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SUMO3 small ubiquitin like modifier 3 [ Homo sapiens (human) ]

Gene ID: 6612, updated on 2-Nov-2024

Summary

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Official Symbol
SUMO3provided by HGNC
Official Full Name
small ubiquitin like modifier 3provided by HGNC
Primary source
HGNC:HGNC:11124
See related
Ensembl:ENSG00000184900 MIM:602231; AllianceGenome:HGNC:11124
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SMT3A; Smt3B; SMT3H1; SUMO-3
Summary
This gene encodes a member of the small ubiquitin-related modifier (SUMO) family of eukaryotic proteins. The encoded protein is covalently conjugated to other proteins via a post-translation modification known as sumoylation. Sumoylation may play a role in a wide variety of cellular processes, including nuclear transport, DNA replication and repair, mitosis, transcriptional regulation, and signal transduction. Alternatively spliced transcript variants encoding distinct proteins have been described. [provided by RefSeq, Feb 2014]
Expression
Ubiquitous expression in brain (RPKM 42.6), bone marrow (RPKM 40.3) and 25 other tissues See more
Orthologs
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Genomic context

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See SUMO3 in Genome Data Viewer
Location:
21q22.3
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (44805617..44818062, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (43165885..43178512, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (46225532..46237977, complement)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 676 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46188940-46189440 Neighboring gene ubiquitin conjugating enzyme E2 G2 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:46208307-46208531 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18575 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:46220961-46221916 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13388 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:46227083-46227236 Neighboring gene long intergenic non-protein coding RNA 1424 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46235315-46235829 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13389 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13390 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13391 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:46243688-46244247 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46254495-46254996 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46265244-46265744 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46265745-46266245 Neighboring gene PTTG1 interacting protein Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46282185-46282898 Neighboring gene uncharacterized LOC124905039 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18577 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18578 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:46292726-46293226 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:46293227-46293727 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46293885-46294562 Neighboring gene Sharpr-MPRA regulatory region 2317 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46317333-46317948 Neighboring gene integrin subunit beta 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46326258-46326823 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46326824-46327388 Neighboring gene uncharacterized LOC107987303 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46329075-46329574

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Down-regulation of SMT3A gene expression in association with DNA synthesis induction after X-ray irradiation in nevoid basal cell carcinoma syndrome (NBCCS) cells. Sugaya S, et al. Mutat Res, 2005 Oct 15. PMID 16154602
  2. Investigation of SUMO pathway genes in the etiology of nonsyndromic cleft lip with or without cleft palate. Carta E, et al. Birth Defects Res A Clin Mol Teratol, 2012 Jun. PMID 22492558
  3. Soluble Production of Human Recombinant VEGF-A121 by Using SUMO Fusion Technology in Escherichia coli. Samuel RVM, et al. Mol Biotechnol, 2018 Aug. PMID 29943150
  4. Analysis of global sumoylation changes occurring during keratinocyte differentiation. Heaton PR, et al. PLoS One, 2012. PMID 22291911, Free PMC Article
  5. The adenovirus E4-ORF3 protein functions as a SUMO E3 ligase for TIF-1γ sumoylation and poly-SUMO chain elongation. Sohn SY, et al. Proc Natl Acad Sci U S A, 2016 Jun 14. PMID 27247387, Free PMC Article

See all (163) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SUMO-3 promotes the ubiquitin-dependent turnover of TRIM55.
    Title: SUMO-3 promotes the ubiquitin-dependent turnover of TRIM55.
  2. SUMO2/3 promotes the progression and oxaliplatin resistance of colorectal cancer through facilitating the SUMOylation at Ku80-K307.
    Title: SUMO2/3 promotes the progression and oxaliplatin resistance of colorectal cancer through facilitating the SUMOylation at Ku80-K307.
  3. NSUN2 modified by SUMO-2/3 promotes gastric cancer progression and regulates mRNA m5C methylation.
    Title: NSUN2 modified by SUMO-2/3 promotes gastric cancer progression and regulates mRNA m5C methylation.
  4. SUMO paralogue-specific functions revealed through systematic analysis of human knockout cell lines and gene expression data.
    Title: SUMO paralogue-specific functions revealed through systematic analysis of human knockout cell lines and gene expression data.
  5. Opposing biological functions of the cytoplasm and nucleus DAXX modified by SUMO-2/3 in gastric cancer.
    Title: Opposing biological functions of the cytoplasm and nucleus DAXX modified by SUMO-2/3 in gastric cancer.
  6. Small ubiquitin-related modifier (SUMO) 3 and SUMO4 gene polymorphisms in Parkinson's disease.
    Title: Small ubiquitin-related modifier (SUMO) 3 and SUMO4 gene polymorphisms in Parkinson's disease.
  7. RNF4-mediated SUMO-targeted ubiquitination relieves PARIS/ZNF746-mediated transcriptional repression.
    Title: RNF4-mediated SUMO-targeted ubiquitination relieves PARIS/ZNF746-mediated transcriptional repression.
  8. The SUMO3 modification of PIAS1 modulates AR cellular distribution and stability.
    Title: SUMO3 modification by PIAS1 modulates androgen receptor cellular distribution and stability.
  9. Formation of SUMO3-conjugated chains of MAVS induced by poly(dA:dT), a ligand of RIG-I, enhances the aggregation of MAVS that drives the secretion of interferon-beta in human keratinocytes.
    Title: Formation of SUMO3-conjugated chains of MAVS induced by poly(dA:dT), a ligand of RIG-I, enhances the aggregation of MAVS that drives the secretion of interferon-β in human keratinocytes.
  10. Study demonstrated for the first time that PKA stimulated OAT3 expression and transport activity by altering the trafficking kinetics of OAT3 possibly through the crosstalk between SUMOylation and ubiquitination. OAT3 is subjected to post-translational modification by SUMO-2 and SUMO-3 not by SUMO-1.
    Title: Activation of Protein Kinase A Stimulates SUMOylation, Expression, and Transport Activity of Organic Anion Transporter 3.
Submit: New GeneRIF Correction See all GeneRIFs (66)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Tat tat Expression of HIV-1 Tat downregulates the abundance of SMT3 suppressor of mif two 3 homolog 3 (SUMO3) in the nucleoli of Jurkat T-cells PubMed
integrase gag-pol SUMOylation of HIV-1 IN at positions K46, K136, and K244 by SUMO involves HIV-1 infectivity PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein tag activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables ubiquitin-like protein ligase binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in negative regulation of DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein sumoylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein sumoylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of protein localization to nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in PML body IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in kinetochore TAS
Traceable Author Statement
more info
 PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
small ubiquitin-related modifier 3
Names
SMT3 suppressor of mif two 3 homolog 1
SMT3 suppressor of mif two 3 homolog 3
ubiquitin-like protein SMT3B

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_033969.1 RefSeqGene

    Range
    5068..17513
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001286416.2 → NP_001273345.1  small ubiquitin-related modifier 3 isoform 2

    See identical proteins and their annotated locations for NP_001273345.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame acceptor splice site compared to variant 1. The resulting longer isoform (2) has an internal protein segment not found in isoform 1.
    Source sequence(s)
    AK300822, BC000036
    Consensus CDS
    CCDS68220.1
    UniProtKB/Swiss-Prot
    P55854
    Related
    ENSP00000409666.2, ENST00000411651.6
    Conserved Domains (2) summary
    cd01763
    Location:7 → 130
    Sumo; Small ubiquitin-related modifier (SUMO)
    smart00213
    Location:17 → 123
    UBQ; Ubiquitin homologues

  2. NM_006936.3 → NP_008867.2  small ubiquitin-related modifier 3 isoform 1 precursor

    See identical proteins and their annotated locations for NP_008867.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the predominant transcript and encodes the shorter isoform (1).
    Source sequence(s)
    BC000036, BC008420
    Consensus CDS
    CCDS33587.1
    UniProtKB/Swiss-Prot
    B2R5X4, B4DUW4, P55854, Q53HI9, Q6FGD4, Q9BWR4
    Related
    ENSP00000330343.7, ENST00000332859.11
    Conserved Domains (1) summary
    cd16115
    Location:16 → 87
    Ubl_SUMO2_3_4; ubiquitin-like (Ubl) domain found in small ubiquitin-related modifier SUMO-2, SUMO-3, SUMO-4, and similar proteins

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    44805617..44818062 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    43165885..43178512 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P55854.2 GenPept UniProtKB/Swiss-Prot:P55854

Gene LinkOut

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