Bves (blood vessel epicardial substance) - Rat Genome Database

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Gene: Bves (blood vessel epicardial substance) Rattus norvegicus
Analyze
Symbol: Bves
Name: blood vessel epicardial substance
RGD ID: 1561100
Description: Predicted to have cAMP binding activity and structural molecule activity. Predicted to be involved in several processes, including animal organ development; positive regulation of receptor recycling; and response to ischemia. Predicted to localize to several cellular components, including bicellular tight junction; lateral plasma membrane; and sarcolemma. Human ortholog(s) of this gene implicated in autosomal recessive limb-girdle muscular dystrophy type 2X. Orthologous to human BVES (blood vessel epicardial substance); INTERACTS WITH 6-propyl-2-thiouracil; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Popdc1; popeye domain-containing 1; popeye domain-containing protein 1; popeye protein 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
mRatBN7.22048,819,241 - 48,860,282 (+)NCBI
Rnor_6.0 Ensembl2050,439,883 - 50,474,678 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02050,439,885 - 50,474,678 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02052,052,628 - 52,086,539 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42049,671,174 - 49,671,683 (+)NCBIRGSC3.4rn4RGSC3.4
Celera2051,164,981 - 51,200,377 (-)NCBICelera
Cytogenetic Map20q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References

Additional References at PubMed
PMID:10882522   PMID:12815060   PMID:16188940   PMID:17662479   PMID:18541910   PMID:20057356   PMID:22354168   PMID:24029230   PMID:24048452   PMID:24066022   PMID:26642364   PMID:27886395  


Genomics

Comparative Map Data
Bves
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22048,819,241 - 48,860,282 (+)NCBI
Rnor_6.0 Ensembl2050,439,883 - 50,474,678 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02050,439,885 - 50,474,678 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02052,052,628 - 52,086,539 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42049,671,174 - 49,671,683 (+)NCBIRGSC3.4rn4RGSC3.4
Celera2051,164,981 - 51,200,377 (-)NCBICelera
Cytogenetic Map20q13NCBI
BVES
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl6105,096,822 - 105,137,157 (-)EnsemblGRCh38hg38GRCh38
GRCh386105,096,822 - 105,137,157 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh376105,544,697 - 105,585,032 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 366105,651,390 - 105,691,236 (-)NCBINCBI36hg18NCBI36
Build 346105,651,393 - 105,690,914NCBI
Celera6106,167,189 - 106,206,693 (-)NCBI
Cytogenetic Map6q21NCBI
HuRef6102,987,978 - 103,028,002 (-)NCBIHuRef
CHM1_16105,806,724 - 105,846,753 (-)NCBICHM1_1
Bves
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391045,211,783 - 45,248,580 (+)NCBIGRCm39mm39
GRCm39 Ensembl1045,211,868 - 45,248,575 (+)Ensembl
GRCm381045,335,735 - 45,372,484 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1045,335,772 - 45,372,479 (+)EnsemblGRCm38mm10GRCm38
MGSCv371045,055,568 - 45,089,514 (+)NCBIGRCm37mm9NCBIm37
MGSCv361045,024,177 - 45,058,123 (+)NCBImm8
Celera1046,209,822 - 46,242,144 (+)NCBICelera
Cytogenetic Map10B2NCBI
cM Map1023.47NCBI
Bves
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541130,517,875 - 30,551,335 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541130,517,917 - 30,548,424 (-)NCBIChiLan1.0ChiLan1.0
BVES
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.16106,784,465 - 106,822,050 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6106,787,615 - 106,822,050 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v06102,915,148 - 102,951,141 (-)NCBIMhudiblu_PPA_v0panPan3
BVES
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11262,542,274 - 62,581,110 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1262,545,666 - 62,579,548 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1262,331,453 - 62,369,673 (-)NCBI
ROS_Cfam_1.01263,393,637 - 63,432,405 (-)NCBI
UMICH_Zoey_3.11262,748,894 - 62,787,110 (-)NCBI
UNSW_CanFamBas_1.01262,590,058 - 62,628,349 (-)NCBI
UU_Cfam_GSD_1.01262,868,831 - 62,907,346 (-)NCBI
Bves
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494697,512,420 - 97,548,660 (-)NCBI
SpeTri2.0NW_0049365641,791,733 - 1,823,421 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
BVES
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl171,314,274 - 71,360,176 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1171,316,354 - 71,360,255 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2180,636,881 - 80,681,079 (-)NCBISscrofa10.2Sscrofa10.2susScr3
BVES
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11368,668,248 - 68,704,661 (+)NCBI
ChlSab1.1 Ensembl1368,668,321 - 68,707,885 (+)Ensembl
Bves
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624952326,812 - 360,790 (-)NCBI

Position Markers
RH143305  
Rat AssemblyChrPosition (strand)SourceJBrowse
RH 3.4 Map11322.3UniSTS
Cytogenetic Map20q13UniSTS
RH143833  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22048,857,447 - 48,857,705 (+)MAPPER
Rnor_6.02050,474,654 - 50,474,911NCBIRnor6.0
Rnor_5.02052,086,515 - 52,086,772UniSTSRnor5.0
RGSC_v3.42049,671,659 - 49,671,916UniSTSRGSC3.4
Celera2051,164,748 - 51,165,005UniSTS
RH 3.4 Map20511.0UniSTS
Cytogenetic Map20q13UniSTS
BI294843  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22048,851,924 - 48,852,076 (+)MAPPER
Rnor_6.02050,468,999 - 50,469,150NCBIRnor6.0
Rnor_5.02052,081,772 - 52,081,923UniSTSRnor5.0
Celera2051,170,174 - 51,170,325UniSTS
RH 3.4 Map20502.9UniSTS
Cytogenetic Map20q13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201383430956205956Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201383430956205956Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201782709656205956Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)202085847056205956Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202660884356205956Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202660884356205956Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202660884356205956Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202671232356205956Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)203091348156205956Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:33
Count of miRNA genes:29
Interacting mature miRNAs:32
Transcripts:ENSRNOT00000066167
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 38 8 11 7 8
Low 3 5 13 10 6 10 71 24 29 11
Below cutoff 24 15 13 15 3 11 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000066167
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2050,439,883 - 50,474,678 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000076504
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2050,447,139 - 50,474,678 (+)Ensembl
RefSeq Acc Id: NM_001077590   ⟹   NP_001071058
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22048,822,312 - 48,857,472 (+)NCBI
Rnor_6.02050,439,885 - 50,474,678 (+)NCBI
Rnor_5.02052,052,628 - 52,086,539 (+)NCBI
RGSC_v3.42049,671,174 - 49,671,683 (+)RGD
Celera2051,164,981 - 51,200,377 (-)RGD
Sequence:
RefSeq Acc Id: XM_039098917   ⟹   XP_038954845
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22048,819,250 - 48,860,282 (+)NCBI
RefSeq Acc Id: XM_039098918   ⟹   XP_038954846
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22048,819,250 - 48,860,282 (+)NCBI
RefSeq Acc Id: XM_039098919   ⟹   XP_038954847
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22048,819,527 - 48,860,282 (+)NCBI
RefSeq Acc Id: XM_039098920   ⟹   XP_038954848
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22048,819,241 - 48,838,828 (+)NCBI
RefSeq Acc Id: XR_005497303
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22048,819,244 - 48,860,282 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001071058   ⟸   NM_001077590
- UniProtKB: Q3BCU4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_038954848   ⟸   XM_039098920
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038954846   ⟸   XM_039098918
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038954845   ⟸   XM_039098917
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038954847   ⟸   XM_039098919
- Peptide Label: isoform X1

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)
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
LL/MavRrrc (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
LN/MavRrrc (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
M520/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
MHS/Gib (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
MNS/Gib (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
MR/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
SBH/Ygl (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: 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)
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: 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)
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
SHRSP/Gcrc (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
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
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:1561100 AgrOrtholog
Ensembl Genes ENSRNOG00000043199 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000066167 ENTREZGENE
Gene3D-CATH 2.60.120.10 UniProtKB/Swiss-Prot
InterPro cNMP-bd-like UniProtKB/Swiss-Prot
  Popeye_prot UniProtKB/Swiss-Prot
  RmlC-like_jellyroll UniProtKB/Swiss-Prot
KEGG Report rno:365603 UniProtKB/Swiss-Prot
NCBI Gene 365603 ENTREZGENE
PANTHER PTHR12101 UniProtKB/Swiss-Prot
Pfam Popeye UniProtKB/Swiss-Prot
PhenoGen Bves PhenoGen
Superfamily-SCOP SSF51206 UniProtKB/Swiss-Prot
UniProt POPD1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-02-09 Bves  blood vessel epicardial substance      Symbol and Name status set to provisional 70820 PROVISIONAL