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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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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