Otud6a (OTU deubiquitinase 6A) - Rat Genome Database

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Gene: Otud6a (OTU deubiquitinase 6A) Rattus norvegicus
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Symbol: Otud6a
Name: OTU deubiquitinase 6A
RGD ID: 1560855
Description: Predicted to enable cysteine-type deubiquitinase activity. Predicted to be involved in protein deubiquitination. Orthologous to human OTUD6A (OTU deubiquitinase 6A); INTERACTS WITH Cuprizon; all-trans-retinoic acid (ortholog); benzo[a]pyrene (ortholog).
Type: protein-coding
RefSeq Status: INFERRED
Previously known as: LOC302426; OTU domain containing 6A; OTU domain-containing protein 6A; RGD1560855; similar to Hin-6 protease
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X69,554,215 - 69,556,389 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX69,554,036 - 69,556,386 (+)EnsemblGRCr8
mRatBN7.2X65,514,113 - 65,516,287 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX65,514,191 - 65,515,063 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX66,997,545 - 66,999,719 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X70,497,935 - 70,500,109 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X68,058,827 - 68,061,001 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X70,256,299 - 70,257,746 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX70,256,737 - 70,257,609 (+)Ensemblrn6Rnor6.0
Rnor_5.0X71,129,608 - 71,130,752 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X88,427,849 - 88,428,721 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX65,874,546 - 65,875,993 (+)NCBICelera
Cytogenetic MapXq22NCBI
JBrowse:




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

Biological Process

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:23827681  


Genomics

Comparative Map Data
Otud6a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X69,554,215 - 69,556,389 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX69,554,036 - 69,556,386 (+)EnsemblGRCr8
mRatBN7.2X65,514,113 - 65,516,287 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX65,514,191 - 65,515,063 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX66,997,545 - 66,999,719 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X70,497,935 - 70,500,109 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X68,058,827 - 68,061,001 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X70,256,299 - 70,257,746 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX70,256,737 - 70,257,609 (+)Ensemblrn6Rnor6.0
Rnor_5.0X71,129,608 - 71,130,752 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X88,427,849 - 88,428,721 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX65,874,546 - 65,875,993 (+)NCBICelera
Cytogenetic MapXq22NCBI
OTUD6A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X70,062,457 - 70,064,179 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX70,062,457 - 70,064,179 (+)Ensemblhg38GRCh38
GRCh37X69,282,307 - 69,284,029 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X69,199,066 - 69,200,754 (+)NCBIBuild 36Build 36hg18NCBI36
CeleraX69,635,707 - 69,637,395 (+)NCBICelera
Cytogenetic MapXq13.1NCBI
HuRefX63,103,165 - 63,104,853 (+)NCBIHuRef
CHM1_1X69,175,955 - 69,177,643 (+)NCBICHM1_1
T2T-CHM13v2.0X68,495,808 - 68,497,530 (+)NCBIT2T-CHM13v2.0
Otud6a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X99,472,514 - 99,474,859 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX99,472,619 - 99,473,491 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38X100,428,908 - 100,429,885 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX100,429,013 - 100,429,885 (+)Ensemblmm10GRCm38
MGSCv37X97,624,352 - 97,625,224 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36X96,631,732 - 96,632,604 (+)NCBIMGSCv36mm8
CeleraX87,354,623 - 87,355,359 (+)NCBICelera
Cytogenetic MapXC3NCBI
cM MapX43.72NCBI
Otud6a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554759,626,733 - 9,629,841 (+)NCBIChiLan1.0ChiLan1.0
OTUD6A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X69,738,016 - 69,743,091 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X69,741,619 - 69,746,694 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X59,331,364 - 59,333,978 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X69,393,964 - 69,394,910 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX69,394,044 - 69,394,910 (+)EnsemblpanPan2panpan1.1
OTUD6A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X54,546,016 - 54,548,379 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX54,546,123 - 54,546,983 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_TashaX45,372,133 - 45,374,509 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0X55,512,419 - 55,514,795 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX55,512,544 - 55,513,404 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X53,481,460 - 53,483,839 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X54,812,259 - 54,814,635 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X54,739,422 - 54,741,798 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Otud6a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X47,616,949 - 47,618,324 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049367771,616,038 - 1,616,913 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
OTUD6A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX56,134,853 - 56,135,722 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1X56,134,479 - 56,137,096 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X63,332,231 - 63,333,313 (+)NCBISscrofa10.2Sscrofa10.2susScr3
OTUD6A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X59,889,957 - 59,893,168 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX59,890,630 - 59,891,496 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660651,753,324 - 1,754,885 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Otud6a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462490327,196 - 28,465 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Otud6a
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1X58,182,483 - 58,183,355 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Otud6a
9 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:36
Count of miRNA genes:36
Interacting mature miRNAs:36
Transcripts:ENSRNOT00000029298
Prediction methods:Miranda, Pita, Rnahybrid
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX45182909117740458Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between duration of physical contact or close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X4493088389930883Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
circulatory system
ectoderm
endocrine system
endoderm
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
1 13 35 5 3 24 19 34 4 50 3

Sequence


Ensembl Acc Id: ENSRNOT00000029298   ⟹   ENSRNOP00000037319
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX69,554,036 - 69,556,386 (+)Ensembl
mRatBN7.2 EnsemblX65,514,191 - 65,515,063 (+)Ensembl
Rnor_6.0 EnsemblX70,256,737 - 70,257,609 (+)Ensembl
RefSeq Acc Id: NM_001401127   ⟹   NP_001388056
RefSeq Status: INFERRED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X69,554,215 - 69,556,389 (+)NCBI
mRatBN7.2X65,514,113 - 65,516,287 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001388056 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000037319
  ENSRNOP00000037319.4
Ensembl Acc Id: ENSRNOP00000037319   ⟸   ENSRNOT00000029298
RefSeq Acc Id: NP_001388056   ⟸   NM_001401127
- UniProtKB: D3ZX46 (UniProtKB/TrEMBL)
Protein Domains
OTU

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZX46-F1-model_v2 AlphaFold D3ZX46 1-290 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:1560855 AgrOrtholog
BioCyc Gene G2FUF-2135 BioCyc
Ensembl Genes ENSRNOG00000042687 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000029298 ENTREZGENE
  ENSRNOT00000029298.6 UniProtKB/TrEMBL
Gene3D-CATH 3.90.70.80 UniProtKB/TrEMBL
InterPro OTU UniProtKB/TrEMBL
  OTU_OTUD6 UniProtKB/TrEMBL
  OTU_ubiquitin_thioesterase UniProtKB/TrEMBL
  Papain_like_cys_pep_sf UniProtKB/TrEMBL
NCBI Gene 302426 ENTREZGENE
PANTHER OTU DOMAIN CONTAINING PROTEIN UniProtKB/TrEMBL
  OTU DOMAIN-CONTAINING PROTEIN 6A UniProtKB/TrEMBL
Pfam OTU UniProtKB/TrEMBL
PhenoGen Otud6a PhenoGen
PROSITE OTU UniProtKB/TrEMBL
RatGTEx ENSRNOG00000042687 RatGTEx
Superfamily-SCOP SSF54001 UniProtKB/TrEMBL
UniProt D3ZX46 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-03-13 Otud6a  OTU deubiquitinase 6A  Otud6a  OTU domain containing 6A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-28 Otud6a  OTU domain containing 6A  RGD1560855_predicted  similar to Hin-6 protease (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1560855_predicted  similar to Hin-6 protease (predicted)  LOC302426  similar to Hin-6 protease  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC302426  similar to Hin-6 protease      Symbol and Name status set to provisional 70820 PROVISIONAL