Usp19 (ubiquitin specific peptidase 19) - Rat Genome Database

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Gene: Usp19 (ubiquitin specific peptidase 19) Rattus norvegicus
Analyze
Symbol: Usp19
Name: ubiquitin specific peptidase 19
RGD ID: 1303276
Description: Predicted to have Hsp90 protein binding activity; ubiquitin protein ligase binding activity; and ubiquitinyl hydrolase activity. Involved in positive regulation of cell cycle process; protein deubiquitination; and regulation of protein stability. Predicted to localize to cytosol and endoplasmic reticulum membrane. Orthologous to human USP19 (ubiquitin specific peptidase 19); INTERACTS WITH 2,4-dinitrotoluene; 2,6-dinitrotoluene; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: deubiquitinating enzyme 19; ubiquitin carboxyl-terminal hydrolase 19; ubiquitin specific protease 19; ubiquitin thioesterase 19; ubiquitin thiolesterase 19; ubiquitin-specific-processing protease 19
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
mRatBN7.28109,190,727 - 109,201,761 (+)NCBI
Rnor_6.0 Ensembl8117,280,705 - 117,291,351 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.08117,280,690 - 117,291,729 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.08116,625,419 - 116,636,432 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera8108,488,932 - 108,497,573 (+)ENTREZGENECelera
Cytogenetic Map8q32NCBI
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:12477932   PMID:19465887   PMID:19773579   PMID:21971047   PMID:22128162   PMID:24356957   PMID:25088257   PMID:25568336   PMID:27156111  


Genomics

Comparative Map Data
Usp19
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28109,190,727 - 109,201,761 (+)NCBI
Rnor_6.0 Ensembl8117,280,705 - 117,291,351 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.08117,280,690 - 117,291,729 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.08116,625,419 - 116,636,432 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera8108,488,932 - 108,497,573 (+)ENTREZGENECelera
Cytogenetic Map8q32NCBI
USP19
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl349,108,046 - 49,120,938 (-)EnsemblGRCh38hg38GRCh38
GRCh38349,108,050 - 49,120,933 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37349,145,483 - 49,158,256 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36349,121,112 - 49,133,217 (-)NCBINCBI36hg18NCBI36
Build 34349,121,111 - 49,133,217NCBI
Celera349,103,060 - 49,115,165 (-)NCBI
Cytogenetic Map3p21.31NCBI
HuRef349,204,015 - 49,216,907 (-)NCBIHuRef
CHM1_1349,098,226 - 49,111,118 (-)NCBICHM1_1
Usp19
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399108,367,806 - 108,379,536 (+)NCBIGRCm39mm39
GRCm39 Ensembl9108,367,801 - 108,379,536 (+)Ensembl
GRCm389108,490,607 - 108,502,337 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9108,490,602 - 108,502,337 (+)EnsemblGRCm38mm10GRCm38
MGSCv379108,393,007 - 108,404,668 (+)NCBIGRCm37mm9NCBIm37
MGSCv369108,348,851 - 108,359,802 (+)NCBImm8
Celera9108,100,140 - 108,111,769 (+)NCBICelera
Cytogenetic Map9F2NCBI
Usp19
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555321,104,591 - 1,113,567 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555321,104,212 - 1,115,267 (-)NCBIChiLan1.0ChiLan1.0
USP19
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1350,112,271 - 50,125,114 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl350,100,216 - 50,125,112 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0349,032,373 - 49,045,238 (-)NCBIMhudiblu_PPA_v0panPan3
USP19
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12040,062,802 - 40,074,221 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2040,064,599 - 40,074,082 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2039,980,975 - 39,992,470 (+)NCBI
ROS_Cfam_1.02040,419,685 - 40,431,184 (+)NCBI
UMICH_Zoey_3.12039,786,538 - 39,798,032 (+)NCBI
UNSW_CanFamBas_1.02040,190,048 - 40,201,538 (+)NCBI
UU_Cfam_GSD_1.02040,470,345 - 40,481,844 (+)NCBI
Usp19
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560264,054,119 - 64,065,492 (-)NCBI
SpeTri2.0NW_004936529814,649 - 826,008 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
USP19
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1331,726,731 - 31,738,770 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11331,726,668 - 31,738,135 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21334,958,907 - 34,968,638 (-)NCBISscrofa10.2Sscrofa10.2susScr3
USP19
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12210,510,554 - 10,523,576 (-)NCBI
ChlSab1.1 Ensembl2210,510,423 - 10,523,487 (-)Ensembl
Vero_WHO_p1.0NW_023666041156,558,381 - 156,571,234 (+)NCBI
Usp19
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247303,134,419 - 3,145,512 (-)NCBI

Position Markers
BI274871  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28109,201,365 - 109,201,557 (+)MAPPER
Rnor_6.08117,291,331 - 117,291,522NCBIRnor6.0
Rnor_5.08116,636,034 - 116,636,225UniSTSRnor5.0
Celera8108,497,873 - 108,498,064UniSTS
RH 3.4 Map81116.09UniSTS


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)mean arterial blood pressure (CMO:0000009)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)absolute change in systolic blood pressure (CMO:0000607)850529480128036471Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)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:48
Count of miRNA genes:38
Interacting mature miRNAs:46
Transcripts:ENSRNOT00000074772
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 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001001516 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006243793 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006243794 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006243795 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006243796 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006243797 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006243798 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006243799 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039081691 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039081692 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005487861 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC128721 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY605065 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC091259 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC168243 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473954 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000200 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000074772   ⟹   ENSRNOP00000067744
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl8117,282,390 - 117,291,031 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000085038   ⟹   ENSRNOP00000069554
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl8117,280,705 - 117,291,351 (+)Ensembl
RefSeq Acc Id: NM_001001516   ⟹   NP_001001516
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28109,192,425 - 109,201,066 (+)NCBI
Rnor_6.08117,282,390 - 117,291,031 (+)NCBI
Rnor_5.08116,625,419 - 116,636,432 (+)NCBI
Celera8108,488,932 - 108,497,573 (+)ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006243793   ⟹   XP_006243855
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28109,190,728 - 109,201,125 (+)NCBI
Rnor_6.08117,280,691 - 117,291,090 (+)NCBI
Rnor_5.08116,625,419 - 116,636,432 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006243794   ⟹   XP_006243856
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28109,190,728 - 109,201,125 (+)NCBI
Rnor_6.08117,280,690 - 117,291,090 (+)NCBI
Rnor_5.08116,625,419 - 116,636,432 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006243795   ⟹   XP_006243857
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28109,190,728 - 109,201,125 (+)NCBI
Rnor_6.08117,280,691 - 117,291,090 (+)NCBI
Rnor_5.08116,625,419 - 116,636,432 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006243796   ⟹   XP_006243858
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28109,190,728 - 109,201,125 (+)NCBI
Rnor_6.08117,280,691 - 117,291,090 (+)NCBI
Rnor_5.08116,625,419 - 116,636,432 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006243797   ⟹   XP_006243859
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28109,190,729 - 109,201,761 (+)NCBI
Rnor_6.08117,280,691 - 117,291,729 (+)NCBI
Rnor_5.08116,625,419 - 116,636,432 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006243798   ⟹   XP_006243860
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28109,190,729 - 109,201,761 (+)NCBI
Rnor_6.08117,280,691 - 117,291,729 (+)NCBI
Rnor_5.08116,625,419 - 116,636,432 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006243799   ⟹   XP_006243861
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28109,190,729 - 109,201,761 (+)NCBI
Rnor_6.08117,280,691 - 117,291,729 (+)NCBI
Rnor_5.08116,625,419 - 116,636,432 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039081691   ⟹   XP_038937619
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28109,190,727 - 109,201,125 (+)NCBI
RefSeq Acc Id: XM_039081692   ⟹   XP_038937620
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28109,190,728 - 109,201,761 (+)NCBI
RefSeq Acc Id: XR_005487861
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28109,190,728 - 109,201,402 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001001516   ⟸   NM_001001516
- UniProtKB: Q6J1Y9 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006243856   ⟸   XM_006243794
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006243860   ⟸   XM_006243798
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_006243855   ⟸   XM_006243793
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006243857   ⟸   XM_006243795
- Peptide Label: isoform X3
- UniProtKB: M0RDN9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006243858   ⟸   XM_006243796
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_006243859   ⟸   XM_006243797
- Peptide Label: isoform X6
- UniProtKB: A0A0G2JVN4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006243861   ⟸   XM_006243799
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: ENSRNOP00000069554   ⟸   ENSRNOT00000085038
RefSeq Acc Id: ENSRNOP00000067744   ⟸   ENSRNOT00000074772
RefSeq Acc Id: XP_038937619   ⟸   XM_039081691
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038937620   ⟸   XM_039081692
- Peptide Label: isoform X9
Protein Domains
CS   MYND-type   USP

Transcriptome

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

Promoters
RGD ID:13696315
Promoter ID:EPDNEW_R6828
Type:initiation region
Name:Usp19_1
Description:ubiquitin specific peptidase 19
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R6829  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08117,280,692 - 117,280,752EPDNEW
RGD ID:13696304
Promoter ID:EPDNEW_R6829
Type:multiple initiation site
Name:Usp19_2
Description:ubiquitin specific peptidase 19
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R6828  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08117,280,813 - 117,280,873EPDNEW

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)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 116633348 116633349 A G snv SR/JrHsd (MCW)
8 116634365 116634366 C A snv F344/NRrrc (SOLiD) (KNAW), F344/Jcl (KyushuU), F344/NHsd (KNAW), F344/DuCrlCrlj (KyushuU), F344/Stm (KyushuU), F344/NRrrc (Illumina) (KNAW), F344/NCrl (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 117289662 117289663 C A snv F344/NCrl (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1303276 AgrOrtholog
Ensembl Genes ENSRNOG00000049531 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000067744 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000069554 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000074772 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000085038 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.790 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro CS_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HSP20-like_chaperone UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Papain-like_cys_pep_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peptidase_C19_UCH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  USP_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  USP_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_MYND UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:361190 UniProtKB/Swiss-Prot
NCBI Gene 361190 ENTREZGENE
Pfam PF04969 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  UCH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  zf-MYND UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Usp19 PhenoGen
PROSITE PS51203 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  USP_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  USP_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  USP_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_MYND_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_MYND_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF49764 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF54001 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JVN4 ENTREZGENE, UniProtKB/TrEMBL
  M0RDN9 ENTREZGENE, UniProtKB/TrEMBL
  Q5BK03_RAT UniProtKB/TrEMBL
  Q6J1Y9 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-04 Usp19  ubiquitin specific peptidase 19  Usp19  ubiquitin specific protease 19  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-09-30 Usp19        Symbol and Name status set to provisional 70820 PROVISIONAL