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    USP38 ubiquitin specific peptidase 38 [ Homo sapiens (human) ]

    Gene ID: 84640, updated on 2-Nov-2024

    Summary

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    Official Symbol
    USP38provided by HGNC
    Official Full Name
    ubiquitin specific peptidase 38provided by HGNC
    Primary source
    HGNC:HGNC:20067
    See related
    Ensembl:ENSG00000170185 MIM:618322; AllianceGenome:HGNC:20067
    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
    HP43.8KD
    Summary
    Enables cysteine-type deubiquitinase activity and protein sequestering activity. Involved in negative regulation of innate immune response; negative regulation of proteasomal ubiquitin-dependent protein catabolic process; and protein K33-linked deubiquitination. Is active in cytoplasm. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in bone marrow (RPKM 7.3), colon (RPKM 5.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See USP38 in Genome Data Viewer
    Location:
    4q31.21
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (143184917..143223874)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (146502094..146541045)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (144106070..144145027)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene USP38 divergent transcript Neighboring gene uncharacterized LOC124900788 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21940 Neighboring gene LysM domain containing 4 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:143992683-143993182 Neighboring gene Sharpr-MPRA regulatory region 2118 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:144105120-144106005 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:144106006-144106890 Neighboring gene NANOG hESC enhancer GRCh37_chr4:144169634-144170135 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21941 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:144257238-144257405 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15719 Neighboring gene uncharacterized LOC124900789 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15720 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:144257955-144258768 Neighboring gene microRNA 3139 Neighboring gene GRB2 associated binding protein 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    Related articles in PubMed

    1. USP38 promotes deubiquitination of K11-linked polyubiquitination of HIF1α at Lys769 to enhance hypoxia signaling. Wang R, et al. J Biol Chem, 2024 Jan. PMID 38072059, Free PMC Article
    2. USP38 regulates inflammatory cardiac remodeling after myocardial infarction. Gong Y, et al. Clin Sci (Lond), 2023 Nov 15. PMID 37903290
    3. USP38 might be a new therapeutic target for glioma via regulation of cancer cell metastasis. Hu T, et al. Folia Neuropathol, 2021. PMID 35114776
    4. Ubiquitin specific peptidase 38 epigenetically regulates KLF transcription factor 5 to augment malignant progression of lung adenocarcinoma. Zhang T, et al. Oncogene, 2024 Apr. PMID 38409551
    5. The deubiquitinase USP38 affects cellular functions through interacting with LSD1. Liu W, et al. Biol Res, 2018 Nov 29. PMID 30497519, Free PMC Article

    See all (37) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Ubiquitin specific peptidase 38 epigenetically regulates KLF transcription factor 5 to augment malignant progression of lung adenocarcinoma.
      Title: Ubiquitin specific peptidase 38 epigenetically regulates KLF transcription factor 5 to augment malignant progression of lung adenocarcinoma.
    2. USP38 promotes deubiquitination of K11-linked polyubiquitination of HIF1alpha at Lys769 to enhance hypoxia signaling.
      Title: USP38 promotes deubiquitination of K11-linked polyubiquitination of HIF1α at Lys769 to enhance hypoxia signaling.
    3. USP38 regulates inflammatory cardiac remodeling after myocardial infarction.
      Title: USP38 regulates inflammatory cardiac remodeling after myocardial infarction.
    4. USP38 inhibits colorectal cancer cell proliferation and migration via downregulating HMX3 ubiquitylation.
      Title: USP38 inhibits colorectal cancer cell proliferation and migration via downregulating HMX3 ubiquitylation.
    5. Reciprocal regulation of IL-33 receptor-mediated inflammatory response and pulmonary fibrosis by TRAF6 and USP38.
      Title: Reciprocal regulation of IL-33 receptor-mediated inflammatory response and pulmonary fibrosis by TRAF6 and USP38.
    6. USP38 might be a new therapeutic target for glioma via regulation of cancer cell metastasis.
      Title: USP38 might be a new therapeutic target for glioma via regulation of cancer cell metastasis.
    7. The deubiquitinase USP38 promotes cell proliferation through stabilizing c-Myc.
      Title: The deubiquitinase USP38 promotes cell proliferation through stabilizing c-Myc.
    8. Genome-wide suppressor screen identifies USP35/USP38 as therapeutic candidates for ciliopathies.
      Title: Genome-wide suppressor screen identifies USP35/USP38 as therapeutic candidates for ciliopathies.
    9. The Deubiquitinase USP38 Promotes NHEJ Repair through Regulation of HDAC1 Activity and Regulates Cancer Cell Response to Genotoxic Insults.
      Title: The Deubiquitinase USP38 Promotes NHEJ Repair through Regulation of HDAC1 Activity and Regulates Cancer Cell Response to Genotoxic Insults.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ35970, KIAA1891

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    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 protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein sequestering activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of innate immune response IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of proteasomal ubiquitin-dependent protein catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein K33-linked deubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of protein stability IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ubiquitin-dependent protein catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in nucleus IC
    Inferred by Curator
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    ubiquitin carboxyl-terminal hydrolase 38
    Names
    deubiquitinating enzyme 38
    ubiquitin specific protease 38
    ubiquitin thioesterase 38
    ubiquitin thiolesterase 38
    ubiquitin-specific-processing protease 38
    NP_001277254.1
    NP_001277255.1
    NP_001397777.1
    NP_115946.2

    NCBI Reference Sequences (RefSeq)

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    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_001290325.1 → NP_001277254.1  ubiquitin carboxyl-terminal hydrolase 38 isoform 2

      See identical proteins and their annotated locations for NP_001277254.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains a 3' terminal exon that extends past a splice site used in variant 1. This results in a novel 3' coding region and 3' UTR, compared to variant 1. It encodes isoform 2 which is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC099549, BC039115
      Consensus CDS
      CCDS77964.1
      UniProtKB/Swiss-Prot
      Q8NB14
      Related
      ENSP00000427647.1, ENST00000510377.5
      Conserved Domains (2) summary
      cd02664
      Location:446 → 947
      Peptidase_C19H; 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:445 → 946
      UCH; Ubiquitin carboxyl-terminal hydrolase

    2. NM_001290326.1 → NP_001277255.1  ubiquitin carboxyl-terminal hydrolase 38 isoform 3

      See identical proteins and their annotated locations for NP_001277255.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. It encodes isoform 3, which is shorter at the N-terminus, compared to isoform 1.
      Source sequence(s)
      AC099549, AK057992, AK093289, AK093754, BC039115
      UniProtKB/Swiss-Prot
      Q8NB14
      UniProtKB/TrEMBL
      B3KSB9
      Conserved Domains (2) summary
      cd02664
      Location:1 → 492
      Peptidase_C19H; 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:1 → 491
      UCH; Ubiquitin carboxyl-terminal hydrolase

    3. NM_001410848.1 → NP_001397777.1  ubiquitin carboxyl-terminal hydrolase 38 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC099549, AC116175
      Consensus CDS
      CCDS93639.1
      UniProtKB/TrEMBL
      A0A804HIT0
      Related
      ENSP00000507210.1, ENST00000682469.2

    4. NM_032557.6 → NP_115946.2  ubiquitin carboxyl-terminal hydrolase 38 isoform 1

      See identical proteins and their annotated locations for NP_115946.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC099549, AK091712, BC039115, BG575871
      Consensus CDS
      CCDS3758.1
      UniProtKB/Swiss-Prot
      B3KX93, Q3ZCV1, Q8NB14, Q8NDF5, Q96DK6, Q96PZ6, Q9BY55
      Related
      ENSP00000303434.4, ENST00000307017.9
      Conserved Domains (1) summary
      cd02664
      Location:446 → 947
      Peptidase_C19H; 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 ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      143184917..143223874
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      146502094..146541045
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NB14.2 GenPept UniProtKB/Swiss-Prot:Q8NB14

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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