Usp38 (ubiquitin specific peptidase 38) - Rat Genome Database

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Gene: Usp38 (ubiquitin specific peptidase 38) Rattus norvegicus
Analyze
Symbol: Usp38
Name: ubiquitin specific peptidase 38
RGD ID: 1311974
Description: Predicted to enable cysteine-type deubiquitinase activity and protein sequestering activity. Predicted to be involved in negative regulation of innate immune response and negative regulation of proteasomal ubiquitin-dependent protein catabolic process. Predicted to be active in cytosol and nucleus. Orthologous to human USP38 (ubiquitin specific peptidase 38); INTERACTS WITH 17beta-estradiol; 2,6-dinitrotoluene; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC307764; ubiquitin carboxyl-terminal hydrolase 38; ubiquitin specific protease 38
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
GRCr81943,910,459 - 43,941,875 (+)NCBIGRCr8
mRatBN7.21927,006,046 - 27,037,449 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1927,006,046 - 27,037,437 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1933,859,775 - 33,891,219 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01934,513,838 - 34,545,280 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01936,738,942 - 36,770,306 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01930,668,258 - 30,699,852 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1930,668,602 - 30,699,859 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01941,576,070 - 41,607,659 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41928,847,283 - 28,879,605 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11928,852,729 - 28,883,368 (+)NCBI
Celera1926,525,530 - 26,557,224 (+)NCBICelera
Cytogenetic Map19q11NCBI
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

Cellular Component
cytoplasm  (ISO)
cytosol  (IBA)
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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:14715245  


Genomics

Comparative Map Data
Usp38
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81943,910,459 - 43,941,875 (+)NCBIGRCr8
mRatBN7.21927,006,046 - 27,037,449 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1927,006,046 - 27,037,437 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1933,859,775 - 33,891,219 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01934,513,838 - 34,545,280 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01936,738,942 - 36,770,306 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01930,668,258 - 30,699,852 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1930,668,602 - 30,699,859 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01941,576,070 - 41,607,659 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41928,847,283 - 28,879,605 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11928,852,729 - 28,883,368 (+)NCBI
Celera1926,525,530 - 26,557,224 (+)NCBICelera
Cytogenetic Map19q11NCBI
USP38
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh384143,184,917 - 143,223,874 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl4143,184,917 - 143,223,874 (+)EnsemblGRCh38hg38GRCh38
GRCh374144,106,070 - 144,145,027 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 364144,325,548 - 144,362,090 (+)NCBINCBI36Build 36hg18NCBI36
Build 344144,463,702 - 144,500,244NCBI
Celera4141,435,984 - 141,473,049 (+)NCBICelera
Cytogenetic Map4q31.21NCBI
HuRef4139,835,778 - 139,872,846 (+)NCBIHuRef
CHM1_14144,083,284 - 144,120,348 (+)NCBICHM1_1
T2T-CHM13v2.04146,502,094 - 146,541,045 (+)NCBIT2T-CHM13v2.0
Usp38
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39881,707,353 - 81,741,631 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl881,707,362 - 81,741,557 (-)EnsemblGRCm39 Ensembl
GRCm38880,980,724 - 81,015,013 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl880,980,733 - 81,014,928 (-)EnsemblGRCm38mm10GRCm38
MGSCv37883,504,632 - 83,538,805 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36883,876,479 - 83,910,652 (-)NCBIMGSCv36mm8
Celera885,259,181 - 85,286,557 (-)NCBICelera
Celera875,127,726 - 75,134,583 (+)NCBICelera
Cytogenetic Map8C2NCBI
cM Map838.68NCBI
Usp38
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955471315,779 - 350,982 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955471316,319 - 350,982 (-)NCBIChiLan1.0ChiLan1.0
USP38
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v23141,060,691 - 141,106,019 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan14141,448,446 - 141,493,761 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v04135,545,818 - 135,582,520 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.14146,844,850 - 146,881,486 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl4146,844,850 - 146,881,486 (+)Ensemblpanpan1.1panPan2
USP38
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.119201,810 - 238,361 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl19210,388 - 238,384 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha19450,450 - 488,291 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.019225,088 - 262,681 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl19233,599 - 262,766 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.119204,694 - 242,742 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.019565,325 - 603,796 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.019919,303 - 957,368 (-)NCBIUU_Cfam_GSD_1.0
Usp38
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530147,708,507 - 47,740,441 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365355,146,327 - 5,178,205 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365355,146,327 - 5,178,184 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
USP38
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl884,567,618 - 84,601,224 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1884,567,476 - 84,601,044 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2889,716,675 - 89,724,274 (-)NCBISscrofa10.2Sscrofa10.2susScr3
USP38
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1790,049,643 - 90,087,152 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl790,049,638 - 90,089,110 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603769,649,470 - 69,688,113 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Usp38
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248532,485,332 - 2,518,070 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248532,485,347 - 2,519,165 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Usp38
118 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:73
Count of miRNA genes:63
Interacting mature miRNAs:67
Transcripts:ENSRNOT00000035084
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054132Srcrt9Stress Responsive Cort QTL 92.870.0017blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19127355345Rat
631678Cm9Cardiac mass QTL 94.270.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)19128982497Rat
631681Cm12Cardiac mass QTL 123.330.00053heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)19128982497Rat
1549847Bss8Bone structure and strength QTL 84lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)19131963836Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19136824771Rat
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19136824771Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19136824771Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19136824771Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)1956937445569374Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)1956937445569374Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19218792746708701Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19231612147316121Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19320477748204777Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19745724942983518Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19997775339654489Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191082797043544039Rat
61407Scl12Serum cholesterol level QTL 120.001blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)191392640130303727Rat
1558656Prcs1Prostate cancer susceptibility QTL 15prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)191511459834521833Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191545586057337602Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191560502346559041Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191563020157337602Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)191715443357337602Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192048357557337602Rat
61328Eae8Experimental allergic encephalomyelitis QTL 84nervous system integrity trait (VT:0010566)percentage of study population developing experimental autoimmune encephalomyelitis during a period of time (CMO:0001047)192481604133061905Rat
1549835Tcas7Tongue tumor susceptibility QTL 70.001tongue integrity trait (VT:0010553)squamous cell carcinoma of the head and neck tumor number (CMO:0001876)192481797839654489Rat

Markers in Region
D19Rat48  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21927,021,131 - 27,021,310 (+)MAPPERmRatBN7.2
Rnor_6.01930,683,540 - 30,683,718NCBIRnor6.0
Rnor_5.01941,591,347 - 41,591,525UniSTSRnor5.0
RGSC_v3.41928,863,284 - 28,863,794RGDRGSC3.4
RGSC_v3.41928,863,299 - 28,863,477UniSTSRGSC3.4
RGSC_v3.11928,868,110 - 28,868,620RGD
Celera1926,540,915 - 26,541,093UniSTS
SHRSP x BN Map1920.2998RGD
SHRSP x BN Map1920.2998UniSTS
Cytogenetic Map19q11UniSTS
RH134797  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21927,036,940 - 27,037,127 (+)MAPPERmRatBN7.2
Rnor_6.01930,699,353 - 30,699,539NCBIRnor6.0
Rnor_5.01941,607,160 - 41,607,346UniSTSRnor5.0
RGSC_v3.41928,879,109 - 28,879,295UniSTSRGSC3.4
Celera1926,556,725 - 26,556,911UniSTS
Cytogenetic Map19q11UniSTS


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 26 56 40 19 40 4 5 71 33 38 11 4
Low 17 1 1 1 4 6 3 2 3 4
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000035084   ⟹   ENSRNOP00000031071
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1927,006,046 - 27,037,437 (+)Ensembl
Rnor_6.0 Ensembl1930,668,602 - 30,699,859 (+)Ensembl
RefSeq Acc Id: NM_001107418   ⟹   NP_001100888
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81943,910,474 - 43,941,869 (+)NCBI
mRatBN7.21927,006,046 - 27,037,440 (+)NCBI
RefSeq Acc Id: XM_039097727   ⟹   XP_038953655
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81943,929,791 - 43,941,875 (+)NCBI
mRatBN7.21927,027,586 - 27,037,449 (+)NCBI
RefSeq Acc Id: XM_039097728   ⟹   XP_038953656
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81943,910,461 - 43,937,004 (+)NCBI
mRatBN7.21927,006,046 - 27,032,575 (+)NCBI
RefSeq Acc Id: XM_063278019   ⟹   XP_063134089
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81943,915,302 - 43,941,875 (+)NCBI
RefSeq Acc Id: XR_005496654
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81943,910,459 - 43,933,579 (+)NCBI
mRatBN7.21927,006,046 - 27,029,150 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001100888 (Get FASTA)   NCBI Sequence Viewer  
  XP_038953655 (Get FASTA)   NCBI Sequence Viewer  
  XP_038953656 (Get FASTA)   NCBI Sequence Viewer  
  XP_063134089 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL92296 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000031071
  ENSRNOP00000031071.4
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000031071   ⟸   ENSRNOT00000035084
RefSeq Acc Id: NP_001100888   ⟸   NM_001107418
- UniProtKB: D3Z8K5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038953656   ⟸   XM_039097728
- Peptide Label: isoform X3
- UniProtKB: A6IYG8 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038953655   ⟸   XM_039097727
- Peptide Label: isoform X2
RefSeq Acc Id: XP_063134089   ⟸   XM_063278019
- Peptide Label: isoform X1
Protein Domains
USP

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3Z8K5-F1-model_v2 AlphaFold D3Z8K5 1-1041 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311974 AgrOrtholog
BioCyc Gene G2FUF-5980 BioCyc
Ensembl Genes ENSRNOG00000026880 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000035084 ENTREZGENE
  ENSRNOT00000035084.7 UniProtKB/TrEMBL
Gene3D-CATH Cysteine proteinases UniProtKB/TrEMBL
InterPro ARM-type_fold UniProtKB/TrEMBL
  Papain_like_cys_pep_sf UniProtKB/TrEMBL
  Pept_C19ubi-hydrolase_C_CS UniProtKB/TrEMBL
  Peptidase_C19 UniProtKB/TrEMBL
  UCH/PAN2 UniProtKB/TrEMBL
  USP38 UniProtKB/TrEMBL
  Usp38-like_N UniProtKB/TrEMBL
NCBI Gene 307764 ENTREZGENE
PANTHER UBIQUITIN CARBOXYL-TERMINAL HYDROLASE UniProtKB/TrEMBL
  UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 38 UniProtKB/TrEMBL
Pfam UCH UniProtKB/TrEMBL
  Usp38-like_N UniProtKB/TrEMBL
PhenoGen Usp38 PhenoGen
PROSITE UCH_2_1 UniProtKB/TrEMBL
  UCH_2_2 UniProtKB/TrEMBL
  UCH_2_3 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000026880 RatGTEx
Superfamily-SCOP ARM repeat UniProtKB/TrEMBL
  SSF54001 UniProtKB/TrEMBL
UniProt A6IYG8 ENTREZGENE, UniProtKB/TrEMBL
  D3Z8K5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-04 Usp38  ubiquitin specific peptidase 38  Usp38_predicted  ubiquitin specific protease 38 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-12 Usp38_predicted  ubiquitin specific protease 38 (predicted)      Symbol and Name status set to approved 70820 APPROVED