Otud6b (OTU deubiquitinase 6B) - Rat Genome Database

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Gene: Otud6b (OTU deubiquitinase 6B) Rattus norvegicus
Analyze
Symbol: Otud6b
Name: OTU deubiquitinase 6B
RGD ID: 1310024
Description: Predicted to enable cysteine-type deubiquitinase activity. Predicted to be involved in cell population proliferation; proteasome assembly; and regulation of translation. Predicted to be part of eukaryotic translation initiation factor 4F complex. Orthologous to human OTUD6B (OTU deubiquitinase 6B); INTERACTS WITH (+)-schisandrin B; 2,4-dinitrotoluene; 3-chloropropane-1,2-diol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: deubiquitinase OTUD6B; LOC297911; OTU domain containing 6B; OTU domain-containing protein 6B; RGD1310024; similar to RIKEN cDNA 2600013N14
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
GRCr8532,979,190 - 33,011,781 (-)NCBIGRCr8
mRatBN7.2528,181,992 - 28,214,486 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl528,023,594 - 28,214,334 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx530,353,872 - 30,369,010 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0531,946,556 - 31,961,694 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0531,906,713 - 31,921,851 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0528,333,019 - 28,350,093 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl528,333,019 - 28,349,927 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0533,017,035 - 33,034,265 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4529,268,066 - 29,283,381 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1529,230,845 - 29,283,260 (-)NCBI
Celera527,450,913 - 27,466,028 (-)NCBICelera
Cytogenetic Map5q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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:21267069   PMID:27864334   PMID:28343629  


Genomics

Comparative Map Data
Otud6b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8532,979,190 - 33,011,781 (-)NCBIGRCr8
mRatBN7.2528,181,992 - 28,214,486 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl528,023,594 - 28,214,334 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx530,353,872 - 30,369,010 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0531,946,556 - 31,961,694 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0531,906,713 - 31,921,851 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0528,333,019 - 28,350,093 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl528,333,019 - 28,349,927 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0533,017,035 - 33,034,265 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4529,268,066 - 29,283,381 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1529,230,845 - 29,283,260 (-)NCBI
Celera527,450,913 - 27,466,028 (-)NCBICelera
Cytogenetic Map5q13NCBI
OTUD6B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38891,070,344 - 91,087,093 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl891,070,196 - 91,087,095 (+)EnsemblGRCh38hg38GRCh38
GRCh37892,082,572 - 92,099,321 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36892,151,600 - 92,168,499 (+)NCBINCBI36Build 36hg18NCBI36
Celera888,277,450 - 88,294,349 (+)NCBICelera
Cytogenetic Map8q21.3NCBI
HuRef887,293,694 - 87,310,590 (+)NCBIHuRef
CHM1_1892,123,085 - 92,139,970 (+)NCBICHM1_1
T2T-CHM13v2.0892,195,269 - 92,212,018 (+)NCBIT2T-CHM13v2.0
Otud6b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39414,809,503 - 14,826,413 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl414,809,498 - 14,826,587 (-)EnsemblGRCm39 Ensembl
GRCm38414,809,505 - 14,826,413 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl414,809,498 - 14,826,587 (-)EnsemblGRCm38mm10GRCm38
MGSCv37414,736,652 - 14,753,734 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36414,736,652 - 14,753,531 (-)NCBIMGSCv36mm8
Celera414,601,182 - 14,626,052 (-)NCBICelera
Cytogenetic Map4A1NCBI
cM Map46.38NCBI
Otud6b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554177,844,292 - 7,858,658 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554177,844,311 - 7,859,032 (+)NCBIChiLan1.0ChiLan1.0
OTUD6B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v27108,440,903 - 108,457,789 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1883,979,464 - 83,996,406 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0887,733,597 - 87,750,481 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1889,685,766 - 89,702,661 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl889,685,766 - 89,702,659 (+)Ensemblpanpan1.1panPan2
OTUD6B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12936,466,596 - 36,485,509 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2936,433,450 - 36,483,222 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2936,618,817 - 36,638,435 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02936,667,557 - 36,687,411 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2936,667,366 - 36,713,018 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12936,687,777 - 36,707,389 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02936,669,466 - 36,689,095 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02937,108,146 - 37,127,799 (+)NCBIUU_Cfam_GSD_1.0
Otud6b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530343,087,401 - 43,104,325 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365444,688,347 - 4,702,591 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365444,688,332 - 4,705,304 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
OTUD6B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl445,772,333 - 45,793,338 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1445,776,776 - 45,793,270 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2449,397,943 - 49,414,516 (-)NCBISscrofa10.2Sscrofa10.2susScr3
OTUD6B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1886,140,202 - 86,156,906 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl886,140,327 - 86,154,676 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603954,706,534 - 54,723,240 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Otud6b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624744885,821 - 901,677 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624744875,658 - 901,540 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Otud6b
185 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:123
Count of miRNA genes:100
Interacting mature miRNAs:108
Transcripts:ENSRNOT00000008725
Prediction methods:Microtar, Miranda, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat
8552954Pigfal14Plasma insulin-like growth factor 1 level QTL 149blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)52122674466226744Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5228222669540447Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
1358353Srcrtb2Stress Responsive Cort Basal QTL 23.480.003blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)51887394774251464Rat
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5384401847869213Rat
1549901Neudeg2Neurodegradation QTL 240nervous system integrity trait (VT:0010566)mononuclear cell count (CMO:0002119)52483871044045280Rat
1641903Alcrsp3Alcohol response QTL 3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)51268928557689285Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
1578767Stresp17Stress response QTL 174.30.01blood aldosterone amount (VT:0005346)plasma aldosterone level (CMO:0000551)52795544072955440Rat
1578776Stresp18Stress response QTL 182.9thymus mass (VT:0004954)thymus wet weight (CMO:0000855)52795544072955440Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
61462Niddm10Non-insulin dependent diabetes mellitus QTL 103.90.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)5511215947171491Rat
2312562Pur18Proteinuria QTL 182.60.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5213896532656739Rat
1600358Mamtr5Mammary tumor resistance QTL 5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)51887394763873947Rat
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5894822853948228Rat


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 38 46 30 19 30 8 10 74 35 41 11 8
Low 5 11 11 11 1
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000008725   ⟹   ENSRNOP00000008726
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl528,197,325 - 28,214,334 (-)Ensembl
Rnor_6.0 Ensembl528,333,019 - 28,349,927 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000093302   ⟹   ENSRNOP00000076285
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl528,023,594 - 28,214,334 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000093477
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl528,334,912 - 28,336,024 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000093698   ⟹   ENSRNOP00000076236
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl528,181,889 - 28,214,175 (-)Ensembl
Rnor_6.0 Ensembl528,338,920 - 28,349,854 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000111015   ⟹   ENSRNOP00000086210
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl528,207,610 - 28,214,175 (-)Ensembl
RefSeq Acc Id: NM_001106639   ⟹   NP_001100109
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8532,996,453 - 33,011,568 (-)NCBI
mRatBN7.2528,199,217 - 28,214,334 (-)NCBI
Rnor_6.0528,334,912 - 28,350,074 (-)NCBI
Rnor_5.0533,017,035 - 33,034,265 (-)NCBI
RGSC_v3.4529,268,066 - 29,283,381 (-)RGD
Celera527,450,913 - 27,466,028 (-)RGD
Sequence:
RefSeq Acc Id: XM_006237914   ⟹   XP_006237976
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8532,994,562 - 33,011,781 (-)NCBI
mRatBN7.2528,197,613 - 28,214,474 (-)NCBI
Rnor_6.0528,334,031 - 28,350,093 (-)NCBI
Rnor_5.0533,017,035 - 33,034,265 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039109423   ⟹   XP_038965351
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8532,979,190 - 33,011,781 (-)NCBI
mRatBN7.2528,181,992 - 28,214,486 (-)NCBI
RefSeq Acc Id: XM_063287293   ⟹   XP_063143363
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8532,979,190 - 33,007,857 (-)NCBI
RefSeq Acc Id: XM_063287294   ⟹   XP_063143364
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8532,994,562 - 33,004,946 (-)NCBI
RefSeq Acc Id: NP_001100109   ⟸   NM_001106639
- UniProtKB: A6II95 (UniProtKB/TrEMBL),   A0A1W2Q6D9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237976   ⟸   XM_006237914
- Peptide Label: isoform X2
- UniProtKB: D3ZGY2 (UniProtKB/TrEMBL),   A0A1W2Q6D9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000008726   ⟸   ENSRNOT00000008725
RefSeq Acc Id: ENSRNOP00000076236   ⟸   ENSRNOT00000093698
RefSeq Acc Id: XP_038965351   ⟸   XM_039109423
- Peptide Label: isoform X1
- UniProtKB: A0A1W2Q6I2 (UniProtKB/TrEMBL),   A0A1W2Q6D9 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000076285   ⟸   ENSRNOT00000093302
RefSeq Acc Id: ENSRNOP00000086210   ⟸   ENSRNOT00000111015
RefSeq Acc Id: XP_063143363   ⟸   XM_063287293
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063143364   ⟸   XM_063287294
- Peptide Label: isoform X4
Protein Domains
OTU

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZGY2-F1-model_v2 AlphaFold D3ZGY2 1-285 view protein structure
AF-A0A1W2Q640-F1-model_v2 AlphaFold A0A1W2Q640 1-347 view protein structure

Transcriptome

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

Promoters
RGD ID:13693581
Promoter ID:EPDNEW_R4100
Type:initiation region
Name:Otud6b_1
Description:OTU domain containing 6B
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_6.0528,349,906 - 28,349,966EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310024 AgrOrtholog
BioCyc Gene G2FUF-41885 BioCyc
Ensembl Genes ENSRNOG00000006636 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000008725.8 UniProtKB/TrEMBL
  ENSRNOT00000093302.2 UniProtKB/TrEMBL
  ENSRNOT00000093698.2 UniProtKB/TrEMBL
  ENSRNOT00000111015.1 UniProtKB/TrEMBL
Gene3D-CATH 3.90.70.80 UniProtKB/TrEMBL
InterPro OTU UniProtKB/TrEMBL
  Papain_like_cys_pep_sf UniProtKB/TrEMBL
KEGG Report rno:297911 UniProtKB/TrEMBL
NCBI Gene 297911 ENTREZGENE
PANTHER DEUBIQUITINASE OTUD6B UniProtKB/TrEMBL
  OTU DOMAIN CONTAINING PROTEIN UniProtKB/TrEMBL
Pfam OTU UniProtKB/TrEMBL
PhenoGen Otud6b PhenoGen
PROSITE OTU UniProtKB/TrEMBL
RatGTEx ENSRNOG00000006636 RatGTEx
Superfamily-SCOP SSF54001 UniProtKB/TrEMBL
UniProt A0A1W2Q6D9 ENTREZGENE, UniProtKB/TrEMBL
  A0A1W2Q6I2 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6A6P1_RAT UniProtKB/TrEMBL
  A6II95 ENTREZGENE, UniProtKB/TrEMBL
  D3ZGY2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-08-09 Otud6b  OTU deubiquitinase 6B  Otud6b  OTU domain containing 6B  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Otud6b  OTU domain containing 6B   Otud6b_predicted  OTU domain containing 6B (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Otud6b_predicted  OTU domain containing 6B (predicted)  RGD1310024_predicted  similar to RIKEN cDNA 2600013N14 (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 RGD1310024_predicted  similar to RIKEN cDNA 2600013N14 (predicted)  LOC297911_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC297911_predicted  similar to RIKEN cDNA 2600013N14 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL