Usp9x (ubiquitin specific peptidase 9, X-linked) - Rat Genome Database

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Gene: Usp9x (ubiquitin specific peptidase 9, X-linked) Rattus norvegicus
Analyze
Symbol: Usp9x
Name: ubiquitin specific peptidase 9, X-linked
RGD ID: 1560056
Description: Predicted to enable co-SMAD binding activity; cysteine-type peptidase activity; and ubiquitin protein ligase binding activity. Predicted to be involved in several processes, including positive regulation of DNA demethylation; protein deubiquitination involved in ubiquitin-dependent protein catabolic process; and transmembrane receptor protein serine/threonine kinase signaling pathway. Predicted to act upstream of or within several processes, including cellular response to transforming growth factor beta stimulus; in utero embryonic development; and nervous system development. Predicted to be located in apical part of cell; cytoplasm; and growth cone. Predicted to be active in cytosol and nucleus. Human ortholog(s) of this gene implicated in female-restricted syndromic X-linked intellectual disability 99 and non-syndromic X-linked intellectual disability 99. Orthologous to human USP9X (ubiquitin specific peptidase 9 X-linked); INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC363445; probable ubiquitin carboxyl-terminal hydrolase FAF-X; RGD1560056; similar to ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila); ubiquitin specific peptidase 9, X chromosome
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X9,588,825 - 9,726,993 (-)NCBImRatBN7.2
mRatBN7.2 EnsemblX9,588,825 - 9,696,711 (-)Ensembl
Rnor_6.0X10,510,033 - 10,660,555 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX10,510,033 - 10,630,297 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X11,308,415 - 11,458,704 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X21,606,330 - 21,718,042 (-)NCBIRGSC3.4rn4RGSC3.4
CeleraX10,119,391 - 10,226,802 (-)NCBICelera
Cytogenetic MapXq12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,6-dinitrotoluene  (EXP)
3-methylcholanthrene  (ISO)
5-fluorouracil  (ISO)
aconitine  (EXP)
acrylamide  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP)
butanal  (ISO)
chlordecone  (ISO)
chlorohydrocarbon  (EXP)
chlorpyrifos  (ISO)
chromium(6+)  (ISO)
cocaine  (ISO)
copper(II) sulfate  (ISO)
dibutyl phthalate  (EXP)
dioxygen  (ISO)
dorsomorphin  (ISO)
elemental selenium  (ISO)
entinostat  (ISO)
enzyme inhibitor  (ISO)
fenofibrate  (ISO)
fipronil  (EXP)
flutamide  (EXP)
folic acid  (ISO)
ivermectin  (ISO)
menadione  (ISO)
methapyrilene  (EXP)
methylmercury chloride  (EXP,ISO)
methylparaben  (ISO)
miconazole  (ISO)
N,N-diethyl-m-toluamide  (EXP)
N-methylformamide  (ISO)
nickel dichloride  (EXP)
nickel subsulfide  (EXP)
nickel sulfate  (ISO)
oxaliplatin  (EXP)
paracetamol  (ISO)
permethrin  (EXP)
phlorizin  (ISO)
potassium chromate  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
sodium arsenate  (ISO)
succimer  (ISO)
tamibarotene  (ISO)
temozolomide  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP)
thapsigargin  (ISO)
topotecan  (EXP)
trichostatin A  (ISO)
valproic acid  (EXP,ISO)
vitamin E  (ISO)

References

Additional References at PubMed
PMID:10704870   PMID:14657369   PMID:15509704   PMID:17728463   PMID:18254724   PMID:18410486   PMID:19135894   PMID:19946888   PMID:20305814   PMID:21173155   PMID:22065755   PMID:22371489  
PMID:22871113   PMID:23146885   PMID:23861879   PMID:24607389   PMID:25763846   PMID:25931508   PMID:25944111   PMID:29626158  


Genomics

Comparative Map Data
Usp9x
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X9,588,825 - 9,726,993 (-)NCBImRatBN7.2
mRatBN7.2 EnsemblX9,588,825 - 9,696,711 (-)Ensembl
Rnor_6.0X10,510,033 - 10,660,555 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX10,510,033 - 10,630,297 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X11,308,415 - 11,458,704 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X21,606,330 - 21,718,042 (-)NCBIRGSC3.4rn4RGSC3.4
CeleraX10,119,391 - 10,226,802 (-)NCBICelera
Cytogenetic MapXq12NCBI
USP9X
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX41,085,445 - 41,236,579 (+)EnsemblGRCh38hg38GRCh38
GRCh38X41,085,420 - 41,236,579 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X40,944,698 - 41,095,832 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X40,829,832 - 40,980,776 (+)NCBINCBI36hg18NCBI36
CeleraX45,085,646 - 45,236,596 (+)NCBI
Cytogenetic MapXp11.4NCBI
HuRefX38,676,295 - 38,826,441 (+)NCBIHuRef
CHM1_1X40,977,600 - 41,128,503 (+)NCBICHM1_1
Usp9x
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X12,937,221 - 13,039,567 (+)NCBIGRCm39mm39
GRCm39 EnsemblX12,937,737 - 13,039,567 (+)Ensembl
GRCm38X13,070,982 - 13,173,328 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX13,071,498 - 13,173,328 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X12,648,624 - 12,750,454 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X12,228,496 - 12,328,745 (+)NCBImm8
CeleraX10,768,972 - 10,871,748 (+)NCBICelera
Cytogenetic MapXA1.1NCBI
cM MapX7.95NCBI
Usp9x
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555651,479,040 - 1,602,070 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555651,479,040 - 1,602,070 (-)NCBIChiLan1.0ChiLan1.0
USP9X
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X41,231,814 - 41,380,569 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX41,232,041 - 41,379,910 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X33,535,543 - 33,683,220 (+)NCBIMhudiblu_PPA_v0panPan3
USP9X
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X35,522,873 - 35,676,086 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX22,845,661 - 23,024,786 (+)NCBI
ROS_Cfam_1.0X35,571,563 - 35,712,343 (+)NCBI
UMICH_Zoey_3.1X35,624,905 - 35,803,984 (+)NCBI
UNSW_CanFamBas_1.0X35,597,545 - 35,776,521 (+)NCBI
UU_Cfam_GSD_1.0X35,640,469 - 35,819,595 (+)NCBI
Usp9x
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X27,780,903 - 27,894,664 (+)NCBI
SpeTri2.0NW_0049365027,649,808 - 7,732,731 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
USP9X
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX36,760,819 - 36,885,275 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X36,736,049 - 36,888,702 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
USP9X
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X38,255,414 - 38,402,855 (+)NCBI
ChlSab1.1 EnsemblX38,256,008 - 38,403,323 (+)Ensembl
Vero_WHO_p1.0NW_0236660763,448,010 - 3,595,885 (+)NCBI
Usp9x
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476214,403,361 - 14,527,854 (-)NCBI

Position Markers
RH127557  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X9,589,002 - 9,589,202 (+)MAPPERmRatBN7.2
Rnor_6.0X10,523,776 - 10,523,975NCBIRnor6.0
Rnor_6.0X10,510,211 - 10,510,410NCBIRnor6.0
Rnor_5.0X11,308,593 - 11,308,792UniSTSRnor5.0
Rnor_5.0X11,322,158 - 11,322,357UniSTSRnor5.0
RGSC_v3.4X21,606,508 - 21,606,707UniSTSRGSC3.4
CeleraX10,119,569 - 10,119,768UniSTS
Cytogenetic MapXq13UniSTS
RH125670  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X9,592,814 - 9,593,046 (+)MAPPERmRatBN7.2
Rnor_6.0X10,526,220 - 10,526,451NCBIRnor6.0
Rnor_5.0X11,324,602 - 11,324,833UniSTSRnor5.0
RGSC_v3.4X21,610,320 - 21,610,551UniSTSRGSC3.4
CeleraX10,123,381 - 10,123,612UniSTS
Cytogenetic MapXq13UniSTS
RH142260  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X9,591,801 - 9,591,955 (+)MAPPERmRatBN7.2
Rnor_6.0X10,513,010 - 10,513,163NCBIRnor6.0
Rnor_5.0X11,311,392 - 11,311,545UniSTSRnor5.0
RGSC_v3.4X21,609,307 - 21,609,460UniSTSRGSC3.4
CeleraX10,122,368 - 10,122,521UniSTS
RH 3.4 MapX21.6UniSTS
Cytogenetic MapXq13UniSTS
BF396338  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X9,640,927 - 9,641,075 (+)MAPPERmRatBN7.2
Rnor_6.0X10,573,812 - 10,573,959NCBIRnor6.0
Rnor_5.0X11,372,194 - 11,372,341UniSTSRnor5.0
RGSC_v3.4X21,660,103 - 21,660,250UniSTSRGSC3.4
CeleraX10,171,446 - 10,171,593UniSTS
RH 3.4 MapX16.2UniSTS
Cytogenetic MapXq13UniSTS
RH141703  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X9,591,548 - 9,591,751 (+)MAPPERmRatBN7.2
Rnor_6.0X10,512,757 - 10,512,959NCBIRnor6.0
Rnor_5.0X11,311,139 - 11,311,341UniSTSRnor5.0
RGSC_v3.4X21,609,054 - 21,609,256UniSTSRGSC3.4
CeleraX10,122,115 - 10,122,317UniSTS
RH 3.4 MapX23.9UniSTS
Cytogenetic MapXq13UniSTS
BG371737  
Rat AssemblyChrPosition (strand)SourceJBrowse
RH 3.4 MapX19.2UniSTS
Cytogenetic MapXq13UniSTS
D20S998  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X9,592,789 - 9,592,908 (+)MAPPERmRatBN7.2
Rnor_6.0X10,526,195 - 10,526,313NCBIRnor6.0
Rnor_5.0X11,324,577 - 11,324,695UniSTSRnor5.0
RGSC_v3.4X21,610,295 - 21,610,413UniSTSRGSC3.4
CeleraX10,123,356 - 10,123,474UniSTS
Cytogenetic MapXq13UniSTS
RH125324  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X9,590,527 - 9,590,706 (+)MAPPERmRatBN7.2
Rnor_6.0X10,525,301 - 10,525,479NCBIRnor6.0
Rnor_6.0X10,511,736 - 10,511,914NCBIRnor6.0
Rnor_5.0X11,310,118 - 11,310,296UniSTSRnor5.0
Rnor_5.0X11,323,683 - 11,323,861UniSTSRnor5.0
RGSC_v3.4X21,608,033 - 21,608,211UniSTSRGSC3.4
CeleraX10,121,094 - 10,121,272UniSTS
Cytogenetic MapXq13UniSTS
USP9X_3261  
Rat AssemblyChrPosition (strand)SourceJBrowse
RGSC_v3.4X21,609,885 - 21,610,490UniSTSRGSC3.4
CeleraX10,122,946 - 10,123,551UniSTS
Cytogenetic MapXq13UniSTS
px-12d6  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X9,589,184 - 9,589,297 (+)MAPPERmRatBN7.2
Rnor_6.0X10,523,958 - 10,524,070NCBIRnor6.0
Rnor_6.0X10,510,393 - 10,510,505NCBIRnor6.0
Rnor_5.0X11,308,775 - 11,308,887UniSTSRnor5.0
Rnor_5.0X11,322,340 - 11,322,452UniSTSRnor5.0
RGSC_v3.4X21,606,690 - 21,606,802UniSTSRGSC3.4
CeleraX10,119,751 - 10,119,863UniSTS
Cytogenetic MapXq13UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X143491017Rat
70166Bp65Blood pressure QTL 655.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X144797211374346Rat
634325Bw13Body weight QTL 130body mass (VT:0001259)body weight (CMO:0000012)X144797220991088Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X144812931706553Rat
631204Gluco15Glucose level QTL 150.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X162371522646544Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X292789847927898Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7440600049406000Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X449454949494549Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1123
Count of miRNA genes:360
Interacting mature miRNAs:492
Transcripts:ENSRNOT00000048980
Prediction methods:Microtar, Miranda, Pita, 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 42 57 41 19 41 8 10 74 35 38 11 8
Low 1 1 3
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000048980   ⟹   ENSRNOP00000043441
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX9,590,589 - 9,696,711 (-)Ensembl
Rnor_6.0 EnsemblX10,511,797 - 10,630,297 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000080651   ⟹   ENSRNOP00000072190
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX9,588,825 - 9,696,695 (-)Ensembl
Rnor_6.0 EnsemblX10,510,033 - 10,630,281 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000093067   ⟹   ENSRNOP00000075990
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX9,594,237 - 9,696,711 (-)Ensembl
RefSeq Acc Id: NM_001135893   ⟹   NP_001129365
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X9,590,589 - 9,696,711 (-)NCBI
Rnor_6.0X10,511,797 - 10,630,297 (-)NCBI
Rnor_5.0X11,308,415 - 11,458,704 (-)NCBI
RGSC_v3.4X21,606,330 - 21,718,042 (-)RGD
CeleraX10,121,155 - 10,226,802 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001135923   ⟹   NP_001129395
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X9,588,825 - 9,696,695 (-)NCBI
Rnor_6.0X10,510,033 - 10,630,281 (-)NCBI
Rnor_5.0X11,308,415 - 11,458,704 (-)NCBI
RGSC_v3.4X21,606,330 - 21,718,042 (-)RGD
CeleraX10,119,391 - 10,226,786 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039099859   ⟹   XP_038955787
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X9,588,943 - 9,696,011 (-)NCBI
RefSeq Acc Id: XM_039099860   ⟹   XP_038955788
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X9,588,943 - 9,726,993 (-)NCBI
RefSeq Acc Id: XM_039099861   ⟹   XP_038955789
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X9,588,943 - 9,726,993 (-)NCBI
RefSeq Acc Id: XM_039099862   ⟹   XP_038955790
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X9,588,943 - 9,695,584 (-)NCBI
RefSeq Acc Id: XM_039099863   ⟹   XP_038955791
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X9,588,943 - 9,696,011 (-)NCBI
RefSeq Acc Id: XM_039099864   ⟹   XP_038955792
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X9,588,943 - 9,696,011 (-)NCBI
RefSeq Acc Id: XM_039099865   ⟹   XP_038955793
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X9,588,943 - 9,696,011 (-)NCBI
RefSeq Acc Id: XM_039099867   ⟹   XP_038955795
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X9,588,943 - 9,674,098 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001129395   ⟸   NM_001135923
- Peptide Label: isoform 2
- UniProtKB: A0A0G2K2C7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001129365   ⟸   NM_001135893
- Peptide Label: isoform 1
- UniProtKB: D3ZC84 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000072190   ⟸   ENSRNOT00000080651
RefSeq Acc Id: ENSRNOP00000043441   ⟸   ENSRNOT00000048980
RefSeq Acc Id: XP_038955789   ⟸   XM_039099861
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955788   ⟸   XM_039099860
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955793   ⟸   XM_039099865
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038955791   ⟸   XM_039099863
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038955792   ⟸   XM_039099864
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038955787   ⟸   XM_039099859
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955790   ⟸   XM_039099862
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955795   ⟸   XM_039099867
- Peptide Label: isoform X4
RefSeq Acc Id: ENSRNOP00000075990   ⟸   ENSRNOT00000093067
Protein Domains
USP

Transcriptome

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

Promoters
RGD ID:13701707
Promoter ID:EPDNEW_R12231
Type:initiation region
Name:Usp9x_1
Description:ubiquitin specific peptidase 9, X-linked
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_6.0X10,630,281 - 10,630,341EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/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)
ACI/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
ACI/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/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
BBDP/Wor (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
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (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
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/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
COP/CrCrl (MCW & UW)
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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)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/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
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
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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)
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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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/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
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1560056 AgrOrtholog
Ensembl Genes ENSRNOG00000003261 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000043441 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000072190 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000048980 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000080651 ENTREZGENE, UniProtKB/TrEMBL
InterPro ARM-type_fold UniProtKB/TrEMBL
  DUF3517 UniProtKB/TrEMBL
  Papain_like_cys_pep_sf UniProtKB/TrEMBL
  Pept_C19ubi-hydrolase_C_CS UniProtKB/TrEMBL
  Peptidase_C19 UniProtKB/TrEMBL
  UCH/PAN2 UniProtKB/TrEMBL
KEGG Report rno:363445 UniProtKB/TrEMBL
NCBI Gene 363445 ENTREZGENE
Pfam DUF3517 UniProtKB/TrEMBL
  UCH UniProtKB/TrEMBL
PhenoGen Usp9x PhenoGen
PROSITE UCH_2_1 UniProtKB/TrEMBL
  UCH_2_2 UniProtKB/TrEMBL
  UCH_2_3 UniProtKB/TrEMBL
Superfamily-SCOP SSF48371 UniProtKB/TrEMBL
  SSF54001 UniProtKB/TrEMBL
UniProt A0A0G2K2C7 ENTREZGENE, UniProtKB/TrEMBL
  D3ZC84 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-23 Usp9x  ubiquitin specific peptidase 9, X-linked  Usp9x  ubiquitin specific peptidase 9, X chromosome   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Usp9x  ubiquitin specific peptidase 9, X chromosome   Usp9x_predicted  ubiquitin specific peptidase 9, X chromosome (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Usp9x_predicted  ubiquitin specific peptidase 9, X chromosome (predicted)  RGD1560056_predicted  similar to ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila) (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1560056_predicted  similar to ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila) (predicted)  LOC363445  similar to ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila)  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC363445  similar to ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila)      Symbol and Name status set to provisional 70820 PROVISIONAL