Obi1 (ORC ubiquitin ligase 1) - Rat Genome Database

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Gene: Obi1 (ORC ubiquitin ligase 1) Rattus norvegicus
Analyze
Symbol: Obi1
Name: ORC ubiquitin ligase 1
RGD ID: 1564706
Description: Predicted to enable chromatin binding activity and ubiquitin-protein transferase activity. Predicted to be involved in protein autoubiquitination; protein monoubiquitination; and regulation of DNA replication. Predicted to act upstream of or within positive regulation of mRNA splicing, via spliceosome. Predicted to be located in chromatin. Orthologous to human OBI1 (ORC ubiquitin ligase 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC361088; RGD1564706; ring finger protein 219; Rnf219; similar to chromosome 13 open reading frame 7
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
mRatBN7.21581,269,413 - 81,308,734 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1581,269,416 - 81,308,734 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1585,260,403 - 85,299,151 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01586,383,456 - 86,422,210 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01583,311,067 - 83,349,817 (-)NCBIRnor_WKY
Rnor_6.01588,632,089 - 88,670,325 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1588,631,794 - 88,670,349 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01592,127,751 - 92,165,948 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41588,548,933 - 88,588,816 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1580,396,575 - 80,435,845 (-)NCBICelera
Cytogenetic Map15q22NCBI
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

Biological Process

Cellular Component
chromatin  (ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:23636947   PMID:31160578  


Genomics

Comparative Map Data
Obi1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21581,269,413 - 81,308,734 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1581,269,416 - 81,308,734 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1585,260,403 - 85,299,151 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01586,383,456 - 86,422,210 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01583,311,067 - 83,349,817 (-)NCBIRnor_WKY
Rnor_6.01588,632,089 - 88,670,325 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1588,631,794 - 88,670,349 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01592,127,751 - 92,165,948 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41588,548,933 - 88,588,816 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1580,396,575 - 80,435,845 (-)NCBICelera
Cytogenetic Map15q22NCBI
OBI1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381378,614,289 - 78,659,155 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1378,614,289 - 78,659,155 (-)EnsemblGRCh38hg38GRCh38
GRCh371379,188,424 - 79,233,290 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361378,086,422 - 78,131,315 (-)NCBINCBI36Build 36hg18NCBI36
Build 341378,086,430 - 78,131,315NCBI
Celera1360,086,863 - 60,131,755 (-)NCBICelera
Cytogenetic Map13q31.1NCBI
HuRef1359,888,745 - 59,933,635 (-)NCBIHuRef
CHM1_11379,156,278 - 79,201,134 (-)NCBICHM1_1
T2T-CHM13v2.01377,840,023 - 77,884,889 (-)NCBIT2T-CHM13v2.0
Obi1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3914104,714,970 - 104,760,148 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl14104,714,972 - 104,760,081 (-)EnsemblGRCm39 Ensembl
GRCm3814104,477,534 - 104,522,712 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl14104,477,536 - 104,522,645 (-)EnsemblGRCm38mm10GRCm38
MGSCv3714104,876,751 - 104,921,883 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3614103,363,213 - 103,408,345 (-)NCBIMGSCv36mm8
Celera14103,091,780 - 103,136,907 (-)NCBICelera
Cytogenetic Map14E2.3NCBI
Obi1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540428,758,918 - 28,804,972 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540428,759,640 - 28,803,257 (+)NCBIChiLan1.0ChiLan1.0
OBI1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11378,874,466 - 78,918,298 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1378,874,466 - 78,918,446 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01359,840,406 - 59,884,765 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
OBI1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12232,006,441 - 32,047,609 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2232,007,210 - 32,047,527 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2231,803,937 - 31,845,113 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02232,327,448 - 32,368,633 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2232,327,801 - 32,368,556 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12231,989,037 - 32,030,201 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02232,026,080 - 32,067,023 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02232,098,203 - 32,139,378 (-)NCBIUU_Cfam_GSD_1.0
Obi1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945127,383,335 - 127,430,516 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365112,800,425 - 2,848,628 (+)EnsemblSpeTri2.0
SpeTri2.0NW_0049365112,800,466 - 2,847,896 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
OBI1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1150,740,916 - 50,786,774 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11150,741,893 - 50,786,824 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21155,430,773 - 55,475,967 (-)NCBISscrofa10.2Sscrofa10.2susScr3
OBI1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1357,683,989 - 57,726,851 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl357,683,746 - 57,726,750 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604613,913,551 - 13,956,671 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Obi1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475121,752,270 - 21,803,930 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475121,752,339 - 21,803,387 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Obi1
66 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:167
Count of miRNA genes:119
Interacting mature miRNAs:142
Transcripts:ENSRNOT00000012881
Prediction methods: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
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)152803066582262678Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)152803066582262678Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)152803066582262678Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)154063126898288169Rat
1576315Schws6Schwannoma susceptibility QTL 60.0069nervous system integrity trait (VT:0010566)post-insult time of death (CMO:0002005)155380615298806152Rat
61477Aia4Adjuvant induced arthritis QTL 43joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)155559608991365858Rat
631516Gluco31Glucose level QTL 317blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)155559608995018120Rat
631655Bp126Blood pressure QTL 1264arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1558156477101769107Rat
731177Uae26Urinary albumin excretion QTL 262.40.025urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1567588667101769107Rat
2300326Plaw1Placental weight QTL 1150.005placenta mass (VT:0004257)placenta wet weight (CMO:0002088)1568327165100062518Rat
1331724Bp223Blood pressure QTL 2233.53715arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)157369051895018228Rat
1641889Colcr6Colorectal carcinoma resistance QTL 62.90.0126intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)157369051899794247Rat
70182BpQTLcluster12Blood pressure QTL cluster 123.53arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)157369065795018120Rat
2317055Aia10Adjuvant induced arthritis QTL 103.41joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1575788062101769107Rat
1549844Bss7Bone structure and strength QTL 76.4femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1575788062101769107Rat
1581555Eae19Experimental allergic encephalomyelitis QTL 194.7nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)157630609990088744Rat
70155Gcs1Gastric cancer susceptibility QTL13.8stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)1576306099101769107Rat


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 14 12 6 14 6 63 16 33 4
Low 3 29 45 35 5 35 8 11 11 19 8 7 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000012881   ⟹   ENSRNOP00000012880
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1581,269,416 - 81,308,734 (-)Ensembl
Rnor_6.0 Ensembl1588,631,794 - 88,670,349 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000109330   ⟹   ENSRNOP00000086618
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1581,269,416 - 81,308,187 (-)Ensembl
RefSeq Acc Id: NM_001108389   ⟹   NP_001101859
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21581,269,416 - 81,308,734 (-)NCBI
Rnor_6.01588,632,089 - 88,670,325 (-)NCBI
Rnor_5.01592,127,751 - 92,165,948 (-)NCBI
RGSC_v3.41588,548,933 - 88,588,816 (-)RGD
Celera1580,396,575 - 80,435,845 (-)RGD
Sequence:
RefSeq Acc Id: XM_039093537   ⟹   XP_038949465
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21581,269,413 - 81,308,534 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001101859 (Get FASTA)   NCBI Sequence Viewer  
  XP_038949465 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM02475 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001101859   ⟸   NM_001108389
- UniProtKB: D3ZAB6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000012880   ⟸   ENSRNOT00000012881
RefSeq Acc Id: XP_038949465   ⟸   XM_039093537
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000086618   ⟸   ENSRNOT00000109330
Protein Domains
RING-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZAB6-F1-model_v2 AlphaFold D3ZAB6 1-724 view protein structure

Transcriptome

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

Promoters
RGD ID:13699865
Promoter ID:EPDNEW_R10388
Type:initiation region
Name:Rnf219_1
Description:ring finger protein 219
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_6.01588,670,272 - 88,670,332EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1564706 AgrOrtholog
BioCyc Gene G2FUF-12650 BioCyc
Ensembl Genes ENSRNOG00000009690 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000012880 ENTREZGENE
  ENSRNOP00000012880.5 UniProtKB/TrEMBL
  ENSRNOP00000086618.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000012881 ENTREZGENE
  ENSRNOT00000012881.7 UniProtKB/TrEMBL
  ENSRNOT00000109330.1 UniProtKB/TrEMBL
Gene3D-CATH 3.30.40.10 UniProtKB/TrEMBL
InterPro RNF219 UniProtKB/TrEMBL
  RNF219_RING-HC UniProtKB/TrEMBL
  Znf_RING UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
KEGG Report rno:361088 UniProtKB/TrEMBL
NCBI Gene 361088 ENTREZGENE
PANTHER PTHR14609 UniProtKB/TrEMBL
PhenoGen Obi1 PhenoGen
PROSITE ZF_RING_2 UniProtKB/TrEMBL
SMART RING UniProtKB/TrEMBL
UniProt A0A8I6A402_RAT UniProtKB/TrEMBL
  D3ZAB6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-08-05 Obi1  ORC ubiquitin ligase 1  Rnf219  ring finger protein 219  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-31 Rnf219  ring finger protein 219  RGD1564706_predicted  similar to chromosome 13 open reading frame 7 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1564706_predicted  similar to chromosome 13 open reading frame 7 (predicted)  LOC361088  similar to chromosome 13 open reading frame 7  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC361088  similar to chromosome 13 open reading frame 7      Symbol and Name status set to provisional 70820 PROVISIONAL