Nvl (nuclear VCP-like) - Rat Genome Database
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Gene: Nvl (nuclear VCP-like) Rattus norvegicus
Analyze
Symbol: Nvl
Name: nuclear VCP-like
RGD ID: 1311270
Description: Predicted to have ATP binding activity; ATPase activity; and preribosome binding activity. Predicted to be involved in several processes, including positive regulation of telomerase activity; regulation of protein localization to nucleolus; and ribosome biogenesis. Predicted to colocalize with nuclear exosome (RNase complex). Orthologous to human NVL (nuclear VCP like); PARTICIPATES IN ribosome biogenesis pathway; INTERACTS WITH (+)-schisandrin B; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC289323; nuclear valosin-containing protein-like
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
mRatBN7.21392,851,023 - 92,906,749 (-)NCBI
Rnor_6.0 Ensembl1399,410,026 - 99,468,778 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01399,410,026 - 99,468,783 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.013104,407,045 - 104,465,204 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41396,862,759 - 96,917,215 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11397,051,898 - 97,105,918 (-)NCBI
Celera1392,394,917 - 92,447,334 (-)NCBICelera
Cytogenetic Map13q26NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:15469983   PMID:16782053   PMID:19946888   PMID:22226966   PMID:22658674   PMID:26166824   PMID:26456651   PMID:29107693  


Genomics

Comparative Map Data
Nvl
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21392,851,023 - 92,906,749 (-)NCBI
Rnor_6.0 Ensembl1399,410,026 - 99,468,778 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01399,410,026 - 99,468,783 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.013104,407,045 - 104,465,204 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41396,862,759 - 96,917,215 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11397,051,898 - 97,105,918 (-)NCBI
Celera1392,394,917 - 92,447,334 (-)NCBICelera
Cytogenetic Map13q26NCBI
NVL
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1224,227,334 - 224,330,189 (-)EnsemblGRCh38hg38GRCh38
GRCh381224,227,345 - 224,330,187 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371224,415,047 - 224,517,874 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh371224,415,036 - 224,517,891 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361222,481,659 - 222,584,495 (-)NCBINCBI36hg18NCBI36
Build 341220,721,771 - 220,824,607NCBI
Celera1197,605,972 - 197,708,808 (-)NCBI
Cytogenetic Map1q42.11NCBI
HuRef1194,934,993 - 195,038,171 (-)NCBIHuRef
CHM1_11225,687,528 - 225,790,385 (-)NCBICHM1_1
Nvl
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391180,914,703 - 180,974,557 (-)NCBIGRCm39mm39
GRCm381181,087,138 - 181,144,214 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1181,087,138 - 181,144,204 (-)EnsemblGRCm38mm10GRCm38
MGSCv371183,023,554 - 183,074,288 (-)NCBIGRCm37mm9NCBIm37
MGSCv361182,930,098 - 182,980,832 (-)NCBImm8
Celera1188,160,290 - 188,211,164 (-)NCBICelera
Cytogenetic Map1H4NCBI
Nvl
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555201,011,621 - 1,062,286 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555201,010,966 - 1,069,176 (+)NCBIChiLan1.0ChiLan1.0
NVL
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11204,704,095 - 204,807,027 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1204,704,371 - 204,806,959 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01199,695,388 - 199,798,080 (-)NCBIMhudiblu_PPA_v0panPan3
NVL
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl740,041,394 - 40,131,823 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1740,041,692 - 40,131,984 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Nvl
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365261,274,760 - 1,381,997 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NVL
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1012,556,060 - 12,670,625 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11012,564,891 - 12,670,641 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
NVL
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1255,455,812 - 5,555,666 (+)NCBI
ChlSab1.1 Ensembl255,455,646 - 5,556,770 (+)Ensembl
Nvl
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248355,896,014 - 5,977,581 (-)NCBI

Position Markers
BE106505  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01399,412,494 - 99,412,646NCBIRnor6.0
Rnor_6.01399,421,865 - 99,422,017NCBIRnor6.0
Rnor_5.013104,417,555 - 104,417,707UniSTSRnor5.0
Rnor_5.013104,409,513 - 104,409,665UniSTSRnor5.0
RGSC_v3.41396,865,227 - 96,865,379UniSTSRGSC3.4
Celera1392,397,385 - 92,397,537UniSTS
RH 3.4 Map13631.1UniSTS
Cytogenetic Map13q26UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131107975663Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)1312193394108478121Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1324502279108770533Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1335301263107975663Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133614753399968921Rat
1641901Alcrsp6Alcohol response QTL 6response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1357903612102903612Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1362975663107975663Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1366971778111971778Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1371230858114033958Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1371230858114033958Rat
7387280Uae43Urinary albumin excretion QTL 435.690.4174urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1372583716114033958Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)777694986114033958Rat
8655959Pur32Proteinuria QTL 328.4total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1379567081103613733Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1380403559108770687Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1386833393114033958Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:200
Count of miRNA genes:147
Interacting mature miRNAs:158
Transcripts:ENSRNOT00000004927
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
Medium 2 8 25 12 18 12 57 18 39 9
Low 1 35 32 29 1 29 8 11 17 17 2 2 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000004927   ⟹   ENSRNOP00000004927
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1399,410,026 - 99,468,778 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000086888   ⟹   ENSRNOP00000070402
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1399,414,193 - 99,468,775 (-)Ensembl
RefSeq Acc Id: NM_001105980   ⟹   NP_001099450
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21392,853,650 - 92,906,049 (-)NCBI
Rnor_6.01399,410,026 - 99,468,778 (-)NCBI
Rnor_5.013104,407,045 - 104,465,204 (-)NCBI
RGSC_v3.41396,862,759 - 96,917,215 (-)RGD
Celera1392,394,917 - 92,447,334 (-)RGD
Sequence:
RefSeq Acc Id: XM_006250367   ⟹   XP_006250429
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21392,851,023 - 92,906,747 (-)NCBI
Rnor_6.01399,410,034 - 99,468,783 (-)NCBI
Rnor_5.013104,407,045 - 104,465,204 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006250370   ⟹   XP_006250432
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21392,851,023 - 92,905,932 (-)NCBI
Rnor_6.01399,410,034 - 99,459,448 (-)NCBI
Rnor_5.013104,407,045 - 104,465,204 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006250372   ⟹   XP_006250434
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21392,851,023 - 92,905,931 (-)NCBI
Rnor_6.01399,410,034 - 99,461,895 (-)NCBI
Rnor_5.013104,407,045 - 104,465,204 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017598728   ⟹   XP_017454217
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21392,851,023 - 92,905,932 (-)NCBI
Rnor_6.01399,410,034 - 99,466,890 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039090561   ⟹   XP_038946489
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21392,856,073 - 92,906,747 (-)NCBI
RefSeq Acc Id: XM_039090562   ⟹   XP_038946490
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21392,851,023 - 92,896,718 (-)NCBI
RefSeq Acc Id: XR_005492226
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21392,869,803 - 92,906,749 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001099450   ⟸   NM_001105980
- UniProtKB: D3ZTY9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006250429   ⟸   XM_006250367
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006250434   ⟸   XM_006250372
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_006250432   ⟸   XM_006250370
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017454217   ⟸   XM_017598728
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000004927   ⟸   ENSRNOT00000004927
RefSeq Acc Id: ENSRNOP00000070402   ⟸   ENSRNOT00000086888
RefSeq Acc Id: XP_038946490   ⟸   XM_039090562
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038946489   ⟸   XM_039090561
- Peptide Label: isoform X1
Protein Domains
AAA

Transcriptome

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

Promoters
RGD ID:13699071
Promoter ID:EPDNEW_R9592
Type:initiation region
Name:Nvl_1
Description:nuclear VCP-like
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01399,468,741 - 99,468,801EPDNEW

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)
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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
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
13 99450248 99450249 G C snv F344/NCrl (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311270 AgrOrtholog
Ensembl Genes ENSRNOG00000003629 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000004927 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000070402 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000004927 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000086888 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.2010 UniProtKB/TrEMBL
InterPro AAA_lid_3 UniProtKB/TrEMBL
  ATPase_AAA+_core UniProtKB/TrEMBL
  ATPase_AAA_core UniProtKB/TrEMBL
  ATPase_AAA_CS UniProtKB/TrEMBL
  NLV2_N_sf UniProtKB/TrEMBL
  NVL2_nucleolin-bd UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
KEGG Report rno:289323 UniProtKB/TrEMBL
NCBI Gene 289323 ENTREZGENE
Pfam AAA UniProtKB/TrEMBL
  AAA_lid_3 UniProtKB/TrEMBL
  Nucleolin_bd UniProtKB/TrEMBL
PhenoGen Nvl PhenoGen
PROSITE AAA UniProtKB/TrEMBL
SMART AAA UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/TrEMBL
UniProt A0A0G2JXU1_RAT UniProtKB/TrEMBL
  D3ZTY9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Nvl  nuclear VCP-like   Nvl_predicted  nuclear VCP-like (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Nvl_predicted  nuclear VCP-like (predicted)      Symbol and Name status set to approved 70820 APPROVED