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USP6 ubiquitin specific peptidase 6 [ Homo sapiens (human) ]

Gene ID: 9098, updated on 3-Apr-2024

Summary

Official Symbol
USP6provided by HGNC
Official Full Name
ubiquitin specific peptidase 6provided by HGNC
Primary source
HGNC:HGNC:12629
See related
Ensembl:ENSG00000129204 MIM:604334; AllianceGenome:HGNC:12629
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
HRP1; TRE2; TRE17; Tre-2; TRESMCR; USP6-short
Summary
Enables thiol-dependent deubiquitinase. Involved in protein deubiquitination and regulation of vesicle-mediated transport. Located in plasma membrane and recycling endosome. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in testis (RPKM 9.4), ovary (RPKM 2.5) and 9 other tissues See more
Orthologs
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Genomic context

See USP6 in Genome Data Viewer
Location:
17p13.2
Exon count:
41
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (5116032..5174991)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (5009412..5068339)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (5019327..5078286)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:4981230-4982101 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11566 Neighboring gene ZFP3 zinc finger protein Neighboring gene ZNF232 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:5033804-5034304 Neighboring gene zinc finger protein 232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:5040130-5040801 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:5040802-5041472 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:5042145-5042815 Neighboring gene MPRA-validated peak2704 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8065 Neighboring gene zinc finger protein 594 Neighboring gene ZNF594 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8066 Neighboring gene MPRA-validated peak2705 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11567 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11568 Neighboring gene SLP adaptor and CSK interacting membrane protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11569 Neighboring gene Sharpr-MPRA regulatory region 14928 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:5157813-5158318 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8067 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:5187866-5188384 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8068 Neighboring gene rabaptin, RAB GTPase binding effector protein 1 Neighboring gene uncharacterized LOC105371505 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr17:5265177-5265872

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?

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of ubiquitin specific peptidase 6 (USP6) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calmodulin binding IEA
Inferred from Electronic Annotation
more info
 
enables cysteine-type deubiquitinase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables cysteine-type deubiquitinase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables cysteine-type endopeptidase activity TAS
Traceable Author Statement
more info
PubMed 
enables nucleic acid binding TAS
Traceable Author Statement
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in protein deubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
involved_in protein modification process NAS
Non-traceable Author Statement
more info
PubMed 
involved_in proteolysis IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of vesicle-mediated transport IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
is_active_in Golgi apparatus IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
located_in lysosome TAS
Traceable Author Statement
more info
PubMed 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in recycling endosome IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
ubiquitin carboxyl-terminal hydrolase 6
Names
TBC1D3 and USP32 fusion
deubiquitinating enzyme 6
hyperpolymorphic gene 1
proto-oncogene TRE-2
ubiquitin specific peptidase 6 (Tre-2 oncogene)
ubiquitin specific protease 6 (Tre-2 oncogene)
ubiquitin thioesterase 6
ubiquitin thiolesterase 6
ubiquitin-specific protease USP6
ubiquitin-specific-processing protease 6
NP_001291213.1
NP_004496.2
XP_011522352.1
XP_011522353.1
XP_011522354.1
XP_011522355.1
XP_011522356.1
XP_011522357.1
XP_011522358.1
XP_011522360.1
XP_011522361.1
XP_047292974.1
XP_054173695.1
XP_054173696.1
XP_054173697.1
XP_054173698.1
XP_054173699.1
XP_054173700.1
XP_054173701.1
XP_054173702.1
XP_054173703.1

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_001304284.2NP_001291213.1  ubiquitin carboxyl-terminal hydrolase 6

    See identical proteins and their annotated locations for NP_001291213.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AC012146
    Consensus CDS
    CCDS11069.2
    UniProtKB/Swiss-Prot
    B9A6N0, P35125, Q15634, Q86WP6, Q8IWT4
    Related
    ENSP00000460380.1, ENST00000574788.6
    Conserved Domains (4) summary
    smart00164
    Location:97312
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    COG5560
    Location:5281114
    UBP12; Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
    cl02553
    Location:10231367
    Peptidase_C19; Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly ...
    pfam15380
    Location:332407
    DUF4607; Domain of unknown function (DUF4607)
  2. NM_004505.4NP_004496.2  ubiquitin carboxyl-terminal hydrolase 6

    See identical proteins and their annotated locations for NP_004496.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AC012146
    Consensus CDS
    CCDS11069.2
    UniProtKB/Swiss-Prot
    B9A6N0, P35125, Q15634, Q86WP6, Q8IWT4
    Related
    ENSP00000250066.6, ENST00000250066.6
    Conserved Domains (4) summary
    smart00164
    Location:97312
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    COG5560
    Location:5281114
    UBP12; Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
    cl02553
    Location:10231367
    Peptidase_C19; Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly ...
    pfam15380
    Location:332407
    DUF4607; Domain of unknown function (DUF4607)

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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    5116032..5174991
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011524059.3XP_011522361.1  ubiquitin carboxyl-terminal hydrolase 6 isoform X4

    UniProtKB/Swiss-Prot
    P35125
    Related
    ENSP00000461581.1, ENST00000572949.5
    Conserved Domains (3) summary
    smart00164
    Location:97312
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    cl02553
    Location:533723
    Peptidase_C19; Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly ...
    pfam15380
    Location:332407
    DUF4607; Domain of unknown function (DUF4607)
  2. XM_011524058.3XP_011522360.1  ubiquitin carboxyl-terminal hydrolase 6 isoform X3

    Conserved Domains (3) summary
    smart00164
    Location:97312
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    cl02553
    Location:533723
    Peptidase_C19; Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly ...
    pfam15380
    Location:332407
    DUF4607; Domain of unknown function (DUF4607)
  3. XM_011524050.2XP_011522352.1  ubiquitin carboxyl-terminal hydrolase 6 isoform X1

    See identical proteins and their annotated locations for XP_011522352.1

    UniProtKB/Swiss-Prot
    B9A6N0, P35125, Q15634, Q86WP6, Q8IWT4
    Conserved Domains (4) summary
    smart00164
    Location:97312
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    COG5560
    Location:5281114
    UBP12; Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
    cl02553
    Location:10231367
    Peptidase_C19; Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly ...
    pfam15380
    Location:332407
    DUF4607; Domain of unknown function (DUF4607)
  4. XM_047437018.1XP_047292974.1  ubiquitin carboxyl-terminal hydrolase 6 isoform X2

  5. XM_011524055.3XP_011522357.1  ubiquitin carboxyl-terminal hydrolase 6 isoform X1

    See identical proteins and their annotated locations for XP_011522357.1

    UniProtKB/Swiss-Prot
    B9A6N0, P35125, Q15634, Q86WP6, Q8IWT4
    Conserved Domains (4) summary
    smart00164
    Location:97312
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    COG5560
    Location:5281114
    UBP12; Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
    cl02553
    Location:10231367
    Peptidase_C19; Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly ...
    pfam15380
    Location:332407
    DUF4607; Domain of unknown function (DUF4607)
  6. XM_011524053.3XP_011522355.1  ubiquitin carboxyl-terminal hydrolase 6 isoform X1

    See identical proteins and their annotated locations for XP_011522355.1

    UniProtKB/Swiss-Prot
    B9A6N0, P35125, Q15634, Q86WP6, Q8IWT4
    Conserved Domains (4) summary
    smart00164
    Location:97312
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    COG5560
    Location:5281114
    UBP12; Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
    cl02553
    Location:10231367
    Peptidase_C19; Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly ...
    pfam15380
    Location:332407
    DUF4607; Domain of unknown function (DUF4607)
  7. XM_011524051.3XP_011522353.1  ubiquitin carboxyl-terminal hydrolase 6 isoform X1

    See identical proteins and their annotated locations for XP_011522353.1

    UniProtKB/Swiss-Prot
    B9A6N0, P35125, Q15634, Q86WP6, Q8IWT4
    Conserved Domains (4) summary
    smart00164
    Location:97312
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    COG5560
    Location:5281114
    UBP12; Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
    cl02553
    Location:10231367
    Peptidase_C19; Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly ...
    pfam15380
    Location:332407
    DUF4607; Domain of unknown function (DUF4607)
  8. XM_011524054.3XP_011522356.1  ubiquitin carboxyl-terminal hydrolase 6 isoform X1

    See identical proteins and their annotated locations for XP_011522356.1

    UniProtKB/Swiss-Prot
    B9A6N0, P35125, Q15634, Q86WP6, Q8IWT4
    Conserved Domains (4) summary
    smart00164
    Location:97312
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    COG5560
    Location:5281114
    UBP12; Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
    cl02553
    Location:10231367
    Peptidase_C19; Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly ...
    pfam15380
    Location:332407
    DUF4607; Domain of unknown function (DUF4607)
  9. XM_011524052.3XP_011522354.1  ubiquitin carboxyl-terminal hydrolase 6 isoform X1

    See identical proteins and their annotated locations for XP_011522354.1

    UniProtKB/Swiss-Prot
    B9A6N0, P35125, Q15634, Q86WP6, Q8IWT4
    Conserved Domains (4) summary
    smart00164
    Location:97312
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    COG5560
    Location:5281114
    UBP12; Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
    cl02553
    Location:10231367
    Peptidase_C19; Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly ...
    pfam15380
    Location:332407
    DUF4607; Domain of unknown function (DUF4607)
  10. XM_011524056.3XP_011522358.1  ubiquitin carboxyl-terminal hydrolase 6 isoform X1

    See identical proteins and their annotated locations for XP_011522358.1

    UniProtKB/Swiss-Prot
    B9A6N0, P35125, Q15634, Q86WP6, Q8IWT4
    Conserved Domains (4) summary
    smart00164
    Location:97312
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    COG5560
    Location:5281114
    UBP12; Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
    cl02553
    Location:10231367
    Peptidase_C19; Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly ...
    pfam15380
    Location:332407
    DUF4607; Domain of unknown function (DUF4607)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    5009412..5068339
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054317728.1XP_054173703.1  ubiquitin carboxyl-terminal hydrolase 6 isoform X4

  2. XM_054317727.1XP_054173702.1  ubiquitin carboxyl-terminal hydrolase 6 isoform X3

  3. XM_054317720.1XP_054173695.1  ubiquitin carboxyl-terminal hydrolase 6 isoform X1

  4. XM_054317726.1XP_054173701.1  ubiquitin carboxyl-terminal hydrolase 6 isoform X2

  5. XM_054317724.1XP_054173699.1  ubiquitin carboxyl-terminal hydrolase 6 isoform X1

  6. XM_054317722.1XP_054173697.1  ubiquitin carboxyl-terminal hydrolase 6 isoform X1

  7. XM_054317721.1XP_054173696.1  ubiquitin carboxyl-terminal hydrolase 6 isoform X1

  8. XM_054317723.1XP_054173698.1  ubiquitin carboxyl-terminal hydrolase 6 isoform X1

  9. XM_054317725.1XP_054173700.1  ubiquitin carboxyl-terminal hydrolase 6 isoform X1

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_005152.1: Suppressed sequence

    Description
    NM_005152.1: This RefSeq was permanently suppressed because it contains the wrong CDS and is a nonsense-mediated mRNA decay (NMD) candidate.