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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
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Genomic context

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See UTP25 in Genome Data Viewer
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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