Usp9y (ubiquitin specific peptidase 9, Y-linked) - Rat Genome Database

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Gene: Usp9y (ubiquitin specific peptidase 9, Y-linked) Rattus norvegicus
Analyze
Symbol: Usp9y
Name: ubiquitin specific peptidase 9, Y-linked
RGD ID: 9087771
Description: Predicted to enable cysteine-type deubiquitinase activity. Predicted to be involved in proteolysis. Human ortholog(s) of this gene implicated in Y-linked spermatogenic failure 2. Orthologous to human USP9Y (ubiquitin specific peptidase 9 Y-linked); INTERACTS WITH aflatoxin B1 (ortholog); arsenite(3-) (ortholog); benzo[a]pyrene (ortholog).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: probable ubiquitin carboxyl-terminal hydrolase FAF-X; ubiquitin specific peptidase 9 Y-linked
RGD Orthologs
Human
Mouse
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8Y1,231,079 - 1,375,897 (-)NCBIGRCr8
mRatBN7.2Y1,156,135 - 1,300,965 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblY1,156,135 - 1,300,943 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxY847,488 - 992,719 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0Y956,943 - 1,101,671 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0Y1,596,613 - 1,741,347 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0Y1,260,512 - 1,403,417 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblY1,258,794 - 1,403,422 (-)EnsemblRnor6.0rn6Rnor6.0
Cytogenetic MapYq11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
cell migration  (IBA,IEA)
proteolysis  (IEA)

Cellular Component
cytosol  (IBA,IEA)
nucleus  (IBA,IEA)

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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:24759410   PMID:24759411  


Genomics

Comparative Map Data
Usp9y
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8Y1,231,079 - 1,375,897 (-)NCBIGRCr8
mRatBN7.2Y1,156,135 - 1,300,965 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblY1,156,135 - 1,300,943 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxY847,488 - 992,719 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0Y956,943 - 1,101,671 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0Y1,596,613 - 1,741,347 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0Y1,260,512 - 1,403,417 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblY1,258,794 - 1,403,422 (-)EnsemblRnor6.0rn6Rnor6.0
Cytogenetic MapYq11NCBI
USP9Y
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38Y12,701,231 - 12,860,839 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblY12,537,650 - 12,860,839 (+)EnsemblGRCh38hg38GRCh38
GRCh37Y14,813,160 - 14,972,764 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36Y13,322,554 - 13,482,162 (+)NCBINCBI36Build 36hg18NCBI36
Build 34Y13,251,290 - 13,410,221NCBI
CeleraX1,806,447 - 1,966,226 (+)NCBICelera
Cytogenetic MapYq11.221NCBI
HuRefY9,466,609 - 9,625,605 (+)NCBIHuRef
T2T-CHM13v2.0Y13,609,504 - 13,769,113 (+)NCBIT2T-CHM13v2.0
Usp9y
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39Y1,298,961 - 1,459,782 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblY1,298,961 - 1,459,782 (-)EnsemblGRCm39 Ensembl
GRCm38Y1,298,961 - 1,459,782 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblY1,298,961 - 1,459,782 (-)EnsemblGRCm38mm10GRCm38
MGSCv37Y635,404 - 796,225 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36Y635,404 - 796,225 (-)NCBIMGSCv36mm8
CeleraY4,124,516 - 4,284,849 (-)NCBICelera
Cytogenetic MapYpterNCBI

Variants

.
Variants in Usp9y
287 total Variants

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 8
Low 11
Below cutoff 2 9 25 9 18 9 8 9 9 9 6 10 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000088719   ⟹   ENSRNOP00000071193
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblY1,159,944 - 1,300,943 (-)Ensembl
Rnor_6.0 EnsemblY1,260,521 - 1,398,030 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092901   ⟹   ENSRNOP00000076011
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblY1,156,135 - 1,300,943 (-)Ensembl
Rnor_6.0 EnsemblY1,258,794 - 1,305,026 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000093067   ⟹   ENSRNOP00000075990
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblY1,305,230 - 1,403,422 (-)Ensembl
RefSeq Acc Id: NM_001329902   ⟹   NP_001316831
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8Y1,231,079 - 1,375,883 (-)NCBI
mRatBN7.2Y1,156,135 - 1,300,943 (-)NCBI
RefSeq Acc Id: XM_039100657   ⟹   XP_038956585
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8Y1,232,796 - 1,375,893 (-)NCBI
mRatBN7.2Y1,157,742 - 1,300,965 (-)NCBI
RefSeq Acc Id: XM_039100658   ⟹   XP_038956586
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8Y1,232,796 - 1,375,897 (-)NCBI
mRatBN7.2Y1,157,742 - 1,300,965 (-)NCBI
RefSeq Acc Id: XM_063280594   ⟹   XP_063136664
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8Y1,232,796 - 1,375,893 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000076011   ⟸   ENSRNOT00000092901
RefSeq Acc Id: ENSRNOP00000075990   ⟸   ENSRNOT00000093067
RefSeq Acc Id: ENSRNOP00000071193   ⟸   ENSRNOT00000088719
RefSeq Acc Id: NP_001316831   ⟸   NM_001329902
- UniProtKB: G4XKZ2 (UniProtKB/TrEMBL),   A0A1B0GWT2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038956585   ⟸   XM_039100657
- Peptide Label: isoform X1
- UniProtKB: A0A1B0GWT2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038956586   ⟸   XM_039100658
- Peptide Label: isoform X2
- UniProtKB: A0A1B0GWT2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063136664   ⟸   XM_063280594
- Peptide Label: isoform X2
Protein Domains
USP

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2JZU8-F1-model_v2 AlphaFold A0A0G2JZU8 1-2551 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:9087771 AgrOrtholog
BioCyc Gene G2FUF-565 BioCyc
Ensembl Genes ENSRNOG00000058664 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000088719.2 UniProtKB/TrEMBL
  ENSRNOT00000092901 ENTREZGENE
  ENSRNOT00000092901.2 UniProtKB/TrEMBL
Gene3D-CATH Cysteine proteinases UniProtKB/TrEMBL
InterPro ARM-type_fold UniProtKB/TrEMBL
  DUF3517 UniProtKB/TrEMBL
  Papain_like_cys_pep_sf UniProtKB/TrEMBL
  Peptidase_C19_UCH UniProtKB/TrEMBL
  USP_CS UniProtKB/TrEMBL
  USP_dom UniProtKB/TrEMBL
KEGG Report rno:103694559 UniProtKB/TrEMBL
NCBI Gene Usp9y ENTREZGENE
PANTHER UBIQUITIN CARBOXYL-TERMINAL HYDROLASE UniProtKB/TrEMBL
  UBIQUITIN CARBOXYL-TERMINAL HYDROLASE FAF-Y-RELATED UniProtKB/TrEMBL
Pfam DUF3517 UniProtKB/TrEMBL
  UCH UniProtKB/TrEMBL
PhenoGen Usp9y PhenoGen
PROSITE USP_1 UniProtKB/TrEMBL
  USP_2 UniProtKB/TrEMBL
  USP_3 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000058664 RatGTEx
Superfamily-SCOP SSF48371 UniProtKB/TrEMBL
  SSF54001 UniProtKB/TrEMBL
UniProt A0A0G2JZU8_RAT UniProtKB/TrEMBL
  A0A1B0GWT2 ENTREZGENE, UniProtKB/TrEMBL
  G4XKZ2 ENTREZGENE, UniProtKB/TrEMBL
  W8CC82_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-08-25 Usp9y  ubiquitin specific peptidase 9, Y-linked      Symbol and Name status set to provisional 70820 PROVISIONAL