11q23UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111901627290463843Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112831466586994795Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)113043533986714631Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)114309033886714631Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)114658320986714631Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114726402386994547Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114726402386994547Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115785881090463843Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115994302390463843Rat
4889521Gluco62Glucose level QTL 622.820.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)116010984287141948Rat
631506Bp104Blood pressure QTL 1042.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)116265336586714475Rat
70208Niddm22Non-insulin dependent diabetes mellitus QTL 223.61blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)116265336586714483Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)116449467190463843Rat
1549848Bvd6Brain ventricular dilatation QTL 63.10.0001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)116934231986312439Rat
1354593Stl12Serum triglyceride level QTL 123.36blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)116964970890463843Rat
1354656Bvd3Brain ventricular dilatation QTL 33.640.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)117272002986994795Rat
10450831Scl80Serum cholesterol level QTL 804.70.01blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)118035840887200449Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:50
Count of miRNA genes:48
Interacting mature miRNAs:50
Transcripts:ENSRNOT00000037612
Prediction methods:Miranda, Rnahybrid
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 50
Low 3 15 36 20 19 20 8 11 24 31 38 11 8
Below cutoff 28 13 13 13 4 3

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001134535 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006248571 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597969 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597970 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597971 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597972 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597973 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597974 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597975 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088278 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088279 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088280 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088281 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088283 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088284 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088285 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088286 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001840417 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005491021 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC110855 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473999 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000222 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000037612   ⟹   ENSRNOP00000035500
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1183,992,076 - 84,008,946 (-)Ensembl
RefSeq Acc Id: NM_001134535   ⟹   NP_001128007
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21180,306,350 - 80,323,220 (-)NCBI
Rnor_6.01183,992,076 - 84,008,946 (-)NCBI
Rnor_5.01187,064,115 - 87,081,268 (-)NCBI
RGSC_v3.41182,535,711 - 82,552,800 (-)RGD
Celera1179,146,019 - 79,162,890 (-)RGD
Sequence:
RefSeq Acc Id: XM_006248571   ⟹   XP_006248633
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21180,306,067 - 80,318,038 (-)NCBI
Rnor_6.01183,991,793 - 84,003,637 (-)NCBI
Rnor_5.01187,064,115 - 87,081,268 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017597969   ⟹   XP_017453458
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21180,306,067 - 80,322,551 (-)NCBI
Rnor_6.01183,991,793 - 84,008,030 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017597970   ⟹   XP_017453459
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01183,991,793 - 84,008,018 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017597971   ⟹   XP_017453460
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01183,991,793 - 84,008,030 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017597972   ⟹   XP_017453461
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21180,306,353 - 80,323,215 (-)NCBI
Rnor_6.01183,991,793 - 84,008,066 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017597973   ⟹   XP_017453462
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01183,991,793 - 84,008,030 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017597974   ⟹   XP_017453463
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21180,306,067 - 80,321,059 (-)NCBI
Rnor_6.01183,991,793 - 84,006,730 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017597975   ⟹   XP_017453464
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01183,992,679 - 84,008,030 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039088278   ⟹   XP_038944206
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21180,306,067 - 80,322,551 (-)NCBI
RefSeq Acc Id: XM_039088279   ⟹   XP_038944207
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21180,306,067 - 80,322,551 (-)NCBI
RefSeq Acc Id: XM_039088280   ⟹   XP_038944208
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21180,306,353 - 80,322,552 (-)NCBI
RefSeq Acc Id: XM_039088281   ⟹   XP_038944209
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21180,306,353 - 80,322,551 (-)NCBI
RefSeq Acc Id: XM_039088283   ⟹   XP_038944211
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21180,306,908 - 80,322,554 (-)NCBI
RefSeq Acc Id: XM_039088284   ⟹   XP_038944212
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21180,310,572 - 80,322,554 (-)NCBI
RefSeq Acc Id: XM_039088285   ⟹   XP_038944213
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21180,310,573 - 80,322,552 (-)NCBI
RefSeq Acc Id: XM_039088286   ⟹   XP_038944214
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21180,306,067 - 80,322,551 (-)NCBI
RefSeq Acc Id: XR_001840417
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01183,992,535 - 84,008,030 (-)NCBI
Sequence:
RefSeq Acc Id: XR_005491021
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21180,306,760 - 80,322,554 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001128007   ⟸   NM_001134535
- UniProtKB: D4A7U5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006248633   ⟸   XM_006248571
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017453461   ⟸   XM_017597972
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017453462   ⟸   XM_017597973
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017453460   ⟸   XM_017597971
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017453458   ⟸   XM_017597969
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017453459   ⟸   XM_017597970
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017453463   ⟸   XM_017597974
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017453464   ⟸   XM_017597975
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: ENSRNOP00000035500   ⟸   ENSRNOT00000037612
RefSeq Acc Id: XP_038944206   ⟸   XM_039088278
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038944214   ⟸   XM_039088286
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038944207   ⟸   XM_039088279
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038944208   ⟸   XM_039088280
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038944209   ⟸   XM_039088281
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038944211   ⟸   XM_039088283
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038944212   ⟸   XM_039088284
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038944213   ⟸   XM_039088285
- Peptide Label: isoform X8
Protein Domains
VIT

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)
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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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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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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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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)
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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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1564491 AgrOrtholog
Ensembl Genes ENSRNOG00000001707 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000035500 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000037612 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.410 UniProtKB/TrEMBL
InterPro VIT UniProtKB/TrEMBL
  VWF_A UniProtKB/TrEMBL
  vWFA_dom_sf UniProtKB/TrEMBL
KEGG Report rno:303812 UniProtKB/TrEMBL
NCBI Gene 303812 ENTREZGENE
Pfam VIT_2 UniProtKB/TrEMBL
  VWA_3 UniProtKB/TrEMBL
PhenoGen Vwa5b2 PhenoGen
PROSITE VIT UniProtKB/TrEMBL
Superfamily-SCOP SSF53300 UniProtKB/TrEMBL
UniProt D4A7U5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-09 Vwa5b2  von Willebrand factor A domain containing 5B2  RGD1564491  RGD1564491   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1564491  RGD1564491   RGD1564491_predicted  RGD1564491 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1564491_predicted  RGD1564491 (predicted)  LOC303812  hypothetical LOC303812  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC303812  hypothetical LOC303812      Symbol and Name status set to provisional 70820 PROVISIONAL