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Aliases for USP48 Gene

Aliases for USP48 Gene

  • Ubiquitin Specific Peptidase 48 2 3 5
  • Ubiquitin-Specific-Processing Protease 48 3 4
  • Ubiquitin Specific Protease 31 2 3
  • Deubiquitinating Enzyme 48 3 4
  • Ubiquitin Thioesterase 48 3 4
  • USP31 3 4
  • Ubiquitin Carboxyl-Terminal Hydrolase 48 3
  • Ubiquitin Specific Protease 48 2
  • Ubiquitin Thiolesterase 48 3
  • EC 3.4.19.12 4
  • EC 3.1.2.15 61
  • RAP1GA1 3

External Ids for USP48 Gene

Previous HGNC Symbols for USP48 Gene

  • USP31

Previous GeneCards Identifiers for USP48 Gene

  • GC01M021475
  • GC01M021877
  • GC01M022004
  • GC01M020248

Summaries for USP48 Gene

Entrez Gene Summary for USP48 Gene

  • 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]

GeneCards Summary for USP48 Gene

USP48 (Ubiquitin Specific Peptidase 48) is a Protein Coding gene. Among its related pathways are Deubiquitination and Ubiquitin-Proteasome Dependent Proteolysis. GO annotations related to this gene include cysteine-type endopeptidase activity and thiol-dependent ubiquitinyl hydrolase activity. An important paralog of this gene is USP47.

UniProtKB/Swiss-Prot for USP48 Gene

  • Recognizes and hydrolyzes the peptide bond at the C-terminal Gly of ubiquitin. Involved in the processing of poly-ubiquitin precursors as well as that of ubiquitinated proteins. May be involved in the regulation of NF-kappa-B activation by TNF receptor superfamily via its interactions with RELA and TRAF2. May also play a regulatory role at postsynaptic sites.

Gene Wiki entry for USP48 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for USP48 Gene

Genomics for USP48 Gene

Regulatory Elements for USP48 Gene

Enhancers for USP48 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01G021760 1.5 Ensembl ENCODE dbSUPER 41.8 +20.1 20060 6.7 HDGF PKNOX1 FOXA2 ATF1 SIN3A FEZF1 ZNF766 GATA2 CBX5 FOS USP48 ENSG00000231978 GC01P021743
GH01G021748 1 dbSUPER 47.7 +33.8 33771 1.8 HDGF PKNOX1 ATF1 ARNT TCF12 ZNF121 ZNF766 ELK1 GATA2 NCOA1 USP48 LDLRAD2 HSPG2 GC01P021743 ENSG00000231978
GH01G021791 1.3 ENCODE dbSUPER 33 -8.2 -8228 1.2 HDGF PKNOX1 CREB3L1 ARNT ZNF766 CBX5 ZNF143 ZNF207 KLF13 ZNF263 USP48 LDLRAD2 GC01P021790
GH01G021779 1.4 ENCODE dbSUPER 27.9 +1.1 1072 6.2 MLX CREB3L1 AGO1 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 TBX21 USP48 CDC42-IT1 ENSG00000271428 ZBTB40-IT1 RAP1GAP ENSG00000231978
GH01G021767 1.3 Ensembl ENCODE dbSUPER 28.5 +15.5 15463 2.3 BCOR HDAC1 HDGF PKNOX1 ESRRA TBL1XR1 TAL1 MAX CEBPG ZNF766 USP48 ENSG00000231978 GC01P021743
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around USP48 on UCSC Golden Path with GeneCards custom track

Promoters for USP48 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000002814 806 2801 MLX CREB3L1 AGO1 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 TBX21

Genomic Location for USP48 Gene

Chromosome:
1
Start:
21,678,298 bp from pter
End:
21,783,606 bp from pter
Size:
105,309 bases
Orientation:
Minus strand

Genomic View for USP48 Gene

Genes around USP48 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
USP48 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for USP48 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for USP48 Gene

Proteins for USP48 Gene

  • Protein details for USP48 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q86UV5-UBP48_HUMAN
    Recommended name:
    Ubiquitin carboxyl-terminal hydrolase 48
    Protein Accession:
    Q86UV5
    Secondary Accessions:
    • B7ZKS7
    • Q2M3I4
    • Q5SZI4
    • Q5T3T5
    • Q6NX53
    • Q8N3F6
    • Q96F64
    • Q96IQ3
    • Q9H5N3
    • Q9H5T7
    • Q9NUJ6
    • Q9NXR0

    Protein attributes for USP48 Gene

    Size:
    1035 amino acids
    Molecular mass:
    119032 Da
    Quaternary structure:
    • Interacts with TRAF2 and RELA.
    SequenceCaution:
    • Sequence=AAH13567.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=AAH67261.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=AAI03725.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=BAA92128.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=CAI12124.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=CAI16260.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Alternative splice isoforms for USP48 Gene

neXtProt entry for USP48 Gene

Selected DME Specific Peptides for USP48 Gene

Q86UV5:
  • APELNVSSSE
  • FYELELNI
  • SLRSWRQLALEQL
  • YSRYGGGP
  • WYKFNDEDIEKMEGKKLQLGIEEDL
  • LRLKNQLNEDYK
  • LQYLFAL
  • HKVVDNKKVMKD
  • KHEEVKELYQRLPA
  • QYFPKAPEFPS
  • SLEWLQKWLDESTP
  • KLHPDKI
  • WFLNLELRQALYLC
  • NAYMLVY

Post-translational modifications for USP48 Gene

  • Ubiquitination at Lys170, posLast=587587, isoforms=2, 3, 8596, Lys681, Lys689, Lys696, isoforms=2, 5, 8868, posLast=945945, and Lys1028
  • Modification sites at PhosphoSitePlus

Domains & Families for USP48 Gene

Gene Families for USP48 Gene

Suggested Antigen Peptide Sequences for USP48 Gene

Graphical View of Domain Structure for InterPro Entry

Q86UV5

UniProtKB/Swiss-Prot:

UBP48_HUMAN :
  • Belongs to the peptidase C19 family.
Family:
  • Belongs to the peptidase C19 family.
genes like me logo Genes that share domains with USP48: view

Function for USP48 Gene

Molecular function for USP48 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
UniProtKB/Swiss-Prot Function:
Recognizes and hydrolyzes the peptide bond at the C-terminal Gly of ubiquitin. Involved in the processing of poly-ubiquitin precursors as well as that of ubiquitinated proteins. May be involved in the regulation of NF-kappa-B activation by TNF receptor superfamily via its interactions with RELA and TRAF2. May also play a regulatory role at postsynaptic sites.

Enzyme Numbers (IUBMB) for USP48 Gene

Gene Ontology (GO) - Molecular Function for USP48 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004843 thiol-dependent ubiquitin-specific protease activity IEA --
GO:0008233 peptidase activity IEA --
GO:0008234 cysteine-type peptidase activity IEA --
GO:0016787 hydrolase activity IEA --
GO:0036459 thiol-dependent ubiquitinyl hydrolase activity IEA --
genes like me logo Genes that share ontologies with USP48: view
genes like me logo Genes that share phenotypes with USP48: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for USP48

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for USP48 Gene

Localization for USP48 Gene

Subcellular locations from UniProtKB/Swiss-Prot for USP48 Gene

Cytoplasm. Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for USP48 gene
Compartment Confidence
mitochondrion 5
nucleus 5
cytosol 5

Gene Ontology (GO) - Cellular Components for USP48 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA --
GO:0005739 mitochondrion IDA --
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with USP48: view

Pathways & Interactions for USP48 Gene

genes like me logo Genes that share pathways with USP48: view

Pathways by source for USP48 Gene

Gene Ontology (GO) - Biological Process for USP48 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006508 proteolysis IEA --
GO:0006511 ubiquitin-dependent protein catabolic process IEA --
GO:0016579 protein deubiquitination TAS --
genes like me logo Genes that share ontologies with USP48: view

No data available for SIGNOR curated interactions for USP48 Gene

Drugs & Compounds for USP48 Gene

No Compound Related Data Available

Transcripts for USP48 Gene

Unigene Clusters for USP48 Gene

Ubiquitin specific peptidase 48:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for USP48

Alternative Splicing Database (ASD) splice patterns (SP) for USP48 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10a · 10b ^ 11 ^ 12a · 12b · 12c ^ 13 ^ 14a · 14b ^ 15a · 15b · 15c ^ 16 ^ 17 ^ 18 ^
SP1: - - - - - -
SP2: - - - - - -
SP3:
SP4: - -
SP5: - - -
SP6: - - -
SP7:
SP8: - - -
SP9: -

ExUns: 19 ^ 20 ^ 21 ^ 22a · 22b ^ 23 ^ 24 ^ 25 ^ 26 ^ 27a · 27b ^ 28
SP1: - -
SP2:
SP3: - - -
SP4:
SP5:
SP6:
SP7: -
SP8:
SP9:

Relevant External Links for USP48 Gene

GeneLoc Exon Structure for
USP48
ECgene alternative splicing isoforms for
USP48

Expression for USP48 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for USP48 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for USP48 Gene

This gene is overexpressed in Lymph node (13.6), CD8 Tcells (6.8), and Ovary (6.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for USP48 Gene



Protein tissue co-expression partners for USP48 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of USP48 Gene:

USP48

SOURCE GeneReport for Unigene cluster for USP48 Gene:

Hs.467524

mRNA Expression by UniProt/SwissProt for USP48 Gene:

Q86UV5-UBP48_HUMAN
Tissue specificity: Widely expressed.

Evidence on tissue expression from TISSUES for USP48 Gene

  • Eye(4.4)
  • Intestine(4.4)
  • Pancreas(4.4)
  • Skin(4.4)
  • Nervous system(2.5)
  • Kidney(2.2)
  • Liver(2.2)
  • Adrenal gland(2.1)
  • Heart(2.1)
  • Muscle(2.1)
  • Thyroid gland(2.1)
  • Bone marrow(2)
  • Lung(2)
  • Lymph node(2)
genes like me logo Genes that share expression patterns with USP48: view

Primer Products

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for USP48 Gene

Orthologs for USP48 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for USP48 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia USP48 34 35
  • 99.74 (n)
oppossum
(Monodelphis domestica)
Mammalia USP48 35
  • 94 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 93 (a)
OneToMany
-- 35
  • 90 (a)
OneToMany
-- 35
  • 90 (a)
OneToMany
-- 35
  • 88 (a)
OneToMany
dog
(Canis familiaris)
Mammalia USP48 34 35
  • 92.66 (n)
cow
(Bos Taurus)
Mammalia USP48 34 35
  • 92.14 (n)
rat
(Rattus norvegicus)
Mammalia Usp48 34
  • 86.73 (n)
mouse
(Mus musculus)
Mammalia Usp48 34 16 35
  • 86.71 (n)
chicken
(Gallus gallus)
Aves USP48 34 35
  • 77.56 (n)
lizard
(Anolis carolinensis)
Reptilia USP48 35
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia usp48 34
  • 71.18 (n)
zebrafish
(Danio rerio)
Actinopterygii usp48 34 35
  • 67.54 (n)
worm
(Caenorhabditis elegans)
Secernentea usp-48 35
  • 13 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes UBP15 35
  • 13 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 40 (a)
OneToOne
Species where no ortholog for USP48 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for USP48 Gene

ENSEMBL:
Gene Tree for USP48 (if available)
TreeFam:
Gene Tree for USP48 (if available)

Paralogs for USP48 Gene

Paralogs for USP48 Gene

genes like me logo Genes that share paralogs with USP48: view

Variants for USP48 Gene

Sequence variations from dbSNP and Humsavar for USP48 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs193921025 Uncertain significance 21,729,761(-) CATAT(A/G)TGTTG nc-transcript-variant, reference, missense
rs1000060288 -- 21,686,114(+) AAAAA(A/C/T)AGCAT intron-variant
rs1000107019 -- 21,709,042(+) GTAGT(C/T)TGGCT intron-variant
rs1000134886 -- 21,759,660(+) CAAAT(C/G/T)TGGCA intron-variant, upstream-variant-2KB
rs1000152195 -- 21,722,455(+) GACTG(C/T)TTAAG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for USP48 Gene

Variant ID Type Subtype PubMed ID
esv2678062 CNV deletion 23128226
esv34155 CNV loss 18971310
nsv1008548 CNV loss 25217958
nsv1126184 CNV deletion 24896259
nsv508470 CNV deletion 20534489
nsv5854 CNV insertion 18451855
nsv5965 CNV insertion 18451855
nsv834391 CNV loss 17160897
nsv999475 CNV loss 25217958

Variation tolerance for USP48 Gene

Residual Variation Intolerance Score: 9.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.34; 41.62% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for USP48 Gene

Human Gene Mutation Database (HGMD)
USP48
SNPedia medical, phenotypic, and genealogical associations of SNPs for
USP48

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for USP48 Gene

Disorders for USP48 Gene

Relevant External Links for USP48

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
USP48

No disorders were found for USP48 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for USP48 Gene

Publications for USP48 Gene

  1. Human ubiquitin specific protease 31 is a deubiquitinating enzyme implicated in activation of nuclear factor-kappaB. (PMID: 16214042) Tzimas C. … Hatzivassiliou E.G. (Cell. Signal. 2006) 3 4 64
  2. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory S.G. … Bentley D.R. (Nature 2006) 3 4 64
  3. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen J.V. … Mann M. (Cell 2006) 3 4 64
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  5. Cloning and enzymatic analysis of 22 novel human ubiquitin-specific proteases. (PMID: 14715245) Quesada V. … Lopez-Otin C. (Biochem. Biophys. Res. Commun. 2004) 3 4 64

Products for USP48 Gene

  • Addgene plasmids for USP48

Sources for USP48 Gene

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