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

Summary

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: mouse all
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Genomic context

Location:: 6q14.1

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (75601880..75718281)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (76778738..76895148)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (76311596..76427997)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

[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].
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.
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.
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.
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.
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.
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.
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.
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.
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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-11925 (e-PCR)
- UniSTS:19203

G63444 (e-PCR)
- UniSTS:140556

D6S1339 (e-PCR)
- UniSTS:54807

RH46771 (e-PCR)
- UniSTS:35610

SENP6__3808 (e-PCR)
- UniSTS:462925

D6S1226E (e-PCR)
- UniSTS:77908

SHGC-34466 (e-PCR)
- UniSTS:19081

STS-R89090 (e-PCR)
- UniSTS:9895

RH69973 (e-PCR)
- UniSTS:46522

SHGC-33979 (e-PCR)
- UniSTS:82669

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

EC 3.4.22.68

NP_001291721.1

EC 3.4.22.68

NP_056386.2

EC 3.4.22.68

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)

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
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]
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