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SENP6 SUMO specific peptidase 6 [ Homo sapiens (human) ]

Gene ID: 26054, updated on 5-Mar-2024

Summary

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Official Symbol
SENP6provided by HGNC
Official Full Name
SUMO specific peptidase 6provided by HGNC
Primary source
HGNC:HGNC:20944
See related
Ensembl:ENSG00000112701 MIM:605003; AllianceGenome:HGNC:20944
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SSP1; SUSP1
Summary
Ubiquitin-like molecules (UBLs), such as SUMO1 (UBL1; MIM 601912), are structurally related to ubiquitin (MIM 191339) and can be ligated to target proteins in a similar manner as ubiquitin. However, covalent attachment of UBLs does not result in degradation of the modified proteins. SUMO1 modification is implicated in the targeting of RANGAP1 (MIM 602362) to the nuclear pore complex, as well as in stabilization of I-kappa-B-alpha (NFKBIA; MIM 164008) from degradation by the 26S proteasome. Like ubiquitin, UBLs are synthesized as precursor proteins, with 1 or more amino acids following the C-terminal glycine-glycine residues of the mature UBL protein. Thus, the tail sequences of the UBL precursors need to be removed by UBL-specific proteases, such as SENP6, prior to their conjugation to target proteins (Kim et al., 2000 [PubMed 10799485]). SENPs also display isopeptidase activity for deconjugation of SUMO-conjugated substrates (Lima and Reverter, 2008 [PubMed 18799455]).[supplied by OMIM, Jun 2009]
Expression
Ubiquitous expression in thyroid (RPKM 14.2), testis (RPKM 12.7) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
6q14.1
Exon count:
24
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (75601880..75718281)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (76778738..76895148)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (76311596..76427997)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:76311385-76311934 Neighboring gene RNA, U6 small nuclear 1338, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17341 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24759 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:76313673-76314202 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:76316827-76317327 Neighboring gene LSM14A, SCD6 homolog A (S. cerevisiae) pseudogene Neighboring gene H3 histone pseudogene 27 Neighboring gene RNA, U6 small nuclear 1016, pseudogene Neighboring gene RN7SK pseudogene 163 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:76397423-76397924 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:76397925-76398424 Neighboring gene oocyte-secreted protein 4B-like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24760 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24761 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17342 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:76466141-76466640 Neighboring gene RNA, U6 small nuclear 155, pseudogene Neighboring gene myosin VI

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
  • 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. Single Cell RNA-Seq Identifies Immune-Related Prognostic Model and Key Signature-SPP1 in Pancreatic Ductal Adenocarcinoma. Chen K, et al. Genes (Basel), 2022 Sep 29. PMID 36292645, Free PMC Article
  2. Genetic screening identifies a SUMO protease dynamically maintaining centromeric chromatin. Mitra S, et al. Nat Commun, 2020 Jan 24. PMID 31980633, Free PMC Article
  3. The SUMO Isopeptidase SENP6 Functions as a Rheostat of Chromatin Residency in Genome Maintenance and Chromosome Dynamics. Wagner K, et al. Cell Rep, 2019 Oct 8. PMID 31597105
  4. The poly-SUMO2/3 protease SENP6 enables assembly of the constitutive centromere-associated network by group deSUMOylation. Liebelt F, et al. Nat Commun, 2019 Sep 4. PMID 31485003, Free PMC Article
  5. SENP6-mediated M18BP1 deSUMOylation regulates CENP-A centromeric localization. Fu H, et al. Cell Res, 2019 Mar. PMID 30631152, Free PMC Article

See all (57) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. [Interaction of SENP6 with PINK1 Promotes Temozolomide Resistance in Neuroglioma Cells via Inducing the Mitophagy].
    Title: [Interaction of SENP6 with PINK1 Promotes Temozolomide Resistance in Neuroglioma Cells via Inducing the Mitophagy].
  2. SENP6-Mediated deSUMOylation of VEGFR2 Enhances Its Cell Membrane Transport in Angiogenesis.
    Title: SENP6-Mediated deSUMOylation of VEGFR2 Enhances Its Cell Membrane Transport in Angiogenesis.
  3. Single Cell RNA-Seq Identifies Immune-Related Prognostic Model and Key Signature-SPP1 in Pancreatic Ductal Adenocarcinoma.
    Title: Single Cell RNA-Seq Identifies Immune-Related Prognostic Model and Key Signature-SPP1 in Pancreatic Ductal Adenocarcinoma.
  4. Genetic alterations of the SUMO isopeptidase SENP6 drive lymphomagenesis and genetic instability in diffuse large B-cell lymphoma.
    Title: Genetic alterations of the SUMO isopeptidase SENP6 drive lymphomagenesis and genetic instability in diffuse large B-cell lymphoma.
  5. The SUMO Isopeptidase SENP6 Functions as a Rheostat of Chromatin Residency in Genome Maintenance and Chromosome Dynamics.
    Title: The SUMO Isopeptidase SENP6 Functions as a Rheostat of Chromatin Residency in Genome Maintenance and Chromosome Dynamics.
  6. SENP6 and FEM1C gene expression in liver transplantation predicts transplantation tolerance.
    Title: Tolerance Biomarkers in Liver Transplantation: Independent External Validation of the Predictive Strength of SENP6 and FEM1C Gene Expression.
  7. The authors conclude that SENP6, a factor important for CENP-A maintenance and assembly, functions in protecting a portion of M18BP1 from PIAS4-mediated SUMOylation and subsequent SUMOylation-dependent ubiquitination and degradation.
    Title: SENP6-mediated M18BP1 deSUMOylation regulates CENP-A centromeric localization.
  8. SENP6 activity is required throughout the cell cycle, suggesting that a dynamic SUMO cycle underlies a continuous surveillance of the centromere complex.
    Title: Genetic screening identifies a SUMO protease dynamically maintaining centromeric chromatin.
  9. SUMO specific peptidase 6 (SENP6) deficient cells are severely compromised for proliferation, accumulate in G2/M and frequently form micronuclei.
    Title: The poly-SUMO2/3 protease SENP6 enables assembly of the constitutive centromere-associated network by group deSUMOylation.
  10. LANA could bind to the promoter region of the SENP6 gene and inhibit SENP6 expression while the regulated SENP6 could in turn modulate the abundance of LANA through desumoylation.
    Title: The Latency-Associated Nuclear Antigen of Kaposi's Sarcoma-Associated Herpesvirus Inhibits Expression of SUMO/Sentrin-Specific Peptidase 6 To Facilitate Establishment of Latency.
Submit: New GeneRIF Correction See all GeneRIFs (18)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Hundreds of variants clustered in genomic loci and biological pathways affect human height.
EBI GWAS Catalog

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ11355, FLJ11887, KIAA0389, KIAA0797

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables SUMO-specific endopeptidase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables SUMO-specific endopeptidase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in protein desumoylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein desumoylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein modification by small protein removal IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein sumoylation IEA
Inferred from Electronic Annotation
more info
  
involved_in proteolysis IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of kinetochore assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of kinetochore assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of spindle assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of spindle assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
sentrin-specific protease 6
Names
2810017C20Rik
SUMO-1-specific protease 1
SUMO1/sentrin specific peptidase 6
SUMO1/sentrin specific protease 6
sentrin/SUMO-specific protease SENP6
NP_001093879.1
NP_001291721.1
NP_056386.2

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.

mRNA and Protein(s)

  1. NM_001100409.3 → NP_001093879.1  sentrin-specific protease 6 isoform 2

    See identical proteins and their annotated locations for NP_001093879.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in a shorter protein (isoform 2), compared to isoform 1.
    Source sequence(s)
    AF307849, AK021417, AL109897, AL356057, BC028583, CR990444
    Consensus CDS
    CCDS43483.1
    UniProtKB/TrEMBL
    B3KX86
    Related
    ENSP00000359027.2, ENST00000370010.6
    Conserved Domains (2) summary
    COG5160
    Location:656 → 767
    ULP1; Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
    cl23802
    Location:966 → 1042
    Peptidase_C48; Ulp1 protease family, C-terminal catalytic domain

  2. NM_001304792.2 → NP_001291721.1  sentrin-specific protease 6 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an exon in the 5' coding region and its 3' terminal exon extends past a splice site that is used in variant 1. This results in a novel 3' coding region and 3' UTR, compared to variant 1. It encodes isoform 3 which has a shorter C-terminus, compared to isoform 1.
    Source sequence(s)
    AA768785, AF306508, AK096455, AL356057, AL589656
    Consensus CDS
    CCDS78158.1
    UniProtKB/TrEMBL
    F8W6D9, H0Y4F4
    Related
    ENSP00000321820.8, ENST00000327284.12
    Conserved Domains (1) summary
    COG5160
    Location:656 → 685
    ULP1; Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]

  3. NM_015571.4 → NP_056386.2  sentrin-specific protease 6 isoform 1

    See identical proteins and their annotated locations for NP_056386.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AF307849, AK021417, AL109897, AL356057, CR990444
    Consensus CDS
    CCDS47454.1
    UniProtKB/Swiss-Prot
    A6NNY9, O94891, Q5VUL3, Q5VUL4, Q8TBY4, Q9GZR1, Q9UJV5
    UniProtKB/TrEMBL
    B3KX86
    Related
    ENSP00000402527.2, ENST00000447266.7
    Conserved Domains (1) summary
    cl23802
    Location:680 → 825
    Peptidase_C48; Ulp1 protease family, C-terminal catalytic domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    75601880..75718281
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    76778738..76895148
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9GZR1.2 GenPept UniProtKB/Swiss-Prot:Q9GZR1

Gene LinkOut

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

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