Yod1 (YOD1 deubiquitinase) - Rat Genome Database

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Gene: Yod1 (YOD1 deubiquitinase) Rattus norvegicus
Analyze
Symbol: Yod1
Name: YOD1 deubiquitinase
RGD ID: 1359726
Description: Predicted to enable K48-linked deubiquitinase activity; cysteine-type deubiquitinase activity; and ubiquitin protein ligase binding activity. Predicted to be involved in several processes, including ERAD pathway; negative regulation of retrograde protein transport, ER to cytosol; and protein deubiquitination. Predicted to be located in cytoplasm. Orthologous to human YOD1 (YOD1 deubiquitinase); PARTICIPATES IN Endoplasmic Reticulum-associated degradation pathway; INTERACTS WITH (+)-schisandrin B; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: HIV-induced protein-7-like protease; hshin7; MGC124915; ubiquitin thioesterase OTU1; YOD1 OTU deubiquinating enzyme 1 homolog; YOD1 OTU deubiquinating enzyme 1 homolog (S. cerevisiae); YOD1 OTU deubiquitinating enzyme 1 homologue; YOD1 OTU deubiquitinating enzyme 1 homologue (S. cerevisiae)
RGD Orthologs
Human
Mouse
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81344,727,319 - 44,733,933 (+)NCBIGRCr8
mRatBN7.21342,175,047 - 42,181,661 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1342,174,820 - 42,177,205 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1344,781,884 - 44,783,601 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01346,070,028 - 46,071,745 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01343,314,718 - 43,316,435 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01347,441,296 - 47,443,013 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1347,440,803 - 47,443,188 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01352,529,960 - 52,531,677 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41343,653,274 - 43,654,991 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11343,667,316 - 43,669,034 (+)NCBI
Celera1342,526,067 - 42,527,784 (+)NCBICelera
Cytogenetic Map13q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (ISO,ISS)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
3. A genomic analysis of rat proteases and protease inhibitors. Puente XS and Lopez-Otin C, Genome Res 2004 Apr;14(4):609-22.
4. GOA pipeline RGD automated data pipeline
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:15489334   PMID:19818707   PMID:21376232   PMID:22871113   PMID:23827681   PMID:24068323   PMID:27753622   PMID:38042492  


Genomics

Comparative Map Data
Yod1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81344,727,319 - 44,733,933 (+)NCBIGRCr8
mRatBN7.21342,175,047 - 42,181,661 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1342,174,820 - 42,177,205 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1344,781,884 - 44,783,601 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01346,070,028 - 46,071,745 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01343,314,718 - 43,316,435 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01347,441,296 - 47,443,013 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1347,440,803 - 47,443,188 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01352,529,960 - 52,531,677 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41343,653,274 - 43,654,991 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11343,667,316 - 43,669,034 (+)NCBI
Celera1342,526,067 - 42,527,784 (+)NCBICelera
Cytogenetic Map13q13NCBI
YOD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381207,043,849 - 207,053,116 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1207,043,849 - 207,052,980 (-)EnsemblGRCh38hg38GRCh38
GRCh371207,217,194 - 207,226,461 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361205,283,817 - 205,291,045 (-)NCBINCBI36Build 36hg18NCBI36
Celera1180,468,698 - 180,475,926 (-)NCBICelera
Cytogenetic Map1q32.1NCBI
HuRef1177,914,550 - 177,923,681 (-)NCBIHuRef
CHM1_11208,489,805 - 208,498,936 (-)NCBICHM1_1
T2T-CHM13v2.01206,309,040 - 206,318,351 (-)NCBIT2T-CHM13v2.0
Yod1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391130,645,064 - 130,652,093 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1130,645,064 - 130,652,095 (+)EnsemblGRCm39 Ensembl
GRCm381130,717,327 - 130,722,073 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1130,717,327 - 130,724,358 (+)EnsemblGRCm38mm10GRCm38
MGSCv371132,613,904 - 132,618,650 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361132,544,873 - 132,549,566 (+)NCBIMGSCv36mm8
Celera1133,340,721 - 133,345,469 (+)NCBICelera
Cytogenetic Map1E4NCBI
cM Map156.89NCBI
YOD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.176,185,650 - 6,194,005 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl76,190,752 - 6,193,284 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha75,749,059 - 5,757,297 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.075,874,444 - 5,882,763 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl75,874,444 - 5,882,058 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.175,808,168 - 5,816,424 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.075,909,780 - 5,918,003 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.075,949,935 - 5,958,184 (-)NCBIUU_Cfam_GSD_1.0
YOD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl967,672,651 - 67,681,826 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1967,672,640 - 67,681,889 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2974,057,174 - 74,061,141 (-)NCBISscrofa10.2Sscrofa10.2susScr3
YOD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12522,307,703 - 22,311,919 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2522,307,778 - 22,309,716 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605522,949,362 - 22,954,186 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Yod1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248074,443,650 - 4,446,373 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248074,443,653 - 4,448,759 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Yod1
12 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:139
Count of miRNA genes:107
Interacting mature miRNAs:123
Transcripts:ENSRNOT00000030476
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
10755495Bp387Blood pressure QTL 3873.78arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133466346187525369Rat
9589141Insul28Insulin level QTL 2810.820.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)13931346554313465Rat
70220Bp55Blood pressure QTL 555.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)133737450982374509Rat
61391Bp5Blood pressure QTL 55.6arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)132230187567301875Rat
4889861Pur29Proteinuria QTL 2913.80.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)133741558480753406Rat
1300163Cardf1Cardiac cell morphology QTL 14.18aorta morphology trait (VT:0000272)artery lesion measurement (CMO:0000975)131192944945417941Rat
2317040Aia21Adjuvant induced arthritis QTL 212.75joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)13983154154831541Rat
631645Bp121Blood pressure QTL 1213.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131491565559915655Rat
2317046Aia8Adjuvant induced arthritis QTL 83.9700000286102295joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)13983154154831541Rat
619615Bp80Blood pressure QTL 800.0354arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133975454484754544Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)138897350101631289Rat
61339Bp24Blood pressure QTL 240.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)13599466844807491Rat
70170Eae14Experimental allergic encephalomyelitis QTL 140.0024nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)132320344868203448Rat
2303032Bp328Blood pressure QTL 328arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134118402245417941Rat
1331784Bp222Blood pressure QTL 2222.944arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131769443653050594Rat
61340Bp25Blood pressure QTL 254.20.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133453521879535218Rat
1581573Uae36Urinary albumin excretion QTL 36urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13599483377046787Rat
1549897Stresp12Stress response QTL 123.35stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)133843340883433408Rat
2302275Gluco37Glucose level QTL 373.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)131192944946193066Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1320605871101339738Rat
1558644Cm45Cardiac mass QTL 453.60.002heart mass (VT:0007028)heart wet weight (CMO:0000069)132369296968692969Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133124133193395974Rat
61349Bp31Blood pressure QTL 315.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)133737450982374509Rat
2303563Bw89Body weight QTL 896body mass (VT:0001259)body weight (CMO:0000012)133228447177284471Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1330395351101056920Rat
2301962Cm72Cardiac mass QTL 724.12heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)133124133158363171Rat
1581554Pur11Proteinuria QTL 11urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13599483377046787Rat
12879477Bp401Blood pressure QTL 401arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133726209282262092Rat
1331750Bp220Blood pressure QTL 2202.98arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133741558482415584Rat
6893338Cm76Cardiac mass QTL 7600.99heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)132369296968692969Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131101056920Rat
9589164Gluco66Glucose level QTL 666.670.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)131515872260158722Rat
738036Lnnr4Liver neoplastic nodule remodeling QTL 43.64liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)13142356786Rat
7411662Foco29Food consumption QTL 2920.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)13931346554313465Rat

Markers in Region
RH144599  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21342,173,824 - 42,173,999 (+)MAPPERmRatBN7.2
Rnor_6.01347,439,808 - 47,439,982NCBIRnor6.0
Rnor_5.01352,528,472 - 52,528,646UniSTSRnor5.0
RGSC_v3.41343,651,786 - 43,651,960UniSTSRGSC3.4
Celera1342,524,579 - 42,524,753UniSTS
RH 3.4 Map13111.2UniSTS
Cytogenetic Map13q13UniSTS
Cytogenetic Map13q24-q25UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000030476   ⟹   ENSRNOP00000031836
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1342,174,820 - 42,177,205 (+)Ensembl
Rnor_6.0 Ensembl1347,440,803 - 47,443,188 (+)Ensembl
RefSeq Acc Id: NM_001008889   ⟹   NP_001008889
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81344,727,319 - 44,733,933 (+)NCBI
mRatBN7.21342,175,047 - 42,181,661 (+)NCBI
Rnor_6.01347,441,296 - 47,443,013 (+)NCBI
Rnor_5.01352,529,960 - 52,531,677 (+)NCBI
RGSC_v3.41343,653,274 - 43,654,991 (+)RGD
Celera1342,526,067 - 42,527,784 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001008889 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI07905 (Get FASTA)   NCBI Sequence Viewer  
  CAE48374 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000031836.2
  ENSRNOP00055029414
  ENSRNOP00060028030
  ENSRNOP00065027488
GenBank Protein Q32Q05 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001008889   ⟸   NM_001008889
- UniProtKB: Q32Q05 (UniProtKB/Swiss-Prot),   Q6IE74 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSRNOP00000031836   ⟸   ENSRNOT00000030476
Protein Domains
OTU

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q32Q05-F1-model_v2 AlphaFold Q32Q05 1-343 view protein structure

Transcriptome

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

Promoters
RGD ID:13698787
Promoter ID:EPDNEW_R9312
Type:single initiation site
Name:Yod1_1
Description:YOD1 deubiquitinase
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_6.01347,440,780 - 47,440,840EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359726 AgrOrtholog
BioCyc Gene G2FUF-18368 BioCyc
Ensembl Genes ENSRNOG00000025704 Ensembl, UniProtKB/Swiss-Prot
  ENSRNOG00055021186 UniProtKB/Swiss-Prot
  ENSRNOG00060019799 UniProtKB/Swiss-Prot
  ENSRNOG00065020327 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000030476.3 UniProtKB/Swiss-Prot
  ENSRNOT00055036203 UniProtKB/Swiss-Prot
  ENSRNOT00060034190 UniProtKB/Swiss-Prot
  ENSRNOT00065034327 UniProtKB/Swiss-Prot
Gene3D-CATH 3.90.70.80 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7454897 IMAGE-MGC_LOAD
InterPro OTU1_Ubl UniProtKB/Swiss-Prot
  OTU_dom UniProtKB/Swiss-Prot
  Papain-like_cys_pep_sf UniProtKB/Swiss-Prot
  Ubiquitin-like_domsf UniProtKB/Swiss-Prot
  Znf_C2H2_type UniProtKB/Swiss-Prot
KEGG Report rno:363982 UniProtKB/Swiss-Prot
MGC_CLONE MGC:124915 IMAGE-MGC_LOAD
NCBI Gene 363982 ENTREZGENE
PANTHER PTHR13312 UniProtKB/Swiss-Prot
  UBIQUITIN THIOESTERASE OTU1 UniProtKB/Swiss-Prot
Pfam OTU UniProtKB/Swiss-Prot
  OTU1_UBXL UniProtKB/Swiss-Prot
PhenoGen Yod1 PhenoGen
PROSITE OTU UniProtKB/Swiss-Prot
  ZINC_FINGER_C2H2_1 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000025704 RatGTEx
  ENSRNOG00055021186 RatGTEx
  ENSRNOG00060019799 RatGTEx
  ENSRNOG00065020327 RatGTEx
Superfamily-SCOP SSF54001 UniProtKB/Swiss-Prot
  SSF54236 UniProtKB/Swiss-Prot
UniProt OTU1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q6IE74 ENTREZGENE
UniProt Secondary Q6IE74 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-06-14 Yod1  YOD1 deubiquitinase  Yod1  YOD1 OTU deubiquinating enzyme 1 homolog (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-10-23 Yod1  YOD1 OTU deubiquinating enzyme 1 homolog (S. cerevisiae)  Yod1  YOD1 OTU deubiquitinating enzyme 1 homologue (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-04 Yod1  YOD1 OTU deubiquitinating enzyme 1 homologue (S. cerevisiae)  hshin7  HIV-induced protein-7-like protease  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-29 hshin7  HIV-induced protein-7-like protease      Symbol and Name status set to provisional 70820 PROVISIONAL