Usp40 (ubiquitin specific peptidase 40) - Rat Genome Database

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Gene: Usp40 (ubiquitin specific peptidase 40) Rattus norvegicus
Analyze
Symbol: Usp40
Name: ubiquitin specific peptidase 40
RGD ID: 1309613
Description: Predicted to enable cysteine-type deubiquitinase activity. Predicted to be involved in proteolysis. Predicted to be active in cytosol and nucleus. Orthologous to human USP40 (ubiquitin specific peptidase 40); INTERACTS WITH (+)-schisandrin B; 1,3-dinitrobenzene; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC100911860; LOC316599; LRRGT00071; sorbitol dehydrogenase-like; ubiquitin carboxyl-terminal hydrolase 40; ubiquitin carboxyl-terminal hydrolase 40-like; ubiquitin specific protease 40; ubiquitin thioesterase 40
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
GRCr8996,055,741 - 96,126,766 (-)NCBIGRCr8
mRatBN7.2988,607,920 - 88,678,940 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl988,607,930 - 88,678,914 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx997,032,175 - 97,103,042 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.09102,168,363 - 102,239,234 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.09100,536,129 - 100,607,106 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0995,072,096 - 95,143,092 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl995,072,112 - 95,143,142 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0994,791,208 - 94,862,210 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4986,897,870 - 86,968,850 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera986,169,618 - 86,240,347 (-)NCBICelera
Cytogenetic Map9q35NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytosol  (IBA)
motile cilium  (IEA)
nucleus  (IBA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Cloning and enzymatic analysis of 22 novel human ubiquitin-specific proteases. Quesada V, etal., Biochem Biophys Res Commun 2004 Jan 30;314(1):54-62.
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Usp40
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8996,055,741 - 96,126,766 (-)NCBIGRCr8
mRatBN7.2988,607,920 - 88,678,940 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl988,607,930 - 88,678,914 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx997,032,175 - 97,103,042 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.09102,168,363 - 102,239,234 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.09100,536,129 - 100,607,106 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0995,072,096 - 95,143,092 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl995,072,112 - 95,143,142 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0994,791,208 - 94,862,210 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4986,897,870 - 86,968,850 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera986,169,618 - 86,240,347 (-)NCBICelera
Cytogenetic Map9q35NCBI
USP40
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382233,475,526 - 233,566,782 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2233,475,526 - 233,566,782 (-)EnsemblGRCh38hg38GRCh38
GRCh372234,384,172 - 234,475,428 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362234,048,904 - 234,134,606 (-)NCBINCBI36Build 36hg18NCBI36
Celera2228,105,436 - 228,195,522 (-)NCBICelera
Cytogenetic Map2q37.1NCBI
HuRef2226,184,857 - 226,274,836 (-)NCBIHuRef
CHM1_12234,390,167 - 234,480,204 (-)NCBICHM1_1
T2T-CHM13v2.02233,964,044 - 234,055,315 (-)NCBIT2T-CHM13v2.0
Usp40
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39187,872,841 - 87,936,308 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl187,872,841 - 87,936,273 (-)EnsemblGRCm39 Ensembl
GRCm38187,945,119 - 88,008,582 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl187,945,119 - 88,008,551 (-)EnsemblGRCm38mm10GRCm38
MGSCv37189,841,696 - 89,905,126 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36189,776,292 - 89,839,722 (-)NCBIMGSCv36mm8
Celera190,903,174 - 90,967,221 (-)NCBICelera
Cytogenetic Map1DNCBI
cM Map144.45NCBI
Usp40
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554532,661,213 - 2,739,146 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554532,661,233 - 2,739,742 (+)NCBIChiLan1.0ChiLan1.0
USP40
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v213136,078,773 - 136,169,973 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B136,093,737 - 136,184,943 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B120,704,893 - 120,796,084 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B239,615,598 - 239,705,721 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B239,617,442 - 239,705,721 (-)Ensemblpanpan1.1panPan2
USP40
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12544,965,276 - 45,021,539 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2545,460,119 - 45,537,523 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02545,224,993 - 45,302,504 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2545,216,601 - 45,302,479 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12545,149,152 - 45,226,628 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02544,995,742 - 45,072,784 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02545,150,957 - 45,228,463 (-)NCBIUU_Cfam_GSD_1.0
Usp40
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303187,113,531 - 187,179,765 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365253,760,280 - 3,826,206 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365253,759,982 - 3,826,190 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
USP40
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15133,870,834 - 133,952,863 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115133,870,831 - 133,952,863 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215148,340,802 - 148,418,018 (+)NCBISscrofa10.2Sscrofa10.2susScr3
USP40
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110119,516,114 - 119,609,519 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl10119,514,754 - 119,609,521 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604079,890,302 - 79,984,155 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Usp40
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248435,961,591 - 6,038,215 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248435,958,316 - 6,042,471 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Usp40
202 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:144
Count of miRNA genes:112
Interacting mature miRNAs:120
Transcripts:ENSRNOT00000064171
Prediction methods:Miranda
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)925661188100929786Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94859825193598251Rat
4889852Pur26Proteinuria QTL 26150.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)977813894101597663Rat
4889943Bss90Bone structure and strength QTL 904.1tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)98636963192058970Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)977813894111552878Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)93696235992058970Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)961381434104821652Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)975712843111552878Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)96207227596470995Rat
1578757Pur6Proteinuria QTL 63.30.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)96207227596470995Rat
61385Edpm9Estrogen-dependent pituitary mass QTL 93.430.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)963869687108869687Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)93696235995410867Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)958163035100929646Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)925268044114175309Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)97927151191616855Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)97927151191616855Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)97927151191616855Rat
12879506Pur33Proteinuria QTL 33urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)94464992189649921Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)964573531109573531Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)956771635101771635Rat
724547Cm21Cardiac mass QTL 212.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)979271511102910209Rat
11353951Bp394Blood pressure QTL 394arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94464992189649921Rat
11353957Bmd92Bone mineral density QTL 920.01tibia mineral mass (VT:1000283)volumetric bone mineral density (CMO:0001553)94611419991114199Rat

Markers in Region
D9Got234  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2988,619,799 - 88,619,947 (+)MAPPERmRatBN7.2
Rnor_6.0995,083,982 - 95,084,129NCBIRnor6.0
Rnor_6.0991,041,375 - 91,041,522NCBIRnor6.0
Rnor_5.0990,778,288 - 90,778,435UniSTSRnor5.0
Rnor_5.0994,803,090 - 94,803,237UniSTSRnor5.0
RGSC_v3.4986,909,740 - 86,909,887UniSTSRGSC3.4
Celera986,181,488 - 86,181,635UniSTS
Cytogenetic Map9q35UniSTS
RH130513  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.0990,799,524 - 90,799,742NCBIRnor5.0
Rnor_5.0994,824,326 - 94,824,544NCBIRnor5.0
Rnor_5.03120,745,107 - 120,745,994NCBIRnor5.0
RGSC_v3.43109,046,603 - 109,047,489UniSTSRGSC3.4
RGSC_v3.4986,930,977 - 86,931,194UniSTSRGSC3.4
Celera3108,112,092 - 108,112,978UniSTS
Celera986,202,725 - 86,202,942UniSTS
Cytogenetic Map9q35UniSTS
Cytogenetic Map3q35UniSTS
RH137157  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2988,608,014 - 88,608,176 (+)MAPPERmRatBN7.2
Rnor_6.0995,072,197 - 95,072,358NCBIRnor6.0
Rnor_5.0994,791,305 - 94,791,466UniSTSRnor5.0
RGSC_v3.4986,897,955 - 86,898,116UniSTSRGSC3.4
Celera986,169,703 - 86,169,864UniSTS
Cytogenetic Map9q35UniSTS
RH141218  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.0990,798,495 - 90,798,697NCBIRnor5.0
Rnor_5.0994,823,297 - 94,823,499NCBIRnor5.0
Rnor_5.03120,746,689 - 120,746,892NCBIRnor5.0
RGSC_v3.43109,048,185 - 109,048,387UniSTSRGSC3.4
RGSC_v3.4986,929,948 - 86,930,149UniSTSRGSC3.4
Celera3108,113,674 - 108,113,876UniSTS
Celera986,201,696 - 86,201,897UniSTS
Cytogenetic Map9q35UniSTS
Cytogenetic Map3q35UniSTS


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 1 12 4 18 4 32 24 34 10
Low 2 43 45 37 1 37 8 11 42 11 7 1 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001134885 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767258 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767259 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767260 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767261 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596489 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083725 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083726 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083727 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083728 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083729 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083730 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083732 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083733 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083734 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083735 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063267293 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063267294 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063267295 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063267296 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001839663 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005488916 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005488917 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_594428 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC092530 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY387057 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473997 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232022 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232863 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000009 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

RefSeq Acc Id: ENSRNOT00000064171   ⟹   ENSRNOP00000060806
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl988,607,930 - 88,678,914 (-)Ensembl
Rnor_6.0 Ensembl995,072,112 - 95,143,092 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000064642   ⟹   ENSRNOP00000059419
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl988,607,930 - 88,678,914 (-)Ensembl
Rnor_6.0 Ensembl991,038,064 - 91,100,482 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000070819   ⟹   ENSRNOP00000064567
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl988,607,930 - 88,644,557 (-)Ensembl
Rnor_6.0 Ensembl995,073,536 - 95,108,739 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000085325   ⟹   ENSRNOP00000074830
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl988,607,930 - 88,678,914 (-)Ensembl
Rnor_6.0 Ensembl995,073,337 - 95,143,142 (-)Ensembl
RefSeq Acc Id: NM_001134885   ⟹   NP_001128357
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8996,055,741 - 96,126,721 (-)NCBI
mRatBN7.2988,607,930 - 88,678,914 (-)NCBI
Rnor_6.0995,072,112 - 95,143,092 (-)NCBI
Rnor_5.0994,791,208 - 94,862,210 (-)NCBI
RGSC_v3.4986,897,870 - 86,968,850 (-)RGD
Celera986,169,618 - 86,240,347 (-)RGD
Sequence:
RefSeq Acc Id: XM_008767261   ⟹   XP_008765483
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8996,060,265 - 96,126,766 (-)NCBI
mRatBN7.2988,612,550 - 88,678,935 (-)NCBI
Rnor_6.0995,076,755 - 95,142,991 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039083725   ⟹   XP_038939653
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8996,055,741 - 96,126,754 (-)NCBI
mRatBN7.2988,607,920 - 88,678,940 (-)NCBI
RefSeq Acc Id: XM_039083726   ⟹   XP_038939654
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8996,055,741 - 96,126,754 (-)NCBI
mRatBN7.2988,607,920 - 88,678,940 (-)NCBI
RefSeq Acc Id: XM_039083727   ⟹   XP_038939655
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8996,055,741 - 96,125,584 (-)NCBI
mRatBN7.2988,607,920 - 88,678,935 (-)NCBI
RefSeq Acc Id: XM_039083728   ⟹   XP_038939656
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8996,055,741 - 96,116,297 (-)NCBI
mRatBN7.2988,607,920 - 88,668,507 (-)NCBI
RefSeq Acc Id: XM_039083729   ⟹   XP_038939657
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8996,071,424 - 96,126,766 (-)NCBI
mRatBN7.2988,623,417 - 88,678,935 (-)NCBI
RefSeq Acc Id: XM_039083730   ⟹   XP_038939658
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8996,055,741 - 96,089,978 (-)NCBI
mRatBN7.2988,607,920 - 88,643,483 (-)NCBI
RefSeq Acc Id: XM_039083732   ⟹   XP_038939660
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8996,055,741 - 96,101,385 (-)NCBI
mRatBN7.2988,607,920 - 88,653,602 (-)NCBI
RefSeq Acc Id: XM_039083733   ⟹   XP_038939661
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8996,055,741 - 96,102,578 (-)NCBI
mRatBN7.2988,607,920 - 88,654,767 (-)NCBI
RefSeq Acc Id: XM_039083734   ⟹   XP_038939662
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8996,087,299 - 96,125,584 (-)NCBI
mRatBN7.2988,639,487 - 88,678,935 (-)NCBI
RefSeq Acc Id: XM_039083735   ⟹   XP_038939663
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8996,055,741 - 96,092,392 (-)NCBI
mRatBN7.2988,607,920 - 88,654,768 (-)NCBI
RefSeq Acc Id: XM_063267293   ⟹   XP_063123363
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8996,058,891 - 96,126,766 (-)NCBI
RefSeq Acc Id: XM_063267294   ⟹   XP_063123364
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8996,070,980 - 96,126,766 (-)NCBI
RefSeq Acc Id: XM_063267295   ⟹   XP_063123365
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8996,055,741 - 96,084,660 (-)NCBI
RefSeq Acc Id: XM_063267296   ⟹   XP_063123366
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8996,055,741 - 96,084,681 (-)NCBI
RefSeq Acc Id: XR_001839663
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8996,061,769 - 96,126,766 (-)NCBI
mRatBN7.2988,612,353 - 88,678,935 (-)NCBI
Rnor_6.0995,076,535 - 95,142,991 (-)NCBI
Sequence:
RefSeq Acc Id: XR_005488916
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8996,075,103 - 96,126,766 (-)NCBI
mRatBN7.2988,627,291 - 88,678,935 (-)NCBI
RefSeq Acc Id: XR_005488917
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8996,075,141 - 96,126,766 (-)NCBI
mRatBN7.2988,627,323 - 88,678,935 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001128357 (Get FASTA)   NCBI Sequence Viewer  
  XP_008765483 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939653 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939654 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939655 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939656 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939657 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939658 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939660 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939661 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939662 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939663 (Get FASTA)   NCBI Sequence Viewer  
  XP_063123363 (Get FASTA)   NCBI Sequence Viewer  
  XP_063123364 (Get FASTA)   NCBI Sequence Viewer  
  XP_063123365 (Get FASTA)   NCBI Sequence Viewer  
  XP_063123366 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAQ91027 (Get FASTA)   NCBI Sequence Viewer  
  EDL92114 (Get FASTA)   NCBI Sequence Viewer  
  EDL92115 (Get FASTA)   NCBI Sequence Viewer  
  EDL92116 (Get FASTA)   NCBI Sequence Viewer  
  EDL92117 (Get FASTA)   NCBI Sequence Viewer  
  EDL92118 (Get FASTA)   NCBI Sequence Viewer  
  EDL92119 (Get FASTA)   NCBI Sequence Viewer  
  EDL92120 (Get FASTA)   NCBI Sequence Viewer  
  EDL92121 (Get FASTA)   NCBI Sequence Viewer  
  EDL92122 (Get FASTA)   NCBI Sequence Viewer  
  EDL92123 (Get FASTA)   NCBI Sequence Viewer  
  EDL92124 (Get FASTA)   NCBI Sequence Viewer  
  EDL92125 (Get FASTA)   NCBI Sequence Viewer  
  EDL92126 (Get FASTA)   NCBI Sequence Viewer  
  EDL92127 (Get FASTA)   NCBI Sequence Viewer  
  EDL92128 (Get FASTA)   NCBI Sequence Viewer  
  EDL92129 (Get FASTA)   NCBI Sequence Viewer  
  EDL92130 (Get FASTA)   NCBI Sequence Viewer  
  EDL92131 (Get FASTA)   NCBI Sequence Viewer  
  EDL92132 (Get FASTA)   NCBI Sequence Viewer  
  EDL92133 (Get FASTA)   NCBI Sequence Viewer  
  EDL92134 (Get FASTA)   NCBI Sequence Viewer  
  EDL92135 (Get FASTA)   NCBI Sequence Viewer  
  EDL92136 (Get FASTA)   NCBI Sequence Viewer  
  EDL92137 (Get FASTA)   NCBI Sequence Viewer  
  EDL92138 (Get FASTA)   NCBI Sequence Viewer  
  EDL92139 (Get FASTA)   NCBI Sequence Viewer  
  EDL92140 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000059419.3
  ENSRNOP00000060806
  ENSRNOP00000060806.1
  ENSRNOP00000064567.3
  ENSRNOP00000074830.2
RefSeq Acc Id: NP_001128357   ⟸   NM_001134885
- UniProtKB: D3ZL95 (UniProtKB/TrEMBL),   A6JQE7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008765483   ⟸   XM_008767261
- Peptide Label: isoform X4
- UniProtKB: A6JQE7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000064567   ⟸   ENSRNOT00000070819
RefSeq Acc Id: ENSRNOP00000074830   ⟸   ENSRNOT00000085325
RefSeq Acc Id: ENSRNOP00000060806   ⟸   ENSRNOT00000064171
RefSeq Acc Id: XP_038939654   ⟸   XM_039083726
- Peptide Label: isoform X1
- UniProtKB: D3ZL95 (UniProtKB/TrEMBL),   A6JQE7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038939653   ⟸   XM_039083725
- Peptide Label: isoform X1
- UniProtKB: D3ZL95 (UniProtKB/TrEMBL),   A6JQE7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038939655   ⟸   XM_039083727
- Peptide Label: isoform X2
- UniProtKB: A6JQE7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038939656   ⟸   XM_039083728
- Peptide Label: isoform X5
- UniProtKB: A6JQF0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038939663   ⟸   XM_039083735
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038939661   ⟸   XM_039083733
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038939660   ⟸   XM_039083732
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038939658   ⟸   XM_039083730
- Peptide Label: isoform X8
- UniProtKB: M0R5A3 (UniProtKB/TrEMBL),   Q6TUH3 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038939657   ⟸   XM_039083729
- Peptide Label: isoform X6
- UniProtKB: A6JQG9 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038939662   ⟸   XM_039083734
- Peptide Label: isoform X11
- UniProtKB: A6JQH0 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000059419   ⟸   ENSRNOT00000064642
RefSeq Acc Id: XP_063123366   ⟸   XM_063267296
- Peptide Label: isoform X13
RefSeq Acc Id: XP_063123365   ⟸   XM_063267295
- Peptide Label: isoform X13
RefSeq Acc Id: XP_063123363   ⟸   XM_063267293
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063123364   ⟸   XM_063267294
- Peptide Label: isoform X7
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A2R6-F1-model_v2 AlphaFold D4A2R6 1-997 view protein structure
AF-D3ZL95-F1-model_v2 AlphaFold D3ZL95 1-1235 view protein structure

Transcriptome

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

Promoters
RGD ID:13696841
Promoter ID:EPDNEW_R7365
Type:multiple initiation site
Name:Usp40_1
Description:ubiquitin specific peptidase 40
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_6.0995,143,096 - 95,143,156EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309613 AgrOrtholog
BioCyc Gene G2FUF-26830 BioCyc
Ensembl Genes ENSRNOG00000018395 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00000049962 Ensembl
Ensembl Transcript ENSRNOT00000064171 ENTREZGENE
  ENSRNOT00000064171.3 UniProtKB/TrEMBL
  ENSRNOT00000064642.4 UniProtKB/TrEMBL
  ENSRNOT00000070819.3 UniProtKB/TrEMBL
  ENSRNOT00000085325.2 UniProtKB/TrEMBL
Gene3D-CATH Cysteine proteinases UniProtKB/TrEMBL
  Medium-chain alcohol dehydrogenases, catalytic domain UniProtKB/TrEMBL
  NAD(P)-binding Rossmann-like Domain UniProtKB/TrEMBL
InterPro ADH_C UniProtKB/TrEMBL
  ADH_GroES-like UniProtKB/TrEMBL
  GroES-like UniProtKB/TrEMBL
  NAD(P)-bd_dom_sf UniProtKB/TrEMBL
  Papain_like_cys_pep_sf UniProtKB/TrEMBL
  Peptidase_C19_UCH UniProtKB/TrEMBL
  SDH-like UniProtKB/TrEMBL
  USP_CS UniProtKB/TrEMBL
  USP_dom UniProtKB/TrEMBL
KEGG Report rno:316599 UniProtKB/TrEMBL
NCBI Gene 316599 ENTREZGENE
PANTHER SORBITOL DEHYDROGENASE UniProtKB/TrEMBL
  SORBITOL DEHYDROGENASE UniProtKB/TrEMBL
  UBIQUITIN CARBOXYL-TERMINAL HYDROLASE UniProtKB/TrEMBL
  UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 40 UniProtKB/TrEMBL
Pfam ADH_N UniProtKB/TrEMBL
  ADH_zinc_N UniProtKB/TrEMBL
  UCH UniProtKB/TrEMBL
PhenoGen Usp40 PhenoGen
PROSITE USP_1 UniProtKB/TrEMBL
  USP_2 UniProtKB/TrEMBL
  USP_3 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000018395 RatGTEx
  ENSRNOG00000049962 RatGTEx
Superfamily-SCOP GroES_like UniProtKB/TrEMBL
  SSF51735 UniProtKB/TrEMBL
  SSF54001 UniProtKB/TrEMBL
UniProt A0A0G2K923_RAT UniProtKB/TrEMBL
  A0A8J8XW61_RAT UniProtKB/TrEMBL
  A6JQE7 ENTREZGENE, UniProtKB/TrEMBL
  A6JQE8_RAT UniProtKB/TrEMBL
  A6JQE9_RAT UniProtKB/TrEMBL
  A6JQF0 ENTREZGENE, UniProtKB/TrEMBL
  A6JQF2_RAT UniProtKB/TrEMBL
  A6JQF6_RAT UniProtKB/TrEMBL
  A6JQF9_RAT UniProtKB/TrEMBL
  A6JQG0_RAT UniProtKB/TrEMBL
  A6JQG8_RAT UniProtKB/TrEMBL
  A6JQG9 ENTREZGENE, UniProtKB/TrEMBL
  A6JQH0 ENTREZGENE, UniProtKB/TrEMBL
  A6JQH1_RAT UniProtKB/TrEMBL
  A6JQH2_RAT UniProtKB/TrEMBL
  A6JQH3_RAT UniProtKB/TrEMBL
  D3ZL95 ENTREZGENE, UniProtKB/TrEMBL
  D4A2R6_RAT UniProtKB/TrEMBL
  M0R5A3 ENTREZGENE
  Q6TUH3 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary M0R5A3 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Usp40  ubiquitin specific peptidase 40  LOC100911860  ubiquitin carboxyl-terminal hydrolase 40-like  Data merged from RGD:6490066 737654 PROVISIONAL
2012-07-05 LOC100911860  ubiquitin carboxyl-terminal hydrolase 40-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-03-04 Usp40  ubiquitin specific peptidase 40  Usp40  ubiquitin specific protease 40  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Usp40  ubiquitin specific protease 40  Usp40_predicted  ubiquitin specific protease 40 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Usp40_predicted  ubiquitin specific protease 40 (predicted)      Symbol and Name status set to approved 70820 APPROVED