Ubn1 (ubinuclein 1) - Rat Genome Database

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Advanced Search (OLGA)
Gene: Ubn1 (ubinuclein 1) Rattus norvegicus
Analyze
Symbol: Ubn1
Name: ubinuclein 1
RGD ID: 1311582
Description: Predicted to be involved in nucleosome assembly. Predicted to be located in bicellular tight junction. Predicted to be active in nucleus. Orthologous to human UBN1 (ubinuclein 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC302935; ubinuclein-1
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
GRCr81011,003,036 - 11,038,466 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1011,003,036 - 11,038,466 (-)EnsemblGRCr8
mRatBN7.21010,496,576 - 10,532,010 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1010,496,576 - 10,532,010 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1015,204,646 - 15,239,996 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01014,693,466 - 14,728,816 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01010,362,719 - 10,398,102 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01010,690,224 - 10,725,655 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1010,690,224 - 10,725,655 (-)Ensemblrn6Rnor6.0
Rnor_5.0109,457,239 - 9,492,668 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41010,612,480 - 10,647,870 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera109,460,580 - 9,495,788 (-)NCBICelera
RGSC_v3.11010,612,474 - 10,647,858 (-)NCBI
Cytogenetic Map10q12NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
bicellular tight junction  (IEA,ISO)
HIR complex  (IEA,ISO)
nuclear body  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IBA,IEA,ISO)

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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
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:10725330   PMID:14718166   PMID:18823282   PMID:19389623  


Genomics

Comparative Map Data
Ubn1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81011,003,036 - 11,038,466 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1011,003,036 - 11,038,466 (-)EnsemblGRCr8
mRatBN7.21010,496,576 - 10,532,010 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1010,496,576 - 10,532,010 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1015,204,646 - 15,239,996 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01014,693,466 - 14,728,816 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01010,362,719 - 10,398,102 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01010,690,224 - 10,725,655 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1010,690,224 - 10,725,655 (-)Ensemblrn6Rnor6.0
Rnor_5.0109,457,239 - 9,492,668 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41010,612,480 - 10,647,870 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera109,460,580 - 9,495,788 (-)NCBICelera
RGSC_v3.11010,612,474 - 10,647,858 (-)NCBI
Cytogenetic Map10q12NCBI
UBN1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38164,847,481 - 4,882,401 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl164,846,665 - 4,882,401 (+)Ensemblhg38GRCh38
GRCh37164,897,482 - 4,932,402 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36164,837,913 - 4,872,364 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34164,842,216 - 4,872,364NCBI
Celera165,106,685 - 5,141,135 (+)NCBICelera
Cytogenetic Map16p13.3NCBI
HuRef164,864,193 - 4,898,486 (+)NCBIHuRef
CHM1_1164,898,810 - 4,933,255 (+)NCBICHM1_1
T2T-CHM13v2.0164,876,971 - 4,911,890 (+)NCBIT2T-CHM13v2.0
Ubn1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39164,867,921 - 4,904,153 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl164,867,921 - 4,904,153 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38165,050,057 - 5,086,289 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl165,050,057 - 5,086,289 (+)Ensemblmm10GRCm38
MGSCv37165,050,161 - 5,086,378 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36164,970,410 - 5,001,608 (+)NCBIMGSCv36mm8
Celera165,681,405 - 5,717,620 (+)NCBICelera
Cytogenetic Map16A1NCBI
cM Map162.49NCBI
Ubn1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544212,627,530 - 12,654,159 (-)Ensembl
ChiLan1.0NW_00495544212,627,530 - 12,654,159 (-)NCBIChiLan1.0ChiLan1.0
UBN1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2185,375,842 - 5,410,621 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1169,166,465 - 9,200,785 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0163,771,623 - 3,806,575 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1164,936,864 - 4,970,992 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl164,942,191 - 4,970,986 (+)EnsemblpanPan2panpan1.1
UBN1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1636,542,266 - 36,581,789 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl636,544,405 - 36,581,797 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha637,934,552 - 37,974,038 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0636,745,422 - 36,784,724 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl636,745,417 - 36,780,193 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1636,540,042 - 36,579,317 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0636,432,947 - 36,472,235 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0636,834,628 - 36,873,909 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Ubn1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344106,950,527 - 106,980,674 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365304,795,968 - 4,826,137 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365304,795,974 - 4,826,217 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
UBN1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl337,512,313 - 37,555,203 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1337,512,306 - 37,555,255 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2338,518,208 - 38,536,586 (-)NCBISscrofa10.2Sscrofa10.2susScr3
UBN1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.154,518,369 - 4,554,687 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl54,525,081 - 4,552,465 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366606826,103,022 - 26,140,180 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ubn1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248242,693,403 - 2,720,305 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248242,693,270 - 2,720,305 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Ubn1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1916,823,796 - 16,859,074 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Ubn1
153 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:1301
Count of miRNA genes:361
Interacting mature miRNAs:496
Transcripts:ENSRNOT00000061236
Prediction methods:Microtar, Miranda, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10589381150893811Rat
631660Hcar1Hepatocarcinoma resistance QTL 13.40.0001liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)10666111835509383Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10666092373950353Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10589381150893811Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10125055464349221Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)10589381150893811Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10687714251877142Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135730538Rat
7387235Uae41Urinary albumin excretion QTL 415.260.1874urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)10130004247Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10589381150893811Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10686461896620484Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1092219745922197Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)10210370847103708Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10589381150893811Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10117749933Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138832698Rat

Markers in Region
AW124741  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21010,520,708 - 10,521,127 (+)MAPPERmRatBN7.2
Rnor_6.01010,714,357 - 10,714,775NCBIRnor6.0
Rnor_5.0109,481,370 - 9,481,788UniSTSRnor5.0
RGSC_v3.41010,636,607 - 10,637,025UniSTSRGSC3.4
Celera109,484,712 - 9,485,130UniSTS
Cytogenetic Map10q12UniSTS
RH124545  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21010,496,649 - 10,496,782 (+)MAPPERmRatBN7.2
Rnor_6.01010,690,298 - 10,690,430NCBIRnor6.0
Rnor_5.0109,457,313 - 9,457,445UniSTSRnor5.0
RGSC_v3.41010,612,549 - 10,612,681UniSTSRGSC3.4
Celera109,460,654 - 9,460,786UniSTS
Cytogenetic Map10q12UniSTS


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 164 91 90 59 92 59 6 356 192 11 143 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000061236   ⟹   ENSRNOP00000057947
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1011,003,036 - 11,038,466 (-)Ensembl
mRatBN7.2 Ensembl1010,496,576 - 10,532,010 (-)Ensembl
Rnor_6.0 Ensembl1010,690,224 - 10,725,655 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000118527   ⟹   ENSRNOP00000096576
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1011,004,207 - 11,038,466 (-)Ensembl
mRatBN7.2 Ensembl1010,496,579 - 10,532,010 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000142345   ⟹   ENSRNOP00000109789
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1011,004,185 - 11,038,466 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000151595   ⟹   ENSRNOP00000100685
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1011,006,117 - 11,038,466 (-)Ensembl
RefSeq Acc Id: NM_001106977   ⟹   NP_001100447
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81011,003,036 - 11,038,466 (-)NCBI
mRatBN7.21010,496,576 - 10,532,010 (-)NCBI
Rnor_6.01010,690,224 - 10,725,655 (-)NCBI
Rnor_5.0109,457,239 - 9,492,668 (-)NCBI
RGSC_v3.41010,612,480 - 10,647,870 (-)RGD
Celera109,460,580 - 9,495,788 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006245787   ⟹   XP_006245849
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81011,003,036 - 11,037,845 (-)NCBI
mRatBN7.21010,496,576 - 10,531,491 (-)NCBI
Rnor_6.01010,690,224 - 10,725,041 (-)NCBI
Rnor_5.0109,457,239 - 9,492,668 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001100447 (Get FASTA)   NCBI Sequence Viewer  
  XP_006245849 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL96265 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000057947
  ENSRNOP00000057947.3
  ENSRNOP00000096576
  ENSRNOP00000096576.1
  ENSRNOP00000100685.1
  ENSRNOP00000109789.1
RefSeq Acc Id: NP_001100447   ⟸   NM_001106977
- UniProtKB: D4A8C6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006245849   ⟸   XM_006245787
- Peptide Label: isoform X1
- UniProtKB: A0A8I6AM22 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000057947   ⟸   ENSRNOT00000061236
Ensembl Acc Id: ENSRNOP00000096576   ⟸   ENSRNOT00000118527
Ensembl Acc Id: ENSRNOP00000100685   ⟸   ENSRNOT00000151595
Ensembl Acc Id: ENSRNOP00000109789   ⟸   ENSRNOT00000142345
Protein Domains
Hpc2-related   Ubinuclein middle

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A8C6-F1-model_v2 AlphaFold D4A8C6 1-1135 view protein structure

Transcriptome

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

Promoters
RGD ID:13696962
Promoter ID:EPDNEW_R7487
Type:initiation region
Name:Ubn1_1
Description:ubinuclein 1
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_6.01010,725,588 - 10,725,648EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311582 AgrOrtholog
BioCyc Gene G2FUF-26059 BioCyc
Ensembl Genes ENSRNOG00000003019 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000061236 ENTREZGENE
  ENSRNOT00000061236.5 UniProtKB/TrEMBL
  ENSRNOT00000118527 ENTREZGENE
  ENSRNOT00000118527.2 UniProtKB/TrEMBL
  ENSRNOT00000142345.1 UniProtKB/TrEMBL
  ENSRNOT00000151595.1 UniProtKB/TrEMBL
InterPro HRD UniProtKB/TrEMBL
  UBN_middle_dom UniProtKB/TrEMBL
KEGG Report rno:302935 UniProtKB/TrEMBL
NCBI Gene 302935 ENTREZGENE
PANTHER CAPZ-INTERACTING PROTEIN AND RELATED PROTEINS UniProtKB/TrEMBL
  PTHR21669:SF12 UniProtKB/TrEMBL
Pfam HRD UniProtKB/TrEMBL
  UBN_AB UniProtKB/TrEMBL
PhenoGen Ubn1 PhenoGen
RatGTEx ENSRNOG00000003019 RatGTEx
UniProt A0A8I6AM22 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0LG85_RAT UniProtKB/TrEMBL
  A0ABK0LHM6_RAT UniProtKB/TrEMBL
  D4A8C6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Ubn1  ubinuclein 1   Ubn1_predicted  ubinuclein 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Ubn1_predicted  ubinuclein 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED