Ubash3a (ubiquitin associated and SH3 domain containing, A) - Rat Genome Database

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Gene: Ubash3a (ubiquitin associated and SH3 domain containing, A) Rattus norvegicus
Analyze
Symbol: Ubash3a
Name: ubiquitin associated and SH3 domain containing, A
RGD ID: 1310305
Description: Predicted to be involved in negative regulation of T cell receptor signaling pathway. Predicted to act upstream of or within regulation of cytokine production. Predicted to be located in cytosol and nuclear speck. Predicted to be active in cytoplasm. Orthologous to human UBASH3A (ubiquitin associated and SH3 domain containing A); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; alpha-Zearalanol; amphetamine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC309666; ubiquitin-associated and SH3 domain-containing protein A
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8209,292,819 - 9,336,036 (+)NCBIGRCr8
mRatBN7.2209,291,471 - 9,334,685 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl209,292,139 - 9,329,224 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx209,987,205 - 10,023,581 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0209,348,375 - 9,384,747 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0209,823,515 - 9,859,888 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0209,941,102 - 9,986,012 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl209,948,908 - 9,985,133 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02012,121,174 - 12,164,639 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4209,583,659 - 9,620,767 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1209,565,754 - 9,620,437 (+)NCBI
Celera2010,813,252 - 10,850,304 (+)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IBA)
cytosol  (IEA,ISO)
nuclear speck  (IEA,ISO)
nucleoplasm  (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:14738763   PMID:16780588   PMID:18570454   PMID:27609517   PMID:34205929  


Genomics

Comparative Map Data
Ubash3a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8209,292,819 - 9,336,036 (+)NCBIGRCr8
mRatBN7.2209,291,471 - 9,334,685 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl209,292,139 - 9,329,224 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx209,987,205 - 10,023,581 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0209,348,375 - 9,384,747 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0209,823,515 - 9,859,888 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0209,941,102 - 9,986,012 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl209,948,908 - 9,985,133 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02012,121,174 - 12,164,639 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4209,583,659 - 9,620,767 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1209,565,754 - 9,620,437 (+)NCBI
Celera2010,813,252 - 10,850,304 (+)NCBICelera
Cytogenetic Map20p12NCBI
UBASH3A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382142,403,902 - 42,447,684 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2142,403,447 - 42,447,684 (+)EnsemblGRCh38hg38GRCh38
GRCh372143,824,011 - 43,867,794 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362142,697,088 - 42,740,843 (+)NCBINCBI36Build 36hg18NCBI36
Build 342142,697,087 - 42,740,843NCBI
Celera2128,972,990 - 29,016,745 (+)NCBICelera
Cytogenetic Map21q22.3NCBI
HuRef2129,250,404 - 29,285,124 (+)NCBIHuRef
HuRef2129,241,532 - 29,247,337 (+)NCBIHuRef
CHM1_12143,384,191 - 43,428,632 (+)NCBICHM1_1
T2T-CHM13v2.02140,793,440 - 40,837,215 (+)NCBIT2T-CHM13v2.0
Ubash3a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391731,426,842 - 31,478,655 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1731,426,847 - 31,465,866 (+)EnsemblGRCm39 Ensembl
GRCm381731,207,868 - 31,259,681 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1731,207,873 - 31,246,892 (+)EnsemblGRCm38mm10GRCm38
MGSCv371731,345,011 - 31,379,348 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361730,939,125 - 30,970,800 (+)NCBIMGSCv36mm8
Celera1732,125,656 - 32,159,759 (+)NCBICelera
Cytogenetic Map17A3.3- B1NCBI
cM Map1715.84NCBI
Ubash3a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540739,290,827 - 39,326,004 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540739,290,025 - 39,325,810 (-)NCBIChiLan1.0ChiLan1.0
UBASH3A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22238,459,784 - 38,503,867 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12133,312,242 - 33,356,325 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02128,711,107 - 28,755,405 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12142,029,709 - 42,073,746 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2142,029,709 - 42,073,746 (+)Ensemblpanpan1.1panPan2
UBASH3A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13136,735,790 - 36,778,405 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3136,735,835 - 36,778,405 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3135,886,662 - 35,929,164 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03136,252,367 - 36,294,753 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3136,252,422 - 36,294,753 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13136,145,154 - 36,187,365 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03136,125,524 - 36,168,052 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03136,620,547 - 36,663,016 (+)NCBIUU_Cfam_GSD_1.0
Ubash3a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440497135,993,083 - 36,030,304 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049365001,437,658 - 1,474,705 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
UBASH3A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13205,744,393 - 205,787,056 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113205,744,395 - 205,786,484 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213216,148,487 - 216,190,648 (+)NCBISscrofa10.2Sscrofa10.2susScr3
UBASH3A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1286,279,762 - 86,330,281 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl286,280,198 - 86,332,756 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605414,240,863 - 14,295,816 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ubash3a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474528,026,274 - 28,057,922 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ubash3a
573 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:601
Count of miRNA genes:259
Interacting mature miRNAs:328
Transcripts:ENSRNOT00000001541
Prediction methods:Microtar, 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
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124159021Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125159026Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat
1331772Cdexp2CD45RC expression in CD8 T cells QTL 25.7CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)20362164910078919Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20362165614101050Rat
4889857Pur27Proteinuria QTL 2712.20.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20460660717617956Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20460660717617956Rat
70154Insul2Insulin level QTL 23.75blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20669170617489458Rat
1581577Pur15Proteinuria QTL 154.380.0002urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)20804241017617956Rat
4889870Pur30Proteinuria QTL 30190.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20804241029322208Rat
631265Iresp1Immunoglobin response QTL18.3blood anti-double stranded DNA antibody amount (VT:0004762)serum anti-DNA antibody level (CMO:0001533)20903971913461775Rat


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 10 2 13 2
Low 2 12 23 20 6 20 13 2 17 11
Below cutoff 1 22 20 15 15 8 8 57 28 24 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000001541   ⟹   ENSRNOP00000001541
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl209,292,139 - 9,328,074 (+)Ensembl
Rnor_6.0 Ensembl209,948,908 - 9,985,133 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000119947   ⟹   ENSRNOP00000094194
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl209,292,139 - 9,329,224 (+)Ensembl
RefSeq Acc Id: NM_001401235   ⟹   NP_001388164
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8209,293,690 - 9,330,491 (+)NCBI
mRatBN7.2209,292,333 - 9,329,143 (+)NCBI
RefSeq Acc Id: XM_039098726   ⟹   XP_038954654
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8209,292,824 - 9,336,036 (+)NCBI
mRatBN7.2209,291,471 - 9,334,685 (+)NCBI
RefSeq Acc Id: XM_039098727   ⟹   XP_038954655
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8209,292,819 - 9,314,647 (+)NCBI
mRatBN7.2209,292,117 - 9,309,113 (+)NCBI
RefSeq Acc Id: XM_063279154   ⟹   XP_063135224
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8209,292,821 - 9,318,146 (+)NCBI
RefSeq Acc Id: XR_005497253
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8209,292,820 - 9,325,930 (+)NCBI
mRatBN7.2209,292,118 - 9,324,580 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001388164 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954654 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954655 (Get FASTA)   NCBI Sequence Viewer  
  XP_063135224 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL97007 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000001541.8
  ENSRNOP00000094194
  ENSRNOP00000094194.1
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000001541   ⟸   ENSRNOT00000001541
RefSeq Acc Id: XP_038954654   ⟸   XM_039098726
- Peptide Label: isoform X1
- UniProtKB: A0A8I6AZI9 (UniProtKB/TrEMBL),   D3ZY64 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038954655   ⟸   XM_039098727
- Peptide Label: isoform X3
RefSeq Acc Id: ENSRNOP00000094194   ⟸   ENSRNOT00000119947
RefSeq Acc Id: NP_001388164   ⟸   NM_001401235
- UniProtKB: A0A8I6AZI9 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135224   ⟸   XM_063279154
- Peptide Label: isoform X2
Protein Domains
SH3   UBA

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZY64-F1-model_v2 AlphaFold D3ZY64 1-624 view protein structure

Transcriptome

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

Promoters
RGD ID:13701473
Promoter ID:EPDNEW_R11997
Type:initiation region
Name:Ubash3a_1
Description:ubiquitin associated and SH3 domain containing, A
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_6.0209,948,904 - 9,948,964EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310305 AgrOrtholog
BioCyc Gene G2FUF-4321 BioCyc
Ensembl Genes ENSRNOG00000001167 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000001541.8 UniProtKB/TrEMBL
  ENSRNOT00000119947 ENTREZGENE
  ENSRNOT00000119947.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.1240 UniProtKB/TrEMBL
  DNA helicase RuvA subunit, C-terminal domain UniProtKB/TrEMBL
  SH3 Domains UniProtKB/TrEMBL
InterPro His_Pase_superF_clade-1 UniProtKB/TrEMBL
  His_PPase_superfam UniProtKB/TrEMBL
  SH3-like_dom UniProtKB/TrEMBL
  SH3_domain UniProtKB/TrEMBL
  UBA UniProtKB/TrEMBL
  UBA-like UniProtKB/TrEMBL
  UBASH3A_SH3 UniProtKB/TrEMBL
NCBI Gene 309666 ENTREZGENE
PANTHER UBIQUITIN-ASSOCIATED AND SH3 DOMAIN-CONTAINING BA-RELATED UniProtKB/TrEMBL
  UBIQUITIN-ASSOCIATED AND SH3 DOMAIN-CONTAINING PROTEIN A UniProtKB/TrEMBL
Pfam PGAM UniProtKB/TrEMBL
  SH3_9 UniProtKB/TrEMBL
PhenoGen Ubash3a PhenoGen
PROSITE SH3 UniProtKB/TrEMBL
  UBA UniProtKB/TrEMBL
RatGTEx ENSRNOG00000001167 RatGTEx
SMART SH3 UniProtKB/TrEMBL
Superfamily-SCOP SH3 UniProtKB/TrEMBL
  SSF46934 UniProtKB/TrEMBL
  SSF53254 UniProtKB/TrEMBL
UniProt A0A8I6AZI9 ENTREZGENE, UniProtKB/TrEMBL
  D3ZY64 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Ubash3a  ubiquitin associated and SH3 domain containing, A   Ubash3a_predicted  ubiquitin associated and SH3 domain containing, A (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Ubash3a_predicted  ubiquitin associated and SH3 domain containing, A (predicted)      Symbol and Name status set to approved 70820 APPROVED