Human Gene SUMO2 (ENST00000420826.7_7) from GENCODE V47lift37
  Description: small ubiquitin like modifier 2, transcript variant 1 (from RefSeq NM_006937.4)
Gencode Transcript: ENST00000420826.7_7
Gencode Gene: ENSG00000188612.12_10
Transcript (Including UTRs)
   Position: hg19 chr17:73,161,681-73,179,054 Size: 17,374 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg19 chr17:73,164,434-73,178,929 Size: 14,496 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:73,161,681-73,179,054)mRNA (may differ from genome)Protein (95 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MGIOMIMPubMedReactomeUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SUMO2_HUMAN
DESCRIPTION: RecName: Full=Small ubiquitin-related modifier 2; Short=SUMO-2; AltName: Full=HSMT3; AltName: Full=SMT3 homolog 2; AltName: Full=SUMO-3; AltName: Full=Sentrin-2; AltName: Full=Ubiquitin-like protein SMT3A; Short=Smt3A; Flags: Precursor;
FUNCTION: Ubiquitin-like protein that can be covalently attached to proteins as a monomer or as a lysine-linked polymer. Covalent attachment via an isopeptide bond to its substrates requires prior activation by the E1 complex SAE1-SAE2 and linkage to the E2 enzyme UBE2I, and can be promoted by an E3 ligase such as PIAS1-4, RANBP2 or CBX4. This post-translational modification on lysine residues of proteins plays a crucial role in a number of cellular processes such as nuclear transport, DNA replication and repair, mitosis and signal transduction. Polymeric SUMO2 chains are also susceptible to polyubiquitination which functions as a signal for proteasomal degradation of modified proteins.
SUBUNIT: Homotrimer (Potential). Crystal packing analysis suggests a possible trimeric assembly, of which the biological significance remains to be determined. Interacts with SAE2 and UBE2I. Covalently attached to a number of proteins. Interacts with PELP1. Interacts with USP25; the interaction sumoylates USP25.
INTERACTION: P10242:MYB; NbExp=3; IntAct=EBI-473220, EBI-298355; Q8N2W9:PIAS4; NbExp=3; IntAct=EBI-473220, EBI-473160;
SUBCELLULAR LOCATION: Nucleus. Note=Nuclear bodies.
TISSUE SPECIFICITY: Broadly expressed.
PTM: Polymeric chains can be formed through Lys-11 cross-linking. Polymeric SUMO2 chains undergo 'Lys-6'-, 'Lys-11'-, 'Lys-48'- and 'Lys-63'-linked polyubiquitination by RNF4.
PTM: Cleavage of precursor form by SENP1 or SENP2 is necessary for function.
SIMILARITY: Belongs to the ubiquitin family. SUMO subfamily.
SIMILARITY: Contains 1 ubiquitin-like domain.
CAUTION: Frequently wrongly assigned as SMT3B in many databases and publications. However, according to initial nomenclature, SUMO2 corresponds to SMT3A (PubMed:10692421).
WEB RESOURCE: Name=Wikipedia; Note=SUMO protein entry; URL="http://en.wikipedia.org/wiki/SUMO_protein";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 181.89 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 3750.45 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -42.40125-0.339 Picture PostScript Text
3' UTR -757.202753-0.275 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR022617 - SUMO
IPR000626 - Ubiquitin
IPR019955 - Ubiquitin_supergroup

Pfam Domains:
PF00240 - Ubiquitin family
PF11976 - Ubiquitin-2 like Rad60 SUMO-like

SCOP Domains:
54236 - Ubiquitin-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1WM2 - X-ray MuPIT 1WM3 - X-ray MuPIT 1WZ0 - NMR MuPIT 1Z5Q - Model 2AWT - NMR MuPIT 2CKH - X-ray MuPIT 2D07 - X-ray MuPIT 2IO0 - X-ray MuPIT 2IO3 - X-ray MuPIT 2IYD - X-ray 2RPQ - NMR MuPIT 3UIN - X-ray MuPIT 3UIO - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P61956
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001222 transcription corepressor binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0031386 protein tag
GO:0031625 ubiquitin protein ligase binding

Biological Process:
GO:0016925 protein sumoylation
GO:0032436 positive regulation of proteasomal ubiquitin-dependent protein catabolic process

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0016605 PML body


-  Descriptions from all associated GenBank mRNAs
  BC002811 - Homo sapiens cDNA clone IMAGE:3636371, partial cds.
JD441179 - Sequence 422203 from Patent EP1572962.
JD254771 - Sequence 235795 from Patent EP1572962.
JD435468 - Sequence 416492 from Patent EP1572962.
BC008450 - Homo sapiens SMT3 suppressor of mif two 3 homolog 2 (S. cerevisiae), mRNA (cDNA clone MGC:14687 IMAGE:4133768), complete cds.
JD550979 - Sequence 532003 from Patent EP1572962.
AK024823 - Homo sapiens cDNA: FLJ21170 fis, clone CAS10946, highly similar to HSSMT3B Homo sapiens mRNA for SMT3B protein.
BC107853 - Homo sapiens SMT3 suppressor of mif two 3 homolog 2 (S. cerevisiae), mRNA (cDNA clone MGC:117191 IMAGE:5772748), complete cds.
AK225090 - Homo sapiens mRNA for SMT3 suppressor of mif two 3 homolog 2 variant, clone: CAS08355.
BC071646 - Homo sapiens SMT3 suppressor of mif two 3 homolog 2 (S. cerevisiae), mRNA (cDNA clone MGC:87809 IMAGE:4369354), complete cds.
BC016775 - Homo sapiens SMT3 suppressor of mif two 3 homolog 2 (S. cerevisiae), mRNA (cDNA clone MGC:23719 IMAGE:4096440), complete cds.
BC022340 - Homo sapiens SMT3 suppressor of mif two 3 homolog 2 (S. cerevisiae), mRNA (cDNA clone MGC:23776 IMAGE:4134531), complete cds.
BC062713 - Homo sapiens SMT3 suppressor of mif two 3 homolog 2 (S. cerevisiae), mRNA (cDNA clone MGC:72004 IMAGE:30404344), complete cds.
BC070159 - Homo sapiens SMT3 suppressor of mif two 3 homolog 2 (S. cerevisiae), mRNA (cDNA clone MGC:88139 IMAGE:6592382), complete cds.
JD063129 - Sequence 44153 from Patent EP1572962.
BC068465 - Homo sapiens SMT3 suppressor of mif two 3 homolog 2 (S. cerevisiae), mRNA (cDNA clone MGC:87071 IMAGE:5277638), complete cds.
JD427947 - Sequence 408971 from Patent EP1572962.
LF328381 - JP 2014500723-A/135884: Polycomb-Associated Non-Coding RNAs.
LF328382 - JP 2014500723-A/135885: Polycomb-Associated Non-Coding RNAs.
X99585 - H.sapiens mRNA for SMT3B protein.
LF328383 - JP 2014500723-A/135886: Polycomb-Associated Non-Coding RNAs.
JD389627 - Sequence 370651 from Patent EP1572962.
JD389628 - Sequence 370652 from Patent EP1572962.
JD080616 - Sequence 61640 from Patent EP1572962.
JD501048 - Sequence 482072 from Patent EP1572962.
JD091627 - Sequence 72651 from Patent EP1572962.
L76416 - Homo sapiens MIF2 suppressor (HSMT3) mRNA, complete cds.
LF326722 - JP 2014500723-A/134225: Polycomb-Associated Non-Coding RNAs.
LF328384 - JP 2014500723-A/135887: Polycomb-Associated Non-Coding RNAs.
AK225263 - Homo sapiens mRNA for SMT3 suppressor of mif two 3 homolog 2 variant, clone: DMC04051.
JD167855 - Sequence 148879 from Patent EP1572962.
AK311837 - Homo sapiens cDNA, FLJ92100, highly similar to Homo sapiens SMT3 suppressor of mif two 3 homolog 2 (yeast)(SUMO2), mRNA.
KJ892164 - Synthetic construct Homo sapiens clone ccsbBroadEn_01558 SUMO2 gene, encodes complete protein.
KJ897587 - Synthetic construct Homo sapiens clone ccsbBroadEn_06981 SUMO2 gene, encodes complete protein.
DQ893036 - Synthetic construct clone IMAGE:100005666; FLH192874.01X; RZPDo839A0478D SMT3 suppressor of mif two 3 homolog 2 (S. cerevisiae) (SUMO2) gene, encodes complete protein.
DQ896277 - Synthetic construct Homo sapiens clone IMAGE:100010737; FLH192870.01L; RZPDo839A0468D SMT3 suppressor of mif two 3 homolog 2 (S. cerevisiae) (SUMO2) gene, encodes complete protein.
AB528658 - Synthetic construct DNA, clone: pF1KB6733, Homo sapiens SUMO2 gene for SMT3 suppressor of mif two 3 homolog 2, without stop codon, in Flexi system.
LF326723 - JP 2014500723-A/134226: Polycomb-Associated Non-Coding RNAs.
LF328386 - JP 2014500723-A/135889: Polycomb-Associated Non-Coding RNAs.
LF343394 - JP 2014500723-A/150897: Polycomb-Associated Non-Coding RNAs.
LF328389 - JP 2014500723-A/135892: Polycomb-Associated Non-Coding RNAs.
JD193100 - Sequence 174124 from Patent EP1572962.
JD261559 - Sequence 242583 from Patent EP1572962.
JD538020 - Sequence 519044 from Patent EP1572962.
MA563958 - JP 2018138019-A/135884: Polycomb-Associated Non-Coding RNAs.
MA563959 - JP 2018138019-A/135885: Polycomb-Associated Non-Coding RNAs.
MA563960 - JP 2018138019-A/135886: Polycomb-Associated Non-Coding RNAs.
MA562299 - JP 2018138019-A/134225: Polycomb-Associated Non-Coding RNAs.
MA563961 - JP 2018138019-A/135887: Polycomb-Associated Non-Coding RNAs.
MA562300 - JP 2018138019-A/134226: Polycomb-Associated Non-Coding RNAs.
MA563963 - JP 2018138019-A/135889: Polycomb-Associated Non-Coding RNAs.
MA578971 - JP 2018138019-A/150897: Polycomb-Associated Non-Coding RNAs.
MA563966 - JP 2018138019-A/135892: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_sumoPathway - Basic Mechanisms of SUMOylation

Reactome (by CSHL, EBI, and GO)

Protein P61956 (Reactome details) participates in the following event(s):

R-HSA-2993784 Conjugation of SUMO2 to UBA2:SAE1
R-HSA-2990842 SEN1,2,5 proteolytically process SUMO2
R-HSA-3000348 RANBP2 SUMOylates SP100 with SUMO2
R-HSA-3000411 RANBP2 SUMOylates PML with SUMO2
R-HSA-4546387 PIAS4 SUMOylates VDR with SUMO2
R-HSA-4570489 SUMOylation of NOP58 with SUMO2
R-HSA-4570499 CBX4 (Pc2) SUMOylates HNRNPK with SUMO2
R-HSA-5684052 PIAS4 SUMOylates MDC1
R-HSA-6804468 PIAS1 SUMOylates SP3 with SUMO2
R-HSA-6804485 PIAS1 SUMOylates L3MBTL2 with SUMO2
R-HSA-2993790 Transfer of SUMO2 from E1 to UBE2I (UBC9)
R-HSA-2997616 PIAS1,4 SUMOylates BRCA1 with SUMO2,3
R-HSA-2997706 MDM2 SUMOylates TP53 with SUMO2,3
R-HSA-3465545 PIAS1,3,4 SUMOylate MTA1 with SUMO2,3
R-HSA-4551616 SUMOylation of RPA1 (RPA70) with SUMO2,3
R-HSA-4551738 SUMOylation of TDG with SUMO2,3
R-HSA-4551768 PIAS4 SUMOylates PARP1 with SUMO2,3
R-HSA-4568914 SUMOylation of BLM with SUMO2,3
R-HSA-4570463 CBX4 (Pc2) SUMOylates CETN2 with SUMO2,3
R-HSA-4570553 SUMOylation of MDC1 with SUMO2,3
R-HSA-4615839 PIAS1 SUMOylates SATB1 with SUMO2,3
R-HSA-4615987 RANBP2 SUMOylates HDAC4 with SUMO2,3
R-HSA-4641350 PIAS4 SUMOylates TOP2A with SUMO2,3
R-HSA-6790454 SUMOylation of XPC
R-HSA-5684071 RNF4 ubiquitinates MDC1
R-HSA-6790487 RNF111 ubiquitinates SUMOylated XPC
R-HSA-3065676 SUMO is conjugated to E1 (UBA2:SAE1)
R-HSA-3065679 SUMO is proteolytically processed
R-HSA-3215018 Processing and activation of SUMO
R-HSA-3108214 SUMOylation of DNA damage response and repair proteins
R-HSA-196791 Vitamin D (calciferol) metabolism
R-HSA-4570464 SUMOylation of RNA binding proteins
R-HSA-5693607 Processing of DNA double-strand break ends
R-HSA-3232118 SUMOylation of transcription factors
R-HSA-4551638 SUMOylation of chromatin organization proteins
R-HSA-3065678 SUMO is transferred from E1 to E2 (UBE2I, UBC9)
R-HSA-2990846 SUMOylation
R-HSA-4615885 SUMOylation of DNA replication proteins
R-HSA-5696395 Formation of Incision Complex in GG-NER
R-HSA-3108232 SUMO E3 ligases SUMOylate target proteins
R-HSA-209943 Steroid hormones
R-HSA-8957322 Metabolism of steroids
R-HSA-5693567 HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA)
R-HSA-597592 Post-translational protein modification
R-HSA-5696399 Global Genome Nucleotide Excision Repair (GG-NER)
R-HSA-556833 Metabolism of lipids
R-HSA-5693538 Homology Directed Repair
R-HSA-392499 Metabolism of proteins
R-HSA-5696398 Nucleotide Excision Repair
R-HSA-1430728 Metabolism
R-HSA-5693532 DNA Double-Strand Break Repair
R-HSA-73894 DNA Repair

-  Other Names for This Gene
  Alternate Gene Symbols: B2R4I2, ENST00000420826.1, ENST00000420826.2, ENST00000420826.3, ENST00000420826.4, ENST00000420826.5, ENST00000420826.6, NM_006937, P55855, P61956, Q32Q42, Q6IPZ6, Q96HK1, SMT3B , SMT3H2, SUMO2 , SUMO2_HUMAN, uc319qgy.1, uc319qgy.2
UCSC ID: ENST00000420826.7_7
RefSeq Accession: NM_006937.4
Protein: P61956 (aka SUMO2_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.