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    USP49 ubiquitin specific peptidase 49 [ Homo sapiens (human) ]

    Gene ID: 25862, updated on 11-Apr-2024

    Summary

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    Official Symbol
    USP49provided by HGNC
    Official Full Name
    ubiquitin specific peptidase 49provided by HGNC
    Primary source
    HGNC:HGNC:20078
    See related
    Ensembl:ENSG00000164663 AllianceGenome:HGNC:20078
    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
    Summary
    Enables cysteine-type endopeptidase activity; histone binding activity; and thiol-dependent deubiquitinase. Involved in histone H2B conserved C-terminal lysine deubiquitination and mRNA splicing, via spliceosome. Predicted to be located in nucleoplasm. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in testis (RPKM 2.1), thyroid (RPKM 1.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See USP49 in Genome Data Viewer
    Location:
    6p21.1
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (41789896..41895375, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (41618461..41723935, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (41757634..41863113, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17194 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41755120-41756119 Neighboring gene prickle planar cell polarity protein 4 Neighboring gene Sharpr-MPRA regulatory region 15280 Neighboring gene translocase of outer mitochondrial membrane 6 Neighboring gene small nucleolar RNA SNORA8 Neighboring gene MPRA-validated peak5805 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41861872-41862386 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:41862979-41863271 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24529 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:41884515-41885714 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24530 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41892998-41893498 Neighboring gene mediator complex subunit 20 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41906017-41906832 Neighboring gene bystin like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41906833-41907648 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24531 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41908777-41909728 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:41928638-41928835 Neighboring gene cyclin D3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:41932711-41933221 Neighboring gene uncharacterized LOC105375059 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24532 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41976875-41977831 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41977832-41978787 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41984389-41984890 Neighboring gene RNA, U6 small nuclear 761, pseudogene

    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
    • 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. USP49 mediates tumor progression and poor prognosis through a YAP1-dependent feedback loop in gastric cancer. Liu Z, et al. Oncogene, 2022 Apr. PMID 35318441
    2. USP49-Mediated Histone H2B Deubiquitination Regulates HCT116 Cell Proliferation through MDM2-p53 Axis. Shi L, et al. Mol Cell Biol, 2022 Mar 17. PMID 35072515, Free PMC Article
    3. Ubiquitin-specific protease 49 attenuates IL-1β-induced rat primary chondrocyte apoptosis by facilitating Axin deubiquitination and subsequent Wnt/β-catenin signaling cascade inhibition. Yang L, et al. Mol Cell Biochem, 2020 Nov. PMID 32737772
    4. The long non-coding RNA HLNC1 potentiates hepatocellular carcinoma progression via interaction with USP49. Qian X, et al. J Clin Lab Anal, 2020 Nov. PMID 32691951, Free PMC Article
    5. USP49 is a novel deubiquitylating enzyme for γ H2AX in DNA double-strand break repair. Matsui M, et al. Gene, 2022 Jul 30. PMID 35598681

    See all (37) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Genome-wide screening for deubiquitinase subfamily identifies ubiquitin-specific protease 49 as a novel regulator of odontogenesis.
      Title: Genome-wide screening for deubiquitinase subfamily identifies ubiquitin-specific protease 49 as a novel regulator of odontogenesis.
    2. USP49 is a novel deubiquitylating enzyme for gamma H2AX in DNA double-strand break repair.
      Title: USP49 is a novel deubiquitylating enzyme for γ H2AX in DNA double-strand break repair.
    3. USP49-Mediated Histone H2B Deubiquitination Regulates HCT116 Cell Proliferation through MDM2-p53 Axis.
      Title: USP49-Mediated Histone H2B Deubiquitination Regulates HCT116 Cell Proliferation through MDM2-p53 Axis.
    4. c-MYC-USP49-BAG2 axis promotes proliferation and chemoresistance of colorectal cancer cells in vitro.
      Title: c-MYC-USP49-BAG2 axis promotes proliferation and chemoresistance of colorectal cancer cells in vitro.
    5. USP49 mediates tumor progression and poor prognosis through a YAP1-dependent feedback loop in gastric cancer.
      Title: USP49 mediates tumor progression and poor prognosis through a YAP1-dependent feedback loop in gastric cancer.
    6. The long non-coding RNA HLNC1 potentiates hepatocellular carcinoma progression via interaction with USP49.
      Title: The long non-coding RNA HLNC1 potentiates hepatocellular carcinoma progression via interaction with USP49.
    7. Ubiquitin-specific protease 49 attenuates IL-1beta-induced rat primary chondrocyte apoptosis by facilitating Axin deubiquitination and subsequent Wnt/beta-catenin signaling cascade inhibition.
      Title: Ubiquitin-specific protease 49 attenuates IL-1β-induced rat primary chondrocyte apoptosis by facilitating Axin deubiquitination and subsequent Wnt/β-catenin signaling cascade inhibition.
    8. USP49 positively regulated dual-specificity protein phosphatases 1 (DUSP1) expression through deubiquitinating DUSP1
      Title: USP49 inhibits ischemia-reperfusion-induced cell viability suppression and apoptosis in human AC16 cardiomyocytes through DUSP1-JNK1/2 signaling.
    9. USP49 inhibits non-small cell lung cancer cell growth by suppressing PIK3R2/AKT signaling.
      Title: Ubiquitin specific peptidase 49 inhibits non-small cell lung cancer cell growth by suppressing PI3K/AKT signaling.
    10. Here, the authors found that USP49 directly interacts with APOBEC3G and efficiently removes ubiquitin, consequently increasing APOBEC3G protein expression and significantly enhancing its anti-HIV-1 activity.
      Title: USP49 potently stabilizes APOBEC3G protein by removing ubiquitin and inhibits HIV-1 replication.
    Submit: New GeneRIF Correction See all GeneRIFs (13)

    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

    EBI GWAS Catalog

    Description
    Genome-wide association study of hematological and biochemical traits in a Japanese population.
    EBI GWAS Catalog
    GWAS of blood cell traits identifies novel associated loci and epistatic interactions in Caucasian and African-American children.
    EBI GWAS Catalog

    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

    Potential readthrough

    Included gene: MED20

    Homology

    Clone Names

    • FLJ13620, MGC20741, DKFZp566J1846

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables cysteine-type deubiquitinase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables cysteine-type deubiquitinase activity TAS
    Traceable Author Statement
    more info
    		  
    enables cysteine-type endopeptidase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables histone H2B deubiquitinase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA splicing, via spliceosome IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein deubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in proteolysis IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in cytoplasm IC
    Inferred by Curator
    more info
    		 PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    ubiquitin carboxyl-terminal hydrolase 49
    Names
    deubiquitinating enzyme 49
    ubiquitin specific protease 49
    ubiquitin thioesterase 49
    ubiquitin thiolesterase 49
    ubiquitin-specific-processing protease 49
    NP_001273483.1
    NP_001371471.1
    NP_061031.2

    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_001286554.2 → NP_001273483.1  ubiquitin carboxyl-terminal hydrolase 49 isoform a

      See identical proteins and their annotated locations for NP_001273483.1

      Status: VALIDATED

      Source sequence(s)
      AL160163, AL365205
      Consensus CDS
      CCDS69111.1
      UniProtKB/Swiss-Prot
      Q5T3D9, Q5T3E0, Q70CQ1, Q96CK4
      UniProtKB/TrEMBL
      Q5T3E1
      Related
      ENSP00000507239.1, ENST00000682992.1
      Conserved Domains (2) summary
      pfam00443
      Location:253 → 654
      UCH; Ubiquitin carboxyl-terminal hydrolase
      pfam02148
      Location:26 → 87
      zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein

    2. NM_001384542.1 → NP_001371471.1  ubiquitin carboxyl-terminal hydrolase 49 isoform a

      Status: VALIDATED

      Source sequence(s)
      AL160163, AL365205
      Consensus CDS
      CCDS69111.1
      UniProtKB/Swiss-Prot
      Q5T3D9, Q5T3E0, Q70CQ1, Q96CK4
      UniProtKB/TrEMBL
      Q5T3E1
      Related
      ENSP00000377797.2, ENST00000394253.7
      Conserved Domains (2) summary
      pfam00443
      Location:253 → 654
      UCH; Ubiquitin carboxyl-terminal hydrolase
      pfam02148
      Location:26 → 87
      zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein

    3. NM_018561.5 → NP_061031.2  ubiquitin carboxyl-terminal hydrolase 49 isoform b

      See identical proteins and their annotated locations for NP_061031.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, and it includes alternate 3' exon structure and thus differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (b) has a distinct C-terminus and is shorter than isoform a.
      Source sequence(s)
      AJ586139, AL160163, BC014176
      Consensus CDS
      CCDS4861.1
      UniProtKB/TrEMBL
      Q5T3E1
      Related
      ENSP00000362097.1, ENST00000373006.5
      Conserved Domains (2) summary
      pfam00443
      Location:253 → 626
      UCH; Ubiquitin carboxyl-terminal hydrolase
      pfam02148
      Location:26 → 87
      zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      41789896..41895375 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      41618461..41723935 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q70CQ1.1 GenPept UniProtKB/Swiss-Prot:Q70CQ1

    Gene LinkOut

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

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