Aliases for USP38 Gene

Aliases for USP38 Gene

  • Ubiquitin Specific Peptidase 38 2 3 5
  • HP43.8KD 2 3 4
  • Ubiquitin-Specific-Processing Protease 38 3 4
  • Ubiquitin Carboxyl-Terminal Hydrolase 38 3 4
  • Ubiquitin Specific Protease 38 2 3
  • Deubiquitinating Enzyme 38 3 4
  • Ubiquitin Thioesterase 38 3 4
  • KIAA1891 2 4
  • Ubiquitin Thiolesterase 38 3
  • EC 3.4.19.12 4
  • USP38 5

External Ids for USP38 Gene

Previous GeneCards Identifiers for USP38 Gene

  • GC04P144572
  • GC04P144683
  • GC04P144463
  • GC04P144325
  • GC04P144106
  • GC04P139835

Summaries for USP38 Gene

GeneCards Summary for USP38 Gene

USP38 (Ubiquitin Specific Peptidase 38) is a Protein Coding gene. Diseases associated with USP38 include Ullrich Congenital Muscular Dystrophy 1. Among its related pathways are Ubiquitin-Proteasome Dependent Proteolysis and Integrated Breast Cancer Pathway. Gene Ontology (GO) annotations related to this gene include cysteine-type endopeptidase activity and thiol-dependent ubiquitinyl hydrolase activity. An important paralog of this gene is USP35.

UniProtKB/Swiss-Prot Summary for USP38 Gene

  • Deubiquitinating enzyme exhibiting a preference towards 'Lys-63'-linked ubiquitin chains.

Additional gene information for USP38 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for USP38 Gene

Genomics for USP38 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for USP38 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH04J143183 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 607.5 +1.9 1884 7.2 CREB1 GATAD2A PRDM10 ZNF629 IKZF1 ZNF692 POLR2A BACH1 JUND ETV6 USP38 ENSG00000250326 LOC105377623 hsa-miR-1273e-055 GAB1
GH04J143373 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 4.6 +193.9 193889 10.6 GATAD2A CTCF PRDM10 ZNF629 IKZF1 FOXA1 PRDM1 RELA RXRB RAD21 GAB1 USP38 lnc-SMARCA5-7 piR-50443-293 SMARCA5
GH04J143472 Enhancer 0.8 Ensembl dbSUPER 11.2 +288.4 288384 2.2 SP1 PKNOX1 FOXA2 YY1 ZBTB33 JUND ELF1 RAD21 HNF4A RXRA ENSG00000250326 USP38 GAB1 piR-38580-226 RF00017-4425 SMARCA5
GH04J143351 Promoter/Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 4.9 +172.4 172439 11.6 SP1 TEAD4 PRDM10 ZNF629 RFX1 FOXA1 DDX20 PRDM1 RELA TCF12 ENSG00000286771 USP38 SMARCA5 GAB1 piR-50443-293
GH04J143386 Enhancer 0.7 dbSUPER 10.6 +203.7 203675 3.3 GATAD2A FOXA1 ZNF600 SOX13 TCF7 EGR1 CEBPB FOXA2 JUND HHEX GAB1 ENSG00000250326 USP38 lnc-SMARCA5-7 lnc-FREM3-5 SMARCA5
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around USP38 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for USP38

Top Transcription factor binding sites by QIAGEN in the USP38 gene promoter:
  • AREB6
  • c-Myc
  • C/EBPalpha
  • E47
  • Egr-2
  • GATA-1
  • Max
  • Meis-1a
  • Meis-1b
  • Zic1

Genomic Locations for USP38 Gene

Genomic Locations for USP38 Gene
chr4:143,184,917-143,224,429
(GRCh38/hg38)
Size:
39,513 bases
Orientation:
Plus strand
chr4:144,106,070-144,144,983
(GRCh37/hg19)
Size:
38,914 bases
Orientation:
Plus strand

Genomic View for USP38 Gene

Genes around USP38 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
USP38 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for USP38 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for USP38 Gene

Proteins for USP38 Gene

  • Protein details for USP38 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8NB14-UBP38_HUMAN
    Recommended name:
    Ubiquitin carboxyl-terminal hydrolase 38
    Protein Accession:
    Q8NB14
    Secondary Accessions:
    • B3KX93
    • Q3ZCV1
    • Q8NDF5
    • Q96DK6
    • Q96PZ6
    • Q9BY55

    Protein attributes for USP38 Gene

    Size:
    1042 amino acids
    Molecular mass:
    116546 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAK26248.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAB71627.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAC03730.1; Type=Miscellaneous discrepancy; Note=The absence of the residues from Tyr-840 to Ser-871 is not the result of an alternative splicing.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for USP38 Gene

    Alternative splice isoforms for USP38 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for USP38 Gene

Post-translational modifications for USP38 Gene

  • Ubiquitination at Lys773
  • Modification sites at PhosphoSitePlus

Other Protein References for USP38 Gene

No data available for DME Specific Peptides for USP38 Gene

Domains & Families for USP38 Gene

Gene Families for USP38 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for USP38 Gene

InterPro:
Blocks:
  • Ubiquitin thiolesterase, family 2
ProtoNet:

Suggested Antigen Peptide Sequences for USP38 Gene

GenScript: Design optimal peptide antigens:
  • Ubiquitin carboxyl-terminal hydrolase (Q3ZCV1_HUMAN)
  • Ubiquitin-specific-processing protease 38 (UBP38_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8NB14

UniProtKB/Swiss-Prot:

UBP38_HUMAN :
  • Belongs to the peptidase C19 family.
Family:
  • Belongs to the peptidase C19 family.
genes like me logo Genes that share domains with USP38: view

Function for USP38 Gene

Molecular function for USP38 Gene

UniProtKB/Swiss-Prot Function:
Deubiquitinating enzyme exhibiting a preference towards 'Lys-63'-linked ubiquitin chains.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=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).; EC=3.4.19.12; Evidence={ECO:0000269|PubMed:14715245};.

Enzyme Numbers (IUBMB) for USP38 Gene

Phenotypes From GWAS Catalog for USP38 Gene

Gene Ontology (GO) - Molecular Function for USP38 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004197 cysteine-type endopeptidase activity IBA 21873635
GO:0004843 thiol-dependent ubiquitin-specific protease activity IDA 14715245
GO:0008233 peptidase activity IEA --
GO:0008234 cysteine-type peptidase activity IEA --
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with USP38: view
genes like me logo Genes that share phenotypes with USP38: view

Animal Models for USP38 Gene

MGI Knock Outs for USP38:
  • Usp38 Usp38<tm1b(EUCOMM)Hmgu>

Animal Model Products

  • Taconic Biosciences Mouse Models for USP38

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for USP38

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for USP38 Gene

Localization for USP38 Gene

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 USP38 gene
Compartment Confidence
nucleus 3
cytosol 3
plasma membrane 1
extracellular 1
cytoskeleton 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Centrosome (2)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for USP38 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA 21873635
GO:0005829 cytosol IBA 21873635
genes like me logo Genes that share ontologies with USP38: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for USP38 Gene

Pathways & Interactions for USP38 Gene

PathCards logo

SuperPathways for USP38 Gene

SuperPathway Contained pathways
1 Ubiquitin-Proteasome Dependent Proteolysis
-
2 Integrated Breast Cancer Pathway
genes like me logo Genes that share pathways with USP38: view

Pathways by source for USP38 Gene

1 BioSystems pathway for USP38 Gene
1 Qiagen pathway for USP38 Gene
  • Ubiquitin-Proteasome Dependent Proteolysis

Gene Ontology (GO) - Biological Process for USP38 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 IDA 14715245
genes like me logo Genes that share ontologies with USP38: view

No data available for SIGNOR curated interactions for USP38 Gene

Drugs & Compounds for USP38 Gene

(1) Drugs for USP38 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Water Approved Pharma 0
genes like me logo Genes that share compounds with USP38: view

Transcripts for USP38 Gene

mRNA/cDNA for USP38 Gene

3 REFSEQ mRNAs :
14 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for USP38

Alternative Splicing Database (ASD) splice patterns (SP) for USP38 Gene

No ASD Table

Relevant External Links for USP38 Gene

GeneLoc Exon Structure for
USP38

Expression for USP38 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for USP38 Gene

mRNA differential expression in normal tissues according to GTEx for USP38 Gene

This gene is overexpressed in Muscle - Skeletal (x6.8).

Protein differential expression in normal tissues from HIPED for USP38 Gene

This gene is overexpressed in Tlymphocyte (67.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for USP38 Gene



Protein tissue co-expression partners for USP38 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for USP38

SOURCE GeneReport for Unigene cluster for USP38 Gene:

Hs.480848

mRNA Expression by UniProt/SwissProt for USP38 Gene:

Q8NB14-UBP38_HUMAN
Tissue specificity: Highly expressed in skeletal muscle. Expressed in adrenal gland.

Evidence on tissue expression from TISSUES for USP38 Gene

  • Nervous system(4.5)
  • Stomach(4.3)
  • Adrenal gland(4.1)
  • Blood(2.3)
  • Muscle(2.1)
genes like me logo Genes that share expression patterns with USP38: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for USP38 Gene

Orthologs for USP38 Gene

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

Orthologs for USP38 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia USP38 30 31
  • 99.46 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia USP38 30 31
  • 91.09 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia USP38 30 31
  • 90.1 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Usp38 30 17 31
  • 87.46 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Usp38 30
  • 87.16 (n)
Oppossum
(Monodelphis domestica)
Mammalia USP38 31
  • 86 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia USP38 31
  • 81 (a)
OneToOne
Chicken
(Gallus gallus)
Aves USP38 30 31
  • 73.82 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia USP38 31
  • 71 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia usp38 30
  • 70.6 (n)
Str.10104 30
Zebrafish
(Danio rerio)
Actinopterygii USP38 31
  • 64 (a)
OneToOne
usp38 30
  • 63.82 (n)
Dr.15383 30
Fruit Fly
(Drosophila melanogaster)
Insecta CG8830 31
  • 29 (a)
OneToMany
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes UBP13 31
  • 18 (a)
ManyToMany
UBP9 31
  • 17 (a)
ManyToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 41 (a)
OneToMany
Species where no ortholog for USP38 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • 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 Vase (Ciona intestinalis)
  • 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)
  • Worm (Caenorhabditis elegans)

Evolution for USP38 Gene

ENSEMBL:
Gene Tree for USP38 (if available)
TreeFam:
Gene Tree for USP38 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for USP38: view image

Paralogs for USP38 Gene

(3) SIMAP similar genes for USP38 Gene using alignment to 3 proteins:

  • UBP38_HUMAN
  • H0Y9H5_HUMAN
  • Q3ZCV1_HUMAN
genes like me logo Genes that share paralogs with USP38: view

Variants for USP38 Gene

Additional dbSNP identifiers (rs#s) for USP38 Gene

Structural Variations from Database of Genomic Variants (DGV) for USP38 Gene

Variant ID Type Subtype PubMed ID
esv3350576 CNV insertion 20981092
nsv1033902 CNV gain 25217958

Variation tolerance for USP38 Gene

Residual Variation Intolerance Score: 2.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.80; 47.51% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for USP38 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
USP38

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for USP38 Gene

Disorders for USP38 Gene

MalaCards: The human disease database

(1) MalaCards diseases for USP38 Gene - From: DISEASES

Disorder Aliases PubMed IDs
ullrich congenital muscular dystrophy 1
  • ucmd1
- elite association - COSMIC cancer census association via MalaCards
Search USP38 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for USP38

genes like me logo Genes that share disorders with USP38: view

No data available for UniProtKB/Swiss-Prot and Genatlas for USP38 Gene

Publications for USP38 Gene

  1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  3. Cloning and enzymatic analysis of 22 novel human ubiquitin-specific proteases. (PMID: 14715245) Quesada V … López-Otín C (Biochemical and biophysical research communications 2004) 3 4
  4. Human and mouse proteases: a comparative genomic approach. (PMID: 12838346) Puente XS … López-Otín C (Nature reviews. Genetics 2003) 2 3
  5. Prediction of the coding sequences of unidentified human genes. XXI. The complete sequences of 60 new cDNA clones from brain which code for large proteins. (PMID: 11572484) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2001) 3 4

Products for USP38 Gene

  • Signalway Proteins for USP38

Sources for USP38 Gene