Ubl4a (ubiquitin-like 4A) - Rat Genome Database

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Gene: Ubl4a (ubiquitin-like 4A) Rattus norvegicus
Analyze
Symbol: Ubl4a
Name: ubiquitin-like 4A
RGD ID: 1563983
Description: Predicted to enable protein-folding chaperone binding activity. Predicted to be involved in establishment of protein localization to membrane; regulation of protein stability; and ubiquitin-dependent protein catabolic process. Predicted to be located in cytosol; membrane; and nucleoplasm. Predicted to be part of BAT3 complex. Orthologous to human UBL4A (ubiquitin like 4A); INTERACTS WITH 2,6-dinitrotoluene; 3-chloropropane-1,2-diol; cadmium dichloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC293864; RGD1563983; similar to Ubiquitin-like protein 4 (Ubiquitin-like protein GDX); ubiquitin-like 4; ubiquitin-like protein 4A; Ubl4
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
GRCr8X157,302,528 - 157,305,380 (-)NCBIGRCr8
mRatBN7.2X152,151,242 - 152,154,094 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX152,151,460 - 152,154,069 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX154,292,367 - 154,295,219 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X157,855,174 - 157,858,026 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X155,527,400 - 155,530,252 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X156,340,919 - 156,343,771 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX156,340,925 - 156,343,777 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01152,081,056 - 152,083,908 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X160,239,300 - 160,242,152 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1135,742,562 - 135,745,414 (+)NCBICelera
Cytogenetic MapXq37NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
BAT3 complex  (IBA,IEA,ISO,ISS)
cytoplasm  (ISO)
cytosol  (ISO,ISS)
membrane  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. The EARP Complex and Its Interactor EIPR-1 Are Required for Cargo Sorting to Dense-Core Vesicles. Topalidou I, etal., PLoS Genet. 2016 May 18;12(5):e1006074. doi: 10.1371/journal.pgen.1006074. eCollection 2016 May.
Additional References at PubMed
PMID:12477932   PMID:20676083   PMID:21636303   PMID:23246001   PMID:25535373   PMID:30053369   PMID:31505169  


Genomics

Comparative Map Data
Ubl4a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X157,302,528 - 157,305,380 (-)NCBIGRCr8
mRatBN7.2X152,151,242 - 152,154,094 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX152,151,460 - 152,154,069 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX154,292,367 - 154,295,219 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X157,855,174 - 157,858,026 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X155,527,400 - 155,530,252 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X156,340,919 - 156,343,771 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX156,340,925 - 156,343,777 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01152,081,056 - 152,083,908 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X160,239,300 - 160,242,152 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1135,742,562 - 135,745,414 (+)NCBICelera
Cytogenetic MapXq37NCBI
UBL4A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X154,483,717 - 154,486,615 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX154,483,717 - 154,486,615 (-)EnsemblGRCh38hg38GRCh38
GRCh37X153,712,056 - 153,714,954 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X153,365,250 - 153,368,126 (-)NCBINCBI36Build 36hg18NCBI36
Build 34X153,275,761 - 153,278,636NCBI
CeleraX153,873,107 - 153,875,983 (-)NCBICelera
Cytogenetic MapXq28NCBI
HuRefX142,288,568 - 142,290,380 (-)NCBIHuRef
CHM1_1X153,623,701 - 153,626,577 (-)NCBICHM1_1
T2T-CHM13v2.0X152,720,226 - 152,723,124 (-)NCBIT2T-CHM13v2.0
Ubl4a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X73,409,324 - 73,412,154 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX73,409,324 - 73,416,824 (-)EnsemblGRCm39 Ensembl
GRCm38X74,365,718 - 74,368,548 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX74,365,718 - 74,373,218 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X71,612,740 - 71,613,866 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X70,620,121 - 70,621,247 (-)NCBIMGSCv36mm8
CeleraX65,621,216 - 65,622,342 (-)NCBICelera
Cytogenetic MapXA7.3NCBI
cM MapX38.0NCBI
Ubl4a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955580997,204 - 1,001,368 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955580998,953 - 1,001,368 (-)NCBIChiLan1.0ChiLan1.0
UBL4A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X154,458,117 - 154,461,095 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X154,461,722 - 154,464,672 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X143,925,494 - 143,928,444 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X153,796,889 - 153,799,214 (-)NCBIpanpan1.1PanPan1.1panPan2
UBL4A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X122,195,500 - 122,196,579 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX122,195,502 - 122,196,577 (-)EnsemblCanFam3.1canFam3CanFam3.1
ROS_Cfam_1.0X125,337,154 - 125,338,233 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX125,335,829 - 125,338,220 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X121,106,157 - 121,107,231 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X123,621,230 - 123,622,309 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X123,383,001 - 123,384,080 (-)NCBIUU_Cfam_GSD_1.0
Ubl4a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X119,500,690 - 119,503,571 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049368091,238,462 - 1,241,318 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049368091,238,459 - 1,241,319 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC10A3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX125,007,122 - 125,013,980 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X125,007,121 - 125,009,657 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X143,575,797 - 143,578,331 (+)NCBISscrofa10.2Sscrofa10.2susScr3
UBL4A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X128,733,219 - 128,736,150 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX128,732,876 - 128,736,077 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606566,722,027 - 66,724,987 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ubl4a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624946955,993 - 958,849 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624946955,993 - 958,424 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ubl4a
2 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:187
Count of miRNA genes:143
Interacting mature miRNAs:156
Transcripts:ENSRNOT00000056313
Prediction methods: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
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X113937816152453651Rat
634346Insul4Insulin level QTL 40blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)X126975089152453651Rat

Markers in Region
Slc10a3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X152,155,056 - 152,155,927 (-)MAPPERmRatBN7.2
Rnor_6.0X156,339,086 - 156,339,956NCBIRnor6.0
Rnor_5.01152,079,223 - 152,080,093UniSTSRnor5.0
RGSC_v3.4X160,237,467 - 160,238,337UniSTSRGSC3.4
Celera1135,740,729 - 135,741,599UniSTS
Cytogenetic MapXq37UniSTS


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 56 41 16 41 8 11 74 35 34 11 8
Low 1 3 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000091810   ⟹   ENSRNOP00000074769
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX152,151,460 - 152,154,069 (-)Ensembl
Rnor_6.0 EnsemblX156,340,925 - 156,343,777 (+)Ensembl
RefSeq Acc Id: NM_001106346   ⟹   NP_001099816
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X157,302,528 - 157,305,380 (-)NCBI
mRatBN7.2X152,151,242 - 152,154,094 (-)NCBI
Rnor_6.0X156,340,919 - 156,343,771 (+)NCBI
Rnor_5.01152,081,056 - 152,083,908 (+)NCBI
RGSC_v3.4X160,239,300 - 160,242,152 (+)RGD
Celera1135,742,562 - 135,745,414 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001099816 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI66513 (Get FASTA)   NCBI Sequence Viewer  
  B2GV38 (Get FASTA)   NCBI Sequence Viewer  
  EDL84970 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000074769
  ENSRNOP00000074769.2
Reference Protein Sequences
RefSeq Acc Id: NP_001099816   ⟸   NM_001106346
- UniProtKB: B2GV38 (UniProtKB/Swiss-Prot),   A0A8L2URF4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000074769   ⟸   ENSRNOT00000091810
Protein Domains
Ubiquitin-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B2GV38-F1-model_v2 AlphaFold B2GV38 1-157 view protein structure

Transcriptome

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

Promoters
RGD ID:13702041
Promoter ID:EPDNEW_R12565
Type:initiation region
Name:Ubl4a_1
Description:ubiquitin-like 4A
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_6.0X156,340,939 - 156,340,999EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1563983 AgrOrtholog
BioCyc Gene G2FUF-622 BioCyc
Ensembl Genes ENSRNOG00000053061 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000091810 ENTREZGENE
  ENSRNOT00000091810.2 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7129152 IMAGE-MGC_LOAD
InterPro Ubiquitin UniProtKB/Swiss-Prot
  Ubiquitin-like_dom UniProtKB/TrEMBL
  Ubiquitin-like_domsf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ubiquitin_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ubiquitin_dom UniProtKB/Swiss-Prot
  Ubiquitin_dom UniProtKB/TrEMBL
  Ubl4_C_TUGS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ubl_UBL4A-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:293864 UniProtKB/Swiss-Prot
MGC_CLONE MGC:188082 IMAGE-MGC_LOAD
NCBI Gene 293864 ENTREZGENE
PANTHER UBIQUITIN-LIKE PROTEIN 4A UniProtKB/Swiss-Prot
  UBIQUITIN-LIKE PROTEIN 4A UniProtKB/Swiss-Prot
  UBIQUITIN-LIKE PROTEIN 4A UniProtKB/TrEMBL
  UBIQUITIN-LIKE PROTEIN 4A UniProtKB/TrEMBL
Pfam Tugs UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ubiquitin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ubl4a PhenoGen
PRINTS UBIQUITIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE UBIQUITIN_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  UBIQUITIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000053061 RatGTEx
SMART UBQ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF54236 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8L2URF4 ENTREZGENE, UniProtKB/TrEMBL
  B2GV38 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-02-02 Ubl4a  ubiquitin-like 4A  Ubl4  ubiquitin-like 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Ubl4  ubiquitin-like 4  Ubl4a_predicted  ubiquitin-like 4a (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Ubl4a_predicted  ubiquitin-like 4a (predicted)  RGD1563983_predicted  similar to Ubiquitin-like protein 4 (Ubiquitin-like protein GDX) (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1563983_predicted  similar to Ubiquitin-like protein 4 (Ubiquitin-like protein GDX) (predicted)  LOC293864  similar to Ubiquitin-like protein 4 (Ubiquitin-like protein GDX)  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC293864  similar to Ubiquitin-like protein 4 (Ubiquitin-like protein GDX)      Symbol and Name status set to provisional 70820 PROVISIONAL