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USP48 ubiquitin specific peptidase 48 [ Homo sapiens (human) ]

Gene ID: 84196, updated on 1-Aug-2020

Summary

Official Symbol
USP48provided by HGNC
Official Full Name
ubiquitin specific peptidase 48provided by HGNC
Primary source
HGNC:HGNC:18533
See related
Ensembl:ENSG00000090686 MIM:617445
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
USP31; RAP1GA1
Summary
This gene encodes a protein containing domains that associate it with the peptidase family C19, also known as family 2 of ubiquitin carboxyl-terminal hydrolases. Family members function as deubiquitinating enzymes, recognizing and hydrolyzing the peptide bond at the C-terminal glycine of ubiquitin. Enzymes in peptidase family C19 are involved in the processing of poly-ubiquitin precursors as well as that of ubiquitinated proteins. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in adrenal (RPKM 9.7), lymph node (RPKM 7.9) and 25 other tissues See more
Orthologs

Genomic context

See USP48 in Genome Data Viewer
Location:
1p36.12
Exon count:
30
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (21678298..21784146, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (22004791..22109688, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2596 Neighboring gene RAP1 GTPase activating protein Neighboring gene low density lipoprotein receptor class A domain containing 2 Neighboring gene heparan sulfate proteoglycan 2 Neighboring gene ribosomal protein L21 pseudogene 29

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?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC14879, MGC132556, DKFZp762M1713

Gene Ontology Provided by GOA

Function Evidence Code Pubs
cysteine-type endopeptidase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
thiol-dependent ubiquitin-specific protease activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
protein deubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein deubiquitination TAS
Traceable Author Statement
more info
 
ubiquitin-dependent protein catabolic process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytosol IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
mitochondrion IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
ubiquitin carboxyl-terminal hydrolase 48
Names
deubiquitinating enzyme 48
ubiquitin specific protease 31
ubiquitin thioesterase 48
ubiquitin thiolesterase 48
ubiquitin-specific-processing protease 48
NP_001027902.1
NP_001317323.1
NP_001337093.1
NP_001337095.1
NP_001337096.1
NP_001337097.1
NP_115612.4
XP_006711018.1
XP_011540566.1
XP_011540567.1
XP_011540569.1
XP_011540570.1
XP_016857985.1
XP_016857986.1
XP_024305935.1

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.

Genomic

  1. NG_047203.1 RefSeqGene

    Range
    5051..109902
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001032730.2NP_001027902.1  ubiquitin carboxyl-terminal hydrolase 48 isoform b

    See identical proteins and their annotated locations for NP_001027902.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the coding region, compared to variant 1. The encoded isoform (b) is much shorter and has a distinct C-terminus compared to isoform a.
    Source sequence(s)
    BC067261, BM462540, CA436959, DB134378
    Consensus CDS
    CCDS44084.1
    UniProtKB/Swiss-Prot
    Q86UV5
    Related
    ENSP00000406256.2, ENST00000421625.6
    Conserved Domains (1) summary
    cd02668
    Location:90419
    Peptidase_C19L; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...
  2. NM_001330394.2NP_001317323.1  ubiquitin carboxyl-terminal hydrolase 48 isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (c) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AF502942, BC104896, BQ027743, DB134378
    Consensus CDS
    CCDS81277.1
    UniProtKB/Swiss-Prot
    Q86UV5
    Related
    ENSP00000383157.1, ENST00000400301.5
    Conserved Domains (4) summary
    cd02668
    Location:90419
    Peptidase_C19L; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...
    pfam00443
    Location:89418
    UCH; Ubiquitin carboxyl-terminal hydrolase
    pfam06337
    Location:484554
    DUSP; DUSP domain
    cl00155
    Location:909983
    UBQ; Ubiquitin-like proteins
  3. NM_001350164.2NP_001337093.1  ubiquitin carboxyl-terminal hydrolase 48 isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate in-frame splice site and lacks an alternate in-frame exon in the central coding region, compared to variant 1. The encoded isoform (d) has the same N- and C-termini, but is shorter compared to isoform a.
    Source sequence(s)
    AF502942, AK226150, AL359815, BQ027743, BQ220710, DB134378
    Conserved Domains (2) summary
    cd01795
    Location:862968
    USP48_C; USP ubiquitin-specific protease
    cd02668
    Location:90418
    Peptidase_C19L; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...
  4. NM_001350166.2NP_001337095.1  ubiquitin carboxyl-terminal hydrolase 48 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses two alternate in-frame splice sites in the central coding region, compared to variant 1. The encoded isoform (e) has the same N- and C-termini, but is two aa shorter than isoform a.
    Source sequence(s)
    AK074247, AL359815, AL834375, BC104896, BQ027743, BQ220710, DB134378
    Conserved Domains (3) summary
    cd01795
    Location:9271033
    USP48_C; USP ubiquitin-specific protease
    cd02668
    Location:90418
    Peptidase_C19L; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...
    pfam06337
    Location:483553
    DUSP; DUSP domain
  5. NM_001350167.2NP_001337096.1  ubiquitin carboxyl-terminal hydrolase 48 isoform f

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) uses an alternate in-frame splice site in the central coding region, compared to variant 1. The encoded isoform (f) has the same N- and C-termini, but is one aa shorter than isoform a. This isoform is the same length as isoform g, but contains a unique sequence.
    Source sequence(s)
    AL359815, AL834375, BC104896, BM928619, BQ027743, BQ220710, DB134378
    Related
    ENSP00000431949.1, ENST00000529637.5
    Conserved Domains (3) summary
    cd01795
    Location:9281034
    USP48_C; USP ubiquitin-specific protease
    cd02668
    Location:90418
    Peptidase_C19L; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...
    pfam06337
    Location:483553
    DUSP; DUSP domain
  6. NM_001350168.2NP_001337097.1  ubiquitin carboxyl-terminal hydrolase 48 isoform g

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) uses an alternate in-frame splice site in the central coding region, compared to variant 1. The encoded isoform (g) has the same N- and C-termini, but is one aa shorter than isoform a. This isoform is the same length as isoform f, but contains a unique sequence.
    Source sequence(s)
    AK074247, AL359815, AL834375, BC104896, BE378955, BQ027743, BQ220710, DB134378
    Conserved Domains (3) summary
    cd01795
    Location:9281034
    USP48_C; USP ubiquitin-specific protease
    cd02668
    Location:90419
    Peptidase_C19L; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...
    pfam06337
    Location:484554
    DUSP; DUSP domain
  7. NM_032236.8NP_115612.4  ubiquitin carboxyl-terminal hydrolase 48 isoform a

    See identical proteins and their annotated locations for NP_115612.4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AF502942, AL359815, BQ027743, DB134378
    Consensus CDS
    CCDS30623.1
    UniProtKB/Swiss-Prot
    Q86UV5
    Related
    ENSP00000309262.9, ENST00000308271.14
    Conserved Domains (4) summary
    cd01795
    Location:9291035
    USP48_C; USP ubiquitin-specific protease
    cd02668
    Location:90419
    Peptidase_C19L; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...
    pfam00443
    Location:89418
    UCH; Ubiquitin carboxyl-terminal hydrolase
    pfam06337
    Location:484554
    DUSP; DUSP domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20200522

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    21678298..21784146 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011542265.3XP_011540567.1  ubiquitin carboxyl-terminal hydrolase 48 isoform X3

    Conserved Domains (5) summary
    cd01795
    Location:802908
    USP48_C; USP ubiquitin-specific protease
    cd02668
    Location:3292
    Peptidase_C19L; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...
    pfam00443
    Location:9291
    UCH; Ubiquitin carboxyl-terminal hydrolase
    pfam06337
    Location:357427
    DUSP; DUSP domain
    cl12116
    Location:610653
    DUSP; DUSP domain
  2. XM_006710955.4XP_006711018.1  ubiquitin carboxyl-terminal hydrolase 48 isoform X1

    See identical proteins and their annotated locations for XP_006711018.1

    Conserved Domains (4) summary
    cd01795
    Location:863969
    USP48_C; USP ubiquitin-specific protease
    cd02668
    Location:90419
    Peptidase_C19L; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...
    pfam00443
    Location:89418
    UCH; Ubiquitin carboxyl-terminal hydrolase
    cl12116
    Location:671714
    DUSP; DUSP domain
  3. XM_024450167.1XP_024305935.1  ubiquitin carboxyl-terminal hydrolase 48 isoform X6

    Conserved Domains (2) summary
    cd01795
    Location:514620
    USP48_C; USP ubiquitin-specific protease
    pfam06337
    Location:70140
    DUSP; DUSP domain
  4. XM_011542267.3XP_011540569.1  ubiquitin carboxyl-terminal hydrolase 48 isoform X5

    See identical proteins and their annotated locations for XP_011540569.1

    Conserved Domains (3) summary
    cd01795
    Location:515621
    USP48_C; USP ubiquitin-specific protease
    pfam06337
    Location:70140
    DUSP; DUSP domain
    cl12116
    Location:323366
    DUSP; DUSP domain
  5. XM_011542264.1XP_011540566.1  ubiquitin carboxyl-terminal hydrolase 48 isoform X2

    Conserved Domains (5) summary
    cd01795
    Location:862968
    USP48_C; USP ubiquitin-specific protease
    cd02668
    Location:23352
    Peptidase_C19L; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...
    pfam00443
    Location:22351
    UCH; Ubiquitin carboxyl-terminal hydrolase
    pfam06337
    Location:417487
    DUSP; DUSP domain
    cl12116
    Location:670713
    DUSP; DUSP domain
  6. XM_011542268.2XP_011540570.1  ubiquitin carboxyl-terminal hydrolase 48 isoform X5

    See identical proteins and their annotated locations for XP_011540570.1

    Conserved Domains (3) summary
    cd01795
    Location:515621
    USP48_C; USP ubiquitin-specific protease
    pfam06337
    Location:70140
    DUSP; DUSP domain
    cl12116
    Location:323366
    DUSP; DUSP domain
  7. XM_017002497.1XP_016857986.1  ubiquitin carboxyl-terminal hydrolase 48 isoform X5

    Conserved Domains (3) summary
    cd01795
    Location:515621
    USP48_C; USP ubiquitin-specific protease
    pfam06337
    Location:70140
    DUSP; DUSP domain
    cl12116
    Location:323366
    DUSP; DUSP domain
  8. XM_017002496.2XP_016857985.1  ubiquitin carboxyl-terminal hydrolase 48 isoform X4

RNA

  1. XR_002957781.1 RNA Sequence

  2. XR_001737480.2 RNA Sequence

  3. XR_001737479.2 RNA Sequence

  4. XR_001737482.2 RNA Sequence

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