Ubxn6 (UBX domain protein 6) - Rat Genome Database

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Gene: Ubxn6 (UBX domain protein 6) Rattus norvegicus
Analyze
Symbol: Ubxn6
Name: UBX domain protein 6
RGD ID: 1590866
Description: Predicted to be involved in ERAD pathway; endosome to lysosome transport via multivesicular body sorting pathway; and macroautophagy. Predicted to be located in bounding membrane of organelle and cytosol. Predicted to be part of protein-containing complex. Predicted to be active in cytoplasm. Orthologous to human UBXN6 (UBX domain protein 6); PARTICIPATES IN Endoplasmic Reticulum-associated degradation pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC363332; similar to UBX domain containing 1; UBX domain containing 1; UBX domain-containing protein 6; Ubxd1
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
GRCr89988,051 - 993,221 (-)NCBIGRCr8
mRatBN7.29900,883 - 906,047 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl9900,884 - 906,124 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx91,347,995 - 1,353,109 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.096,694,563 - 6,699,666 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.095,653,032 - 5,658,146 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0910,995,516 - 11,000,643 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl910,995,198 - 11,000,642 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.099,982,433 - 9,987,589 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera97,601,054 - 7,606,148 (+)NCBICelera
Cytogenetic Map9q11NCBI
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

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
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:19056867   PMID:19275885   PMID:21822278   PMID:26475856   PMID:27753622  


Genomics

Comparative Map Data
Ubxn6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr89988,051 - 993,221 (-)NCBIGRCr8
mRatBN7.29900,883 - 906,047 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl9900,884 - 906,124 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx91,347,995 - 1,353,109 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.096,694,563 - 6,699,666 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.095,653,032 - 5,658,146 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0910,995,516 - 11,000,643 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl910,995,198 - 11,000,642 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.099,982,433 - 9,987,589 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera97,601,054 - 7,606,148 (+)NCBICelera
Cytogenetic Map9q11NCBI
UBXN6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38194,445,006 - 4,457,879 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl194,444,999 - 4,457,794 (-)EnsemblGRCh38hg38GRCh38
GRCh37194,445,003 - 4,457,791 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36194,396,261 - 4,408,790 (-)NCBINCBI36Build 36hg18NCBI36
Build 34194,396,260 - 4,408,790NCBI
Celera194,383,244 - 4,396,018 (-)NCBICelera
Cytogenetic Map19p13.3NCBI
HuRef194,207,464 - 4,220,339 (-)NCBIHuRef
CHM1_1194,444,589 - 4,457,323 (-)NCBICHM1_1
T2T-CHM13v2.0194,428,463 - 4,442,199 (-)NCBIT2T-CHM13v2.0
Ubxn6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391756,374,045 - 56,386,333 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1756,374,045 - 56,382,028 (-)EnsemblGRCm39 Ensembl
GRCm381756,067,045 - 56,079,333 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1756,067,045 - 56,075,028 (-)EnsemblGRCm38mm10GRCm38
MGSCv371756,207,676 - 56,214,412 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361755,661,546 - 55,668,282 (-)NCBIMGSCv36mm8
Celera1759,486,915 - 59,493,651 (-)NCBICelera
Cytogenetic Map17DNCBI
cM Map1729.14NCBI
Ubxn6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554954,456,308 - 4,466,254 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554954,456,182 - 4,465,954 (+)NCBIChiLan1.0ChiLan1.0
UBXN6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2208,838,347 - 8,851,379 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1198,067,462 - 8,079,687 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0193,463,259 - 3,475,428 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1194,410,952 - 4,423,113 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl194,410,952 - 4,423,092 (-)Ensemblpanpan1.1panPan2
UBXN6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12055,228,026 - 55,246,333 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2055,227,729 - 55,245,940 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2054,956,629 - 54,974,574 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02055,886,799 - 55,904,984 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2055,894,672 - 55,904,980 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12054,955,806 - 54,966,063 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02055,429,034 - 55,446,964 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02055,627,722 - 55,645,668 (+)NCBIUU_Cfam_GSD_1.0
Ubxn6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118215,253,780 - 215,269,310 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365882,565,461 - 2,578,624 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365882,565,473 - 2,578,721 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
UBXN6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl274,357,517 - 74,378,592 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1274,357,522 - 74,378,600 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2274,858,008 - 74,871,543 (+)NCBISscrofa10.2Sscrofa10.2susScr3
UBXN6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.164,175,858 - 4,188,687 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl64,175,108 - 4,188,649 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660814,011,232 - 4,024,463 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ubxn6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248285,258,023 - 5,264,989 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248285,257,960 - 5,265,371 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ubxn6
3 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:42
Count of miRNA genes:38
Interacting mature miRNAs:42
Transcripts:ENSRNOT00000070986
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
10054141Gmadr4Adrenal mass QTL 42.450.0074adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)9114209783Rat
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9125661317Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9137999212Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9137999212Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9137999212Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9140594091Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9143718459Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9143718459Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat

Markers in Region
RH134524  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.29901,259 - 901,723 (-)MAPPERmRatBN7.2
Rnor_6.0910,999,803 - 11,000,266NCBIRnor6.0
Rnor_5.099,986,750 - 9,987,213UniSTSRnor5.0
Celera97,605,309 - 7,605,772UniSTS
AU040909  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.29901,143 - 901,288 (-)MAPPERmRatBN7.2
Rnor_6.0911,000,238 - 11,000,382NCBIRnor6.0
Rnor_5.099,987,185 - 9,987,329UniSTSRnor5.0
Celera97,605,744 - 7,605,888UniSTS
RH141481  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.29900,438 - 900,639 (-)MAPPERmRatBN7.2
Rnor_6.0911,000,887 - 11,001,087NCBIRnor6.0
Rnor_5.099,987,834 - 9,988,034UniSTSRnor5.0
Celera97,606,393 - 7,606,593UniSTS
RH141680  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.29902,833 - 903,409 (-)MAPPERmRatBN7.2
Rnor_6.0910,998,117 - 10,998,692NCBIRnor6.0
Rnor_5.099,985,064 - 9,985,639UniSTSRnor5.0
Celera97,603,623 - 7,604,198UniSTS


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 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000070986   ⟹   ENSRNOP00000066490
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl9900,884 - 905,978 (-)Ensembl
Rnor_6.0 Ensembl910,995,548 - 11,000,642 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000089071   ⟹   ENSRNOP00000071261
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl9900,887 - 906,124 (-)Ensembl
Rnor_6.0 Ensembl910,995,198 - 11,000,632 (+)Ensembl
RefSeq Acc Id: NM_001399140   ⟹   NP_001386069
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr89988,051 - 993,154 (-)NCBI
mRatBN7.29900,883 - 905,986 (-)NCBI
RefSeq Acc Id: NM_001399141   ⟹   NP_001386070
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr89988,051 - 993,154 (-)NCBI
mRatBN7.29900,883 - 905,986 (-)NCBI
RefSeq Acc Id: XM_039083941   ⟹   XP_038939869
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr89989,898 - 993,215 (-)NCBI
mRatBN7.29902,730 - 906,047 (-)NCBI
RefSeq Acc Id: XM_063267481   ⟹   XP_063123551
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr89989,898 - 993,221 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000066490   ⟸   ENSRNOT00000070986
RefSeq Acc Id: ENSRNOP00000071261   ⟸   ENSRNOT00000089071
RefSeq Acc Id: XP_038939869   ⟸   XM_039083941
- Peptide Label: isoform X1
RefSeq Acc Id: NP_001386070   ⟸   NM_001399141
- Peptide Label: isoform 2
- UniProtKB: A6KR06 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001386069   ⟸   NM_001399140
- Peptide Label: isoform 1
RefSeq Acc Id: XP_063123551   ⟸   XM_063267481
- Peptide Label: isoform X2
Protein Domains
UBX

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K012-F1-model_v2 AlphaFold A0A0G2K012 1-524 view protein structure

Transcriptome

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

Promoters
RGD ID:13696470
Promoter ID:EPDNEW_R6995
Type:initiation region
Name:Ubxn6_1
Description:UBX domain protein 6
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_6.0910,995,562 - 10,995,622EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1590866 AgrOrtholog
BioCyc Gene G2FUF-28565 BioCyc
Ensembl Genes ENSRNOG00000048509 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000070986.2 UniProtKB/TrEMBL
  ENSRNOT00000089071 ENTREZGENE
  ENSRNOT00000089071.2 UniProtKB/TrEMBL
Gene3D-CATH 1.20.58.2190 UniProtKB/TrEMBL
InterPro PUB-like_dom UniProtKB/TrEMBL
  PUB_domain UniProtKB/TrEMBL
  Ubiquitin-rel_dom UniProtKB/TrEMBL
  UBX UniProtKB/TrEMBL
  UBXN6_PUB UniProtKB/TrEMBL
KEGG Report rno:363332 UniProtKB/TrEMBL
NCBI Gene 363332 ENTREZGENE
PANTHER UBX DOMAIN-CONTAINING PROTEIN 6 UniProtKB/TrEMBL
  UBX-RELATED UniProtKB/TrEMBL
Pfam PUB UniProtKB/TrEMBL
  UBX UniProtKB/TrEMBL
PhenoGen Ubxn6 PhenoGen
PROSITE UBX UniProtKB/TrEMBL
RatGTEx ENSRNOG00000048509 RatGTEx
SMART PUG UniProtKB/TrEMBL
  UBX UniProtKB/TrEMBL
Superfamily-SCOP SSF143503 UniProtKB/TrEMBL
  SSF54236 UniProtKB/TrEMBL
UniProt A0A0G2K012_RAT UniProtKB/TrEMBL
  A6KR06 ENTREZGENE, UniProtKB/TrEMBL
  A6KR07_RAT UniProtKB/TrEMBL
  M0RAE4_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-09 Ubxn6  UBX domain protein 6  Ubxd1  UBX domain containing 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-05 Ubxd1  UBX domain containing 1  LOC363332  similar to UBX domain containing 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC363332  similar to UBX domain containing 1      Symbol and Name status set to provisional 70820 PROVISIONAL