Uba6 (ubiquitin-like modifier activating enzyme 6) - Rat Genome Database

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Pathways
Gene: Uba6 (ubiquitin-like modifier activating enzyme 6) Rattus norvegicus
Analyze
Symbol: Uba6
Name: ubiquitin-like modifier activating enzyme 6
RGD ID: 1308324
Description: Predicted to enable nucleotidyltransferase activity; thiosulfate sulfurtransferase activity; and ubiquitin-like modifier activating enzyme activity. Predicted to be involved in protein ubiquitination. Predicted to act upstream of or within several processes, including dendritic spine development; limbic system development; and ubiquitin-dependent protein catabolic process. Predicted to be active in cytoplasm. Orthologous to human UBA6 (ubiquitin like modifier activating enzyme 6); PARTICIPATES IN ubiquitin/proteasome degradation pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC305268; RGD1308324; similar to RIKEN cDNA 5730469D23; Ube1l2; ubiquitin-activating enzyme E1-like 2; ubiquitin-like modifier-activating enzyme 6
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
mRatBN7.21421,884,039 - 21,947,857 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1421,884,039 - 21,947,857 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1422,240,675 - 22,304,454 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01423,553,105 - 23,616,884 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01422,084,204 - 22,147,983 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01423,507,628 - 23,571,446 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1423,507,628 - 23,571,446 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01423,412,097 - 23,475,036 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41423,666,102 - 23,729,920 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11423,666,122 - 23,728,497 (+)NCBI
Celera1421,357,573 - 21,421,374 (+)NCBICelera
Cytogenetic Map14p21NCBI
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

Cellular Component
cytoplasm  (IBA,ISO)

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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:17889673   PMID:23499007   PMID:32497710  


Genomics

Comparative Map Data
Uba6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21421,884,039 - 21,947,857 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1421,884,039 - 21,947,857 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1422,240,675 - 22,304,454 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01423,553,105 - 23,616,884 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01422,084,204 - 22,147,983 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01423,507,628 - 23,571,446 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1423,507,628 - 23,571,446 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01423,412,097 - 23,475,036 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41423,666,102 - 23,729,920 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11423,666,122 - 23,728,497 (+)NCBI
Celera1421,357,573 - 21,421,374 (+)NCBICelera
Cytogenetic Map14p21NCBI
UBA6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38467,612,652 - 67,701,155 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl467,612,652 - 67,701,155 (-)EnsemblGRCh38hg38GRCh38
GRCh37468,478,370 - 68,566,873 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36468,164,074 - 68,249,484 (-)NCBINCBI36Build 36hg18NCBI36
Celera465,943,873 - 66,029,283 (-)NCBICelera
Cytogenetic Map4q13.2NCBI
HuRef464,394,643 - 64,480,109 (-)NCBIHuRef
CHM1_1468,518,622 - 68,603,987 (-)NCBICHM1_1
T2T-CHM13v2.0471,055,730 - 71,144,265 (-)NCBIT2T-CHM13v2.0
Uba6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39586,258,579 - 86,320,602 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl586,257,146 - 86,320,662 (-)EnsemblGRCm39 Ensembl
GRCm38586,110,720 - 86,172,743 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl586,109,287 - 86,172,803 (-)EnsemblGRCm38mm10GRCm38
MGSCv37586,539,745 - 86,601,768 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36587,185,281 - 87,247,304 (-)NCBIMGSCv36mm8
Celera583,342,275 - 83,404,045 (-)NCBICelera
Cytogenetic Map5E1NCBI
cM Map543.56NCBI
Uba6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554475,213,146 - 5,284,553 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554475,213,792 - 5,282,266 (+)NCBIChiLan1.0ChiLan1.0
UBA6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1462,403,942 - 62,519,729 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0456,348,370 - 56,433,433 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1462,741,812 - 62,826,197 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl462,741,812 - 62,826,197 (+)Ensemblpanpan1.1panPan2
UBA6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11358,148,935 - 58,231,194 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1358,013,212 - 58,231,200 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1358,064,591 - 58,146,589 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01358,760,633 - 58,843,785 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1358,723,823 - 58,843,817 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11358,486,500 - 58,568,429 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01357,976,685 - 58,058,696 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01358,987,100 - 59,069,355 (-)NCBIUU_Cfam_GSD_1.0
Uba6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528518,217,712 - 18,305,172 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936582780,892 - 869,026 (+)EnsemblSpeTri2.0
SpeTri2.0NW_004936582780,911 - 901,734 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
UBA6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl865,381,061 - 65,488,925 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1865,381,058 - 65,470,829 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2869,806,159 - 69,894,716 (-)NCBISscrofa10.2Sscrofa10.2susScr3
UBA6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.171,246,462 - 1,320,919 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl71,246,500 - 1,321,056 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660661,333,242 - 1,407,666 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Uba6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247611,262,345 - 1,349,964 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247611,262,172 - 1,351,606 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Uba6
147 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:448
Count of miRNA genes:242
Interacting mature miRNAs:302
Transcripts:ENSRNOT00000037509
Prediction methods:Microtar, Miranda
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
2300159Bmd61Bone mineral density QTL 615.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
2300183Bmd60Bone mineral density QTL 605.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
619619Rf4Renal disease susceptibility QTL 44.10.002urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14132754612Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
70195Mcs8Mammary carcinoma susceptibility QTL 84.28mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)14381307424531477Rat
1331740Bw26Body weight QTL 263.028body mass (VT:0001259)body weight (CMO:0000012)14381307430767156Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14908897839057237Rat
2302277Gluco38Glucose level QTL 385.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062228035204Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
631212Bw5Body weight QTL55.43retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)141103081230320092Rat
1300140Srn3Serum renin concentration QTL 33.19blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)141487516830883947Rat
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)141759376142336881Rat
631262Tcas4Tongue tumor susceptibility QTL 47.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)141762256142337007Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141854133263541332Rat
61420Pia6Pristane induced arthritis QTL 64.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)141863134542337007Rat
10755459Coatc15Coat color QTL 150.01681coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)141983694464836944Rat

Markers in Region
BB446153  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21421,944,685 - 21,944,788 (+)MAPPERmRatBN7.2
Rnor_6.01423,568,275 - 23,568,377NCBIRnor6.0
Rnor_5.01423,471,865 - 23,471,967UniSTSRnor5.0
RGSC_v3.41423,726,749 - 23,726,851UniSTSRGSC3.4
Celera1421,418,203 - 21,418,305UniSTS
Cytogenetic Map14p21UniSTS
RH137881  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21421,944,619 - 21,944,796 (+)MAPPERmRatBN7.2
Rnor_6.01423,568,209 - 23,568,385NCBIRnor6.0
Rnor_5.01423,471,799 - 23,471,975UniSTSRnor5.0
RGSC_v3.41423,726,683 - 23,726,859UniSTSRGSC3.4
Celera1421,418,137 - 21,418,313UniSTS
Cytogenetic Map14p21UniSTS


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 1 12 29 13 18 13 74 32 38 11
Low 2 31 28 28 1 28 8 10 3 3 8
Below cutoff 1

Sequence


RefSeq Acc Id: ENSRNOT00000037509   ⟹   ENSRNOP00000030667
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1421,884,039 - 21,947,857 (+)Ensembl
Rnor_6.0 Ensembl1423,507,628 - 23,571,446 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000102184   ⟹   ENSRNOP00000077997
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1421,884,039 - 21,944,860 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000114947   ⟹   ENSRNOP00000094765
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1421,884,039 - 21,936,615 (+)Ensembl
RefSeq Acc Id: NM_001107213   ⟹   NP_001100683
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21421,884,039 - 21,947,857 (+)NCBI
Rnor_6.01423,507,628 - 23,571,446 (+)NCBI
Rnor_5.01423,412,097 - 23,475,036 (+)NCBI
RGSC_v3.41423,666,102 - 23,729,920 (+)RGD
Celera1421,357,573 - 21,421,374 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001100683 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL89840 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001100683   ⟸   NM_001107213
- UniProtKB: D4A8H3 (UniProtKB/TrEMBL),   A6JCR8 (UniProtKB/TrEMBL),   A0A8I6AS92 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000030667   ⟸   ENSRNOT00000037509
RefSeq Acc Id: ENSRNOP00000077997   ⟸   ENSRNOT00000102184
RefSeq Acc Id: ENSRNOP00000094765   ⟸   ENSRNOT00000114947
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A8H3-F1-model_v2 AlphaFold D4A8H3 1-1053 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:1308324 AgrOrtholog
BioCyc Gene G2FUF-16065 BioCyc
BioCyc Pathway PWY-7511 [protein ubiquitination] BioCyc
Ensembl Genes ENSRNOG00000021931 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000030667 ENTREZGENE
  ENSRNOP00000030667.4 UniProtKB/TrEMBL
  ENSRNOP00000077997.1 UniProtKB/TrEMBL
  ENSRNOP00000094765.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000037509 ENTREZGENE
  ENSRNOT00000037509.6 UniProtKB/TrEMBL
  ENSRNOT00000102184.1 UniProtKB/TrEMBL
  ENSRNOT00000114947.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.2660 UniProtKB/TrEMBL
  2.40.30.180 UniProtKB/TrEMBL
  3.10.290.60 UniProtKB/TrEMBL
  3.50.50.80 UniProtKB/TrEMBL
  NAD(P)-binding Rossmann-like Domain UniProtKB/TrEMBL
  Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 2 UniProtKB/TrEMBL
InterPro E1_4HB UniProtKB/TrEMBL
  E1_FCCH UniProtKB/TrEMBL
  E1_FCCH_sf UniProtKB/TrEMBL
  ThiF/MoeB/HesA UniProtKB/TrEMBL
  ThiF_NAD_FAD-bd UniProtKB/TrEMBL
  Ub-activating_enz_e1_C UniProtKB/TrEMBL
  Ub-E1_IAD_1 UniProtKB/TrEMBL
  UBA_E1_C_sf UniProtKB/TrEMBL
  Ubi_acti_E1_SCCH UniProtKB/TrEMBL
  Ubiquitin-activating_enz UniProtKB/TrEMBL
  Ubiquitin-activating_enzyme UniProtKB/TrEMBL
  UBQ-activ_enz_E1 UniProtKB/TrEMBL
  UBQ-activ_enz_E1-like UniProtKB/TrEMBL
KEGG Report rno:305268 UniProtKB/TrEMBL
NCBI Gene 305268 ENTREZGENE
PANTHER PTHR10953 UniProtKB/TrEMBL
  SUMO-ACTIVATING ENZYME SUBUNIT 1 UniProtKB/TrEMBL
Pfam E1_4HB UniProtKB/TrEMBL
  E1_FCCH UniProtKB/TrEMBL
  ThiF UniProtKB/TrEMBL
  UBA_e1_C UniProtKB/TrEMBL
  UBA_e1_thiolCys UniProtKB/TrEMBL
PhenoGen Uba6 PhenoGen
PRINTS UBIQUITINACT UniProtKB/TrEMBL
SMART UBA_e1_C UniProtKB/TrEMBL
Superfamily-SCOP MoeB UniProtKB/TrEMBL
UniProt A0A8I5Y6L1_RAT UniProtKB/TrEMBL
  A0A8I6AS92 ENTREZGENE, UniProtKB/TrEMBL
  A6JCR8 ENTREZGENE, UniProtKB/TrEMBL
  D4A8H3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-05-02 Uba6  ubiquitin-like modifier activating enzyme 6  Ube1l2  ubiquitin-activating enzyme E1-like 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-26 Ube1l2  ubiquitin-activating enzyme E1-like 2  RGD1308324_predicted  similar to RIKEN cDNA 5730469D23 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 RGD1308324_predicted  similar to RIKEN cDNA 5730469D23 (predicted)  LOC305268_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC305268_predicted  similar to RIKEN cDNA 5730469D23 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL