Sumo4 (small ubiquitin-like modifier 4) - Rat Genome Database

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Gene: Sumo4 (small ubiquitin-like modifier 4) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Sumo4
Name: small ubiquitin-like modifier 4
RGD ID: 1595256
Description: Predicted to enable protein tag and ubiquitin-like protein ligase binding activity. Predicted to be involved in protein sumoylation. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in type 1 diabetes mellitus 5. Orthologous to human SUMO4 (small ubiquitin like modifier 4).
Type: pseudo (Ensembl: protein-coding)
RefSeq Status: INFERRED
Previously known as: LOC682787; similar to SMT3 suppressor of mif two 3 homolog 2; small ubiquitin-related modifier 2; SMT3 suppressor of mif two 3 homolog 2-like; Sumo2l
RGD Orthologs
Alliance Genes
More Info homologs ...
Related Functional Gene: Sumo2  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2515,099,322 - 15,099,913 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl515,099,419 - 15,099,706 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0514,983,382 - 14,984,134 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl514,983,371 - 14,984,364 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0519,767,464 - 19,768,205 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4515,325,457 - 15,325,943 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera514,481,140 - 14,481,890 (+)NCBICelera
Cytogenetic Map5q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleus  (IBA)

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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
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:15247916   PMID:16236267   PMID:18708028   PMID:22082260   PMID:24173240  


Genomics

Variants

.
Variants in Sumo4
5 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:351
Count of miRNA genes:195
Interacting mature miRNAs:212
Transcripts:ENSRNOT00000049609
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
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
631827Alc4Alcohol consumption QTL 43.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)5818750118616199Rat
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


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 2
Medium 3 43 57 41 19 41 8 11 72 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000049609   ⟹   ENSRNOP00000044856
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl514,983,371 - 14,984,364 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000100244   ⟹   ENSRNOP00000084127
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl515,099,419 - 15,099,706 (+)Ensembl
RefSeq Acc Id: XM_002729458   ⟹   XP_002729504
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2515,099,322 - 15,099,913 (+)NCBI
Rnor_6.0514,983,382 - 14,984,134 (+)NCBI
Rnor_5.0519,767,464 - 19,768,205 (+)NCBI
RGSC_v3.4515,325,457 - 15,325,943 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs XP_002729504 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_002729504   ⟸   XM_002729458
- UniProtKB: F1LN30 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000044856   ⟸   ENSRNOT00000049609
RefSeq Acc Id: ENSRNOP00000084127   ⟸   ENSRNOT00000100244
Protein Domains
Ubiquitin-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LN30-F1-model_v2 AlphaFold F1LN30 1-95 view protein structure

Transcriptome

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

Promoters
RGD ID:13693551
Promoter ID:EPDNEW_R4071
Type:initiation region
Name:Sumo4_1
Description:small ubiquitin-like modifier 4
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_6.0514,983,382 - 14,983,442EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1595256 AgrOrtholog
BioCyc Gene G2FUF-42145 BioCyc
Ensembl Genes ENSRNOG00000032840 Ensembl, UniProtKB/TrEMBL
  ENSRNOG00000069967 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000044856 UniProtKB/TrEMBL
  ENSRNOP00000084127 ENTREZGENE
  ENSRNOP00000084127.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000049609 UniProtKB/TrEMBL
  ENSRNOT00000100244 ENTREZGENE
  ENSRNOT00000100244.1 UniProtKB/TrEMBL
InterPro SUMO UniProtKB/TrEMBL
  Ubiquitin UniProtKB/TrEMBL
  Ubiquitin-rel_dom UniProtKB/TrEMBL
KEGG Report rno:682787 UniProtKB/TrEMBL
NCBI Gene 682787 ENTREZGENE
PANTHER SMALL UBIQUITIN-RELATED MODIFIER UniProtKB/TrEMBL
  SMALL UBIQUITIN-RELATED MODIFIER 3-RELATED UniProtKB/TrEMBL
Pfam Rad60-SLD UniProtKB/TrEMBL
PhenoGen Sumo4 PhenoGen
PROSITE UBIQUITIN_2 UniProtKB/TrEMBL
SMART UBQ UniProtKB/TrEMBL
Superfamily-SCOP SSF54236 UniProtKB/TrEMBL
UniProt F1LN30 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-02 Sumo4  small ubiquitin-like modifier 4  Sumo4  small ubiquitin-like modifier 4  Data Merged 737654 PROVISIONAL
2021-08-09 Sumo4  small ubiquitin-like modifier 4      Symbol and Name status set to provisional 45752 PROVISIONAL
2015-10-08 Sumo4  small ubiquitin-like modifier 4  Sumo2l  SMT3 suppressor of mif two 3 homolog 2-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-09-26 Sumo2l  SMT3 suppressor of mif two 3 homolog 2-like  LOC682787  similar to SMT3 suppressor of mif two 3 homolog 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC682787  similar to SMT3 suppressor of mif two 3 homolog 2      Symbol and Name status set to provisional 70820 PROVISIONAL