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

Gene ID: 26054, updated on 13-Mar-2020

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
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

Genomic context

See SENP6 in Genome Data Viewer
Location:
6q14.1
Exon count:
27
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (75601509..75718281)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (76311596..76427997)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 1338, pseudogene 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 RNA, U6 small nuclear 155, pseudogene Neighboring gene myosin VI Neighboring gene RNA, 5S ribosomal pseudogene 209

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ11355, FLJ11887, KIAA0389, KIAA0797

Gene Ontology Provided by GOA

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

General protein information

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
XP_006715520.1
XP_011534048.1
XP_011534049.1
XP_016866208.1
XP_016866210.1
XP_016866212.1
XP_016866213.1
XP_016866214.1
XP_024302168.1

NCBI Reference Sequences (RefSeq)

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_001100409.3NP_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/Swiss-Prot
    Q9GZR1
    UniProtKB/TrEMBL
    B3KMM0
    Related
    ENSP00000359027.2, ENST00000370010.6
    Conserved Domains (2) summary
    COG5160
    Location:656767
    ULP1; Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
    cl23802
    Location:9661042
    Peptidase_C48; Ulp1 protease family, C-terminal catalytic domain
  2. NM_001304792.1NP_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/Swiss-Prot
    Q9GZR1
    UniProtKB/TrEMBL
    F8W6D9
    Related
    ENSP00000321820.8, ENST00000327284.12
    Conserved Domains (1) summary
    COG5160
    Location:656685
    ULP1; Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
  3. NM_015571.4NP_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
    Q9GZR1
    UniProtKB/TrEMBL
    B3KMM0
    Related
    ENSP00000402527.2, ENST00000447266.7
    Conserved Domains (1) summary
    cl23802
    Location:680825
    Peptidase_C48; Ulp1 protease family, C-terminal catalytic domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    75601509..75718281
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017010724.2XP_016866213.1  sentrin-specific protease 6 isoform X5

    Conserved Domains (1) summary
    cl23802
    Location:570694
    Peptidase_C48; Ulp1 protease family, C-terminal catalytic domain
  2. XM_024446400.1XP_024302168.1  sentrin-specific protease 6 isoform X2

    Conserved Domains (2) summary
    COG5160
    Location:637748
    ULP1; Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
    cl23802
    Location:9471023
    Peptidase_C48; Ulp1 protease family, C-terminal catalytic domain
  3. XM_011535747.3XP_011534049.1  sentrin-specific protease 6 isoform X5

    Conserved Domains (1) summary
    cl23802
    Location:570694
    Peptidase_C48; Ulp1 protease family, C-terminal catalytic domain
  4. XM_017010725.2XP_016866214.1  sentrin-specific protease 6 isoform X6

    Conserved Domains (1) summary
    cl23802
    Location:564688
    Peptidase_C48; Ulp1 protease family, C-terminal catalytic domain
  5. XM_011535746.2XP_011534048.1  sentrin-specific protease 6 isoform X3

    Conserved Domains (1) summary
    cl23802
    Location:649773
    Peptidase_C48; Ulp1 protease family, C-terminal catalytic domain
  6. XM_017010723.2XP_016866212.1  sentrin-specific protease 6 isoform X5

    Conserved Domains (1) summary
    cl23802
    Location:570694
    Peptidase_C48; Ulp1 protease family, C-terminal catalytic domain
  7. XM_006715457.4XP_006715520.1  sentrin-specific protease 6 isoform X4

    Conserved Domains (1) summary
    cl23802
    Location:624748
    Peptidase_C48; Ulp1 protease family, C-terminal catalytic domain
  8. XM_017010719.2XP_016866208.1  sentrin-specific protease 6 isoform X1

  9. XM_017010721.1XP_016866210.1  sentrin-specific protease 6 isoform X4

    Conserved Domains (1) summary
    cl23802
    Location:624748
    Peptidase_C48; Ulp1 protease family, C-terminal catalytic domain

RNA

  1. XR_001743331.2 RNA Sequence

  2. XR_241847.4 RNA Sequence

  3. XR_001743330.2 RNA Sequence

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