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    UTP25 UTP25 small subunit processome component [ Homo sapiens (human) ]

    Gene ID: 27042, updated on 5-Mar-2024

    Summary

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    Official Symbol
    UTP25provided by HGNC
    Official Full Name
    UTP25 small subunit processome componentprovided by HGNC
    Primary source
    HGNC:HGNC:28440
    See related
    Ensembl:ENSG00000117597 MIM:619663; AllianceGenome:HGNC:28440
    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
    DEF; DIEXF; C1orf107; DJ434O14.5
    Summary
    Enables RNA binding activity. Involved in several processes, including protein catabolic process; protein destabilization; and protein localization to nucleolus. Located in nucleolus. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in ovary (RPKM 3.8), thyroid (RPKM 2.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    1q32.2
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (209827972..209857565)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (209074743..209104338)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (210001317..210030910)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene TRAF3 interacting protein 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:209957609-209958226 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:209958227-209958842 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:209979409-209979752 Neighboring gene chromosome 1 open reading frame 74 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_2681 Neighboring gene VISTA enhancer hs932 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2477 Neighboring gene Sharpr-MPRA regulatory region 1786 Neighboring gene interferon regulatory factor 6 Neighboring gene NANOG hESC enhancer GRCh37_chr1:210048900-210049401 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:210068740-210069939 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:210071837-210072364 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_2736 Neighboring gene Sharpr-MPRA regulatory region 13960 Neighboring gene synaptotagmin 14 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:210166703-210167203 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_2861 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_2872 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_2922 Neighboring gene NANOG hESC enhancer GRCh37_chr1:210284477-210284996 Neighboring gene MPRA-validated peak677 silencer Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_2948 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:210406019-210406552 Neighboring gene SERTAD4 antisense RNA 1 Neighboring gene SERTA domain containing 4

    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. Tissue and cancer-specific expression of DIEXF is epigenetically mediated by an Alu repeat. Martín B, et al. Epigenetics, 2020 Jun-Jul. PMID 32041475, Free PMC Article
    2. MiR-195 affects cell migration and cell proliferation by down-regulating DIEXF in Hirschsprung's disease. Lei H, et al. BMC Gastroenterol, 2014 Jul 9. PMID 25007945, Free PMC Article
    3. Phosphorylation of Def Regulates Nucleolar p53 Turnover and Cell Cycle Progression through Def Recruitment of Calpain3. Guan Y, et al. PLoS Biol, 2016 Sep. PMID 27657329, Free PMC Article
    4. The pre-rRNA processing factor DEF is rate limiting for the pathogenesis of MYCN-driven neuroblastoma. Tao T, et al. Oncogene, 2017 Jul 6. PMID 28263972, Free PMC Article
    5. Def defines a conserved nucleolar pathway that leads p53 to proteasome-independent degradation. Tao T, et al. Cell Res, 2013 May. PMID 23357851, Free PMC Article

    See all (47) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Tissue and cancer-specific expression of DIEXF is epigenetically mediated by an Alu repeat.
      Title: Tissue and cancer-specific expression of DIEXF is epigenetically mediated by an Alu repeat.
    2. DEF is highly expressed in human neuroblastoma, and its depletion in human neuroblastoma cell lines induces apoptosis.
      Title: The pre-rRNA processing factor DEF is rate limiting for the pathogenesis of MYCN-driven neuroblastoma.
    3. Colonic tissue from patients with Hirschsprung's disease showed lower expression levels of digestive-organ expansion factor (DIEXF).
      Title: MiR-195 affects cell migration and cell proliferation by down-regulating DIEXF in Hirschsprung's disease.
    4. characterization of the related zebrafish protein
      Title: Loss of function of def selectively up-regulates Delta113p53 expression to arrest expansion growth of digestive organs in zebrafish.
    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

    • FLJ12704, FLJ41680, MGC29875, DKFZp686E19106

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables U3 snoRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables rRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in embryonic organ development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of embryonic development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein destabilization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein localization to nucleolus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in nucleolus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    part_of small-subunit processome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    U3 small nucleolar RNA-associated protein 25 homolog
    Names
    UTP25 small subunit processor component
    digestive-organ expansion factor homolog

    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_014388.7 → NP_055203.4  U3 small nucleolar RNA-associated protein 25 homolog

      See identical proteins and their annotated locations for NP_055203.4

      Status: VALIDATED

      Source sequence(s)
      AL022398, AL022728, BC022964, CR749825, DA256510
      Consensus CDS
      CCDS1493.1
      UniProtKB/Swiss-Prot
      O75992, Q4VY00, Q63HL9, Q68CQ4
      UniProtKB/TrEMBL
      A8K0P8
      Related
      ENSP00000419005.1, ENST00000491415.7
      Conserved Domains (1) summary
      pfam06862
      Location:276 → 751
      UTP25; Utp25, U3 small nucleolar RNA-associated SSU processome protein 25

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      209827972..209857565
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006711275.4 → XP_006711338.1  U3 small nucleolar RNA-associated protein 25 homolog isoform X1

      Conserved Domains (1) summary
      pfam06862
      Location:276 → 561
      UTP25; Utp25, U3 small nucleolar RNA-associated SSU processome protein 25

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      209074743..209104338
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054336003.1 → XP_054191978.1  U3 small nucleolar RNA-associated protein 25 homolog isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q68CQ4.2 GenPept UniProtKB/Swiss-Prot:Q68CQ4

    Gene LinkOut

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

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