Ubxn2b (UBX domain protein 2B) - Rat Genome Database

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Gene: Ubxn2b (UBX domain protein 2B) Rattus norvegicus
Analyze
Symbol: Ubxn2b
Name: UBX domain protein 2B
RGD ID: 1308557
Description: Predicted to enable ubiquitin binding activity. Predicted to be involved in several processes, including establishment of mitotic spindle orientation; negative regulation of protein localization to centrosome; and positive regulation of mitotic centrosome separation. Predicted to be located in spindle pole centrosome. Predicted to be active in cytosol and nucleus. Orthologous to human UBXN2B (UBX domain protein 2B); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC312965; NSFL1 cofactor p37; p97 cofactor p37; RGD1308557; similar to homolog of rat p47 ; UBX domain-containing protein 2B
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
mRatBN7.2519,303,634 - 19,333,181 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl519,303,682 - 19,326,849 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx521,510,779 - 21,533,944 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0523,096,194 - 23,119,370 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0522,876,496 - 22,899,682 (+)NCBIRnor_WKY
Rnor_6.0519,285,368 - 19,314,199 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl519,284,548 - 19,311,088 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0524,070,783 - 24,098,774 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4519,631,847 - 19,655,014 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1519,631,871 - 19,654,541 (+)NCBI
Celera518,604,281 - 18,627,448 (+)NCBICelera
Cytogenetic Map5q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

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:17141156   PMID:23649807  


Genomics

Comparative Map Data
Ubxn2b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2519,303,634 - 19,333,181 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl519,303,682 - 19,326,849 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx521,510,779 - 21,533,944 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0523,096,194 - 23,119,370 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0522,876,496 - 22,899,682 (+)NCBIRnor_WKY
Rnor_6.0519,285,368 - 19,314,199 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl519,284,548 - 19,311,088 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0524,070,783 - 24,098,774 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4519,631,847 - 19,655,014 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1519,631,871 - 19,654,541 (+)NCBI
Celera518,604,281 - 18,627,448 (+)NCBICelera
Cytogenetic Map5q12NCBI
UBXN2B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38858,411,361 - 58,451,501 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl858,411,359 - 58,451,501 (+)EnsemblGRCh38hg38GRCh38
GRCh37859,323,920 - 59,364,060 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36859,486,377 - 59,526,614 (+)NCBINCBI36Build 36hg18NCBI36
Celera855,316,857 - 55,357,075 (+)NCBICelera
Cytogenetic Map8q12.1NCBI
HuRef854,811,019 - 54,851,280 (+)NCBIHuRef
CHM1_1859,375,721 - 59,415,949 (+)NCBICHM1_1
T2T-CHM13v2.0858,832,480 - 58,872,635 (+)NCBIT2T-CHM13v2.0
Ubxn2b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3946,191,105 - 6,219,788 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl46,191,098 - 6,221,688 (+)EnsemblGRCm39 Ensembl
GRCm3846,191,105 - 6,219,788 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl46,191,098 - 6,221,688 (+)EnsemblGRCm38mm10GRCm38
MGSCv3746,118,252 - 6,146,935 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3646,118,252 - 6,146,935 (+)NCBIMGSCv36mm8
Celera46,110,040 - 6,138,678 (+)NCBICelera
Cytogenetic Map4A1NCBI
Ubxn2b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545416,929,917 - 16,956,588 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495545416,929,816 - 16,978,706 (+)NCBIChiLan1.0ChiLan1.0
UBXN2B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1856,516,601 - 56,556,489 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl856,516,601 - 56,556,489 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0854,865,251 - 54,905,243 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
UBXN2B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1299,229,070 - 9,258,269 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl299,228,985 - 9,259,372 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha299,541,980 - 9,571,171 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0299,314,507 - 9,343,660 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl299,314,521 - 9,343,656 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1299,312,339 - 9,341,685 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0299,438,305 - 9,467,577 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0299,717,333 - 9,746,587 (+)NCBIUU_Cfam_GSD_1.0
Ubxn2b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530370,221,115 - 70,265,143 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364964,532,714 - 4,559,562 (+)EnsemblSpeTri2.0
SpeTri2.0NW_0049364964,520,334 - 4,564,358 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
UBXN2B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl474,405,902 - 74,437,615 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1474,405,876 - 74,437,650 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2481,200,231 - 81,232,255 (-)NCBISscrofa10.2Sscrofa10.2susScr3
UBXN2B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1854,397,523 - 54,436,468 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl854,397,601 - 54,432,523 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603987,290,626 - 87,329,624 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ubxn2b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474433,696,129 - 33,725,383 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474433,676,900 - 33,725,388 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ubxn2b
175 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:465
Count of miRNA genes:252
Interacting mature miRNAs:294
Transcripts:ENSRNOT00000012551
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
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
2312562Pur18Proteinuria QTL 182.60.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5213896532656739Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
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
2313085Bss59Bone structure and strength QTL 592.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)5384401826141981Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5384401847869213Rat
61462Niddm10Non-insulin dependent diabetes mellitus QTL 103.90.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)5511215947171491Rat
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5894822853948228Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
1641903Alcrsp3Alcohol response QTL 3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)51268928557689285Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat
1600358Mamtr5Mammary tumor resistance QTL 5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)51887394763873947Rat
1358353Srcrtb2Stress Responsive Cort Basal QTL 23.480.003blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)51887394774251464Rat

Markers in Region
RH140001  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2519,323,815 - 19,323,995 (+)MAPPERmRatBN7.2
Rnor_6.0519,305,530 - 19,305,709NCBIRnor6.0
Rnor_5.0524,090,924 - 24,091,103UniSTSRnor5.0
RGSC_v3.4519,651,981 - 19,652,160UniSTSRGSC3.4
Celera518,624,415 - 18,624,594UniSTS
RH 3.4 Map2860.4UniSTS
Cytogenetic Map5q12UniSTS


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 4 10 4 9 4 74 14 33
Low 3 38 47 37 10 37 8 9 21 8 11 8
Below cutoff 1 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000012551   ⟹   ENSRNOP00000012551
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl519,284,548 - 19,311,088 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093925   ⟹   ENSRNOP00000076685
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl519,303,682 - 19,326,849 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000095748   ⟹   ENSRNOP00000092042
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl519,303,682 - 19,326,849 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000096591   ⟹   ENSRNOP00000087315
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl519,307,726 - 19,326,849 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000117943   ⟹   ENSRNOP00000090006
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl519,305,061 - 19,326,849 (+)Ensembl
RefSeq Acc Id: NM_001107905   ⟹   NP_001101375
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2519,303,682 - 19,326,849 (+)NCBI
Rnor_6.0519,285,396 - 19,308,563 (+)NCBI
Rnor_5.0524,070,783 - 24,098,774 (+)NCBI
RGSC_v3.4519,631,847 - 19,655,014 (+)RGD
Celera518,604,281 - 18,627,448 (+)RGD
Sequence:
RefSeq Acc Id: XM_017593330   ⟹   XP_017448819
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2519,303,634 - 19,333,175 (+)NCBI
Rnor_6.0519,285,368 - 19,312,523 (+)NCBI
Sequence:
RefSeq Acc Id: XR_005504427
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2519,303,634 - 19,333,181 (+)NCBI
RefSeq Acc Id: XR_005504428
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2519,303,634 - 19,320,670 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001101375 (Get FASTA)   NCBI Sequence Viewer  
  XP_017448819 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM11633 (Get FASTA)   NCBI Sequence Viewer  
  P0C627 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001101375   ⟸   NM_001107905
- UniProtKB: P0C627 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017448819   ⟸   XM_017593330
- Peptide Label: isoform X1
- UniProtKB: A0A8I6AH29 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000012551   ⟸   ENSRNOT00000012551
RefSeq Acc Id: ENSRNOP00000087315   ⟸   ENSRNOT00000096591
RefSeq Acc Id: ENSRNOP00000090006   ⟸   ENSRNOT00000117943
RefSeq Acc Id: ENSRNOP00000076685   ⟸   ENSRNOT00000093925
RefSeq Acc Id: ENSRNOP00000092042   ⟸   ENSRNOT00000095748
Protein Domains
SEP   UBX

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P0C627-F1-model_v2 AlphaFold P0C627 1-331 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:1308557 AgrOrtholog
BioCyc Gene G2FUF-42082 BioCyc
Ensembl Genes ENSRNOG00000009137 Ensembl
  ENSRNOG00000071045 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000076685 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000087315.1 UniProtKB/TrEMBL
  ENSRNOP00000090006.1 UniProtKB/TrEMBL
  ENSRNOP00000092042 ENTREZGENE
  ENSRNOP00000092042.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000093925 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000095748 ENTREZGENE
  ENSRNOT00000095748.1 UniProtKB/TrEMBL
  ENSRNOT00000096591.1 UniProtKB/TrEMBL
  ENSRNOT00000117943.1 UniProtKB/TrEMBL
Gene3D-CATH 3.30.420.210 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro NSFL1C_SEP_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SEP_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ubiquitin-like_domsf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  UBX_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:312965 UniProtKB/Swiss-Prot
NCBI Gene 312965 ENTREZGENE
Pfam SEP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  UBX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ubxn2b PhenoGen
PROSITE SEP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  UBX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SEP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  UBX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF102848 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF54236 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I6ADM0_RAT UniProtKB/TrEMBL
  A0A8I6AGB9_RAT UniProtKB/TrEMBL
  A0A8I6AH29 ENTREZGENE, UniProtKB/TrEMBL
  P0C627 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-09 Ubxn2b  UBX domain protein 2B  RGD1308557  similar to homolog of rat p47   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1308557  similar to homolog of rat p47   RGD1308557_predicted  similar to homolog of rat p47 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1308557_predicted  similar to homolog of rat p47 (predicted)  LOC312965_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC312965_predicted  similar to homolog of rat p47 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL