Usp25 (ubiquitin specific peptidase 25) - Rat Genome Database

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Gene: Usp25 (ubiquitin specific peptidase 25) Rattus norvegicus
Analyze
Symbol: Usp25
Name: ubiquitin specific peptidase 25
RGD ID: 1309003
Description: Predicted to enable SUMO binding activity; cysteine-type deubiquitinase activity; and enzyme binding activity. Predicted to be involved in several processes, including interleukin-17-mediated signaling pathway; negative regulation of ERAD pathway; and stress-activated protein kinase signaling cascade. Predicted to be located in endoplasmic reticulum. Predicted to be active in cytosol and nucleus. Orthologous to human USP25 (ubiquitin specific peptidase 25); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene; 3-chloropropane-1,2-diol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC108348050; LOC304150; ubiquitin carboxyl-terminal hydrolase 25; ubiquitin carboxyl-terminal hydrolase 25-like; ubiquitin specific protease 25
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
GRCr81129,088,283 - 29,198,323 (+)NCBIGRCr8
mRatBN7.21115,603,654 - 15,711,356 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1115,603,881 - 15,711,348 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1124,255,854 - 24,365,169 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01116,968,816 - 17,078,074 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01116,131,552 - 16,240,866 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01115,436,080 - 15,558,646 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1115,436,269 - 15,558,646 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1115,081,774 - 15,089,850 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01118,721,858 - 18,745,175 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01119,095,215 - 19,215,613 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41115,799,829 - 15,907,792 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11115,799,997 - 15,906,598 (+)NCBI
Celera1115,609,163 - 15,716,459 (+)NCBICelera
Cytogenetic Map11p11-q11NCBI
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,ISO)
endoplasmic reticulum  (ISO)
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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:18538659   PMID:22590560   PMID:22871113   PMID:35202642   PMID:37814350  


Genomics

Comparative Map Data
Usp25
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81129,088,283 - 29,198,323 (+)NCBIGRCr8
mRatBN7.21115,603,654 - 15,711,356 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1115,603,881 - 15,711,348 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1124,255,854 - 24,365,169 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01116,968,816 - 17,078,074 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01116,131,552 - 16,240,866 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01115,436,080 - 15,558,646 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1115,436,269 - 15,558,646 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1115,081,774 - 15,089,850 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01118,721,858 - 18,745,175 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01119,095,215 - 19,215,613 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41115,799,829 - 15,907,792 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11115,799,997 - 15,906,598 (+)NCBI
Celera1115,609,163 - 15,716,459 (+)NCBICelera
Cytogenetic Map11p11-q11NCBI
USP25
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382115,729,982 - 15,880,064 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2115,729,982 - 15,880,064 (+)EnsemblGRCh38hg38GRCh38
GRCh372117,102,301 - 17,252,383 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362116,024,367 - 16,174,248 (+)NCBINCBI36Build 36hg18NCBI36
Build 342116,024,366 - 16,174,248NCBI
Celera212,272,740 - 2,422,618 (+)NCBICelera
Cytogenetic Map21q21.1NCBI
HuRef212,481,855 - 2,631,589 (+)NCBIHuRef
CHM1_12116,663,002 - 16,812,990 (+)NCBICHM1_1
T2T-CHM13v2.02114,085,398 - 14,235,467 (+)NCBIT2T-CHM13v2.0
Usp25
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391676,810,573 - 76,913,671 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1676,810,594 - 76,913,668 (+)EnsemblGRCm39 Ensembl
GRCm381677,013,684 - 77,116,783 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1677,013,706 - 77,116,780 (+)EnsemblGRCm38mm10GRCm38
MGSCv371677,014,314 - 77,117,025 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361676,896,661 - 76,999,372 (+)NCBIMGSCv36mm8
Celera1677,241,870 - 77,344,813 (+)NCBICelera
Cytogenetic Map16C3.1NCBI
cM Map1644.4NCBI
Usp25
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540717,429,299 - 17,575,262 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540717,429,299 - 17,572,138 (+)NCBIChiLan1.0ChiLan1.0
USP25
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22212,219,944 - 12,367,486 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1217,053,528 - 7,201,118 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0212,468,993 - 2,618,200 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12115,834,158 - 15,982,182 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2115,724,729 - 15,982,182 (+)Ensemblpanpan1.1panPan2
USP25
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13112,555,614 - 12,692,765 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3112,555,595 - 12,691,694 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3112,567,579 - 12,704,519 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03112,582,490 - 12,719,684 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3112,582,034 - 12,718,862 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13112,553,996 - 12,690,361 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03112,592,012 - 12,728,277 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03112,989,867 - 13,126,766 (+)NCBIUU_Cfam_GSD_1.0
Usp25
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440497113,693,817 - 13,762,699 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365058,548,677 - 8,681,232 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365058,613,588 - 8,683,560 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
USP25
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13180,571,342 - 180,712,435 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113180,571,019 - 180,708,966 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213190,890,832 - 191,008,377 (+)NCBISscrofa10.2Sscrofa10.2susScr3
USP25
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1276,660,926 - 76,805,153 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl276,662,159 - 76,791,688 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605077,159,534 - 77,305,841 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Usp25
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247454,169,938 - 4,305,122 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247454,170,328 - 4,306,604 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Usp25
757 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:526
Count of miRNA genes:267
Interacting mature miRNAs:312
Transcripts:ENSRNOT00000002150
Prediction methods:Microtar, 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
634341Bw121Body weight QTL 1213.56abdominal fat pad mass (VT:1000711)abdominal fat pad weight (CMO:0000088)11121836709Rat
1598842Glom10Glomerulus QTL 103.4kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)11135331169Rat
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11169446234Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)11104193166113562Rat
1641927Alcrsp10Alcohol response QTL 10alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)11843667453436674Rat
2290451Scl58Serum cholesterol level QTL 583.48blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)111283104625121472Rat


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 43 27 19 27 8 10 74 35 41 11 8
Low 1 14 14 14 1
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000002150   ⟹   ENSRNOP00000002150
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1115,603,881 - 15,711,348 (+)Ensembl
Rnor_6.0 Ensembl1115,436,269 - 15,558,638 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000009911   ⟹   ENSRNOP00000009911
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1115,081,774 - 15,089,850 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000084928   ⟹   ENSRNOP00000071094
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1115,624,409 - 15,711,348 (+)Ensembl
Rnor_6.0 Ensembl1115,436,382 - 15,558,646 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000104051   ⟹   ENSRNOP00000080323
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1115,603,881 - 15,711,348 (+)Ensembl
RefSeq Acc Id: NM_001107114   ⟹   NP_001100584
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81129,090,653 - 29,198,316 (+)NCBI
mRatBN7.21115,603,695 - 15,711,349 (+)NCBI
Rnor_6.01115,436,269 - 15,558,638 (+)NCBI
Rnor_5.01119,095,215 - 19,215,613 (+)NCBI
RGSC_v3.41115,799,829 - 15,907,792 (+)RGD
Celera1115,609,163 - 15,716,459 (+)RGD
Sequence:
RefSeq Acc Id: XM_063270602   ⟹   XP_063126672
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81129,090,610 - 29,198,323 (+)NCBI
RefSeq Acc Id: XM_063270603   ⟹   XP_063126673
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81129,090,655 - 29,198,323 (+)NCBI
RefSeq Acc Id: XM_063270604   ⟹   XP_063126674
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81129,090,610 - 29,195,322 (+)NCBI
RefSeq Acc Id: XM_063270605   ⟹   XP_063126675
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81129,088,283 - 29,198,323 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001100584   ⟸   NM_001107114
- UniProtKB: D4ACD3 (UniProtKB/TrEMBL),   A6JL28 (UniProtKB/TrEMBL),   A0A0G2JZL5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000071094   ⟸   ENSRNOT00000084928
RefSeq Acc Id: ENSRNOP00000002150   ⟸   ENSRNOT00000002150
RefSeq Acc Id: ENSRNOP00000009911   ⟸   ENSRNOT00000009911
RefSeq Acc Id: ENSRNOP00000080323   ⟸   ENSRNOT00000104051
RefSeq Acc Id: XP_063126675   ⟸   XM_063270605
- Peptide Label: isoform X4
RefSeq Acc Id: XP_063126672   ⟸   XM_063270602
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZPF8 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063126674   ⟸   XM_063270604
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063126673   ⟸   XM_063270603
- Peptide Label: isoform X2
Protein Domains
USP

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZWN5-F1-model_v2 AlphaFold D3ZWN5 1-249 view protein structure
AF-D4ACD3-F1-model_v2 AlphaFold D4ACD3 1-1055 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:1309003 AgrOrtholog
BioCyc Gene G2FUF-22182 BioCyc
Ensembl Genes ENSRNOG00000001573 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00000050713 Ensembl
Ensembl Transcript ENSRNOT00000002150 ENTREZGENE
  ENSRNOT00000002150.7 UniProtKB/TrEMBL
  ENSRNOT00000084928.2 UniProtKB/TrEMBL
  ENSRNOT00000104051.1 UniProtKB/TrEMBL
Gene3D-CATH 6.10.250.1720 UniProtKB/TrEMBL
  Cysteine proteinases UniProtKB/TrEMBL
  DNA helicase RuvA subunit, C-terminal domain UniProtKB/TrEMBL
InterPro Papain_like_cys_pep_sf UniProtKB/TrEMBL
  Pept_C19ubi-hydrolase_C_CS UniProtKB/TrEMBL
  Peptidase_C19 UniProtKB/TrEMBL
  UBA-like UniProtKB/TrEMBL
  Ubiquitin-int_motif UniProtKB/TrEMBL
  UBP14-like UniProtKB/TrEMBL
  UCH/PAN2 UniProtKB/TrEMBL
KEGG Report rno:304150 UniProtKB/TrEMBL
NCBI Gene 304150 ENTREZGENE
PANTHER UBIQUITIN CARBOXYL-TERMINAL HYDROLASE UniProtKB/TrEMBL
  UBIQUITIN CARBOXYL-TERMINAL HYDROLASE UniProtKB/TrEMBL
  UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 2-RELATED UniProtKB/TrEMBL
  UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 25 UniProtKB/TrEMBL
Pfam UCH UniProtKB/TrEMBL
  UIM UniProtKB/TrEMBL
PhenoGen Usp25 PhenoGen
PROSITE UCH_2_1 UniProtKB/TrEMBL
  UCH_2_2 UniProtKB/TrEMBL
  UCH_2_3 UniProtKB/TrEMBL
  UIM UniProtKB/TrEMBL
RatGTEx ENSRNOG00000001573 RatGTEx
  ENSRNOG00000050713 RatGTEx
SMART UIM UniProtKB/TrEMBL
Superfamily-SCOP SSF54001 UniProtKB/TrEMBL
  UBA_like UniProtKB/TrEMBL
UniProt A0A0G2JZL5 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZPF8 ENTREZGENE, UniProtKB/TrEMBL
  A6JL28 ENTREZGENE, UniProtKB/TrEMBL
  D4ACD3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Usp25  ubiquitin specific peptidase 25  LOC108348050  ubiquitin carboxyl-terminal hydrolase 25-like  Data merged from RGD:11392568 737654 PROVISIONAL
2016-08-02 LOC108348050  ubiquitin carboxyl-terminal hydrolase 25-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-03-04 Usp25  ubiquitin specific peptidase 25  Usp25_predicted  ubiquitin specific protease 25 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-12 Usp25_predicted  ubiquitin specific protease 25 (predicted)      Symbol and Name status set to approved 70820 APPROVED