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    UTP15 UTP15 small subunit processome component [ Homo sapiens (human) ]

    Gene ID: 84135, updated on 27-Nov-2024

    Summary

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    Official Symbol
    UTP15provided by HGNC
    Official Full Name
    UTP15 small subunit processome componentprovided by HGNC
    Primary source
    HGNC:HGNC:25758
    See related
    Ensembl:ENSG00000164338 MIM:616194; AllianceGenome:HGNC:25758
    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
    NET21
    Summary
    Enables RNA binding activity. Involved in positive regulation of rRNA processing; positive regulation of transcription by RNA polymerase I; and ribosomal small subunit biogenesis. Located in endoplasmic reticulum and fibrillar center. Part of small-subunit processome. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in bone marrow (RPKM 3.2), thyroid (RPKM 2.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See UTP15 in Genome Data Viewer
    Location:
    5q13.2
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (73565741..73583380)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (74047053..74064689)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (72861566..72879205)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16090 Neighboring gene FUN14 domain containing 2 pseudogene 1 Neighboring gene H3K27ac hESC enhancers GRCh37_chr5:72860724-72861278 and GRCh37_chr5:72861279-72861833 Neighboring gene ankyrin repeat family A member 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:72895316-72895509 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16091 Neighboring gene uncharacterized LOC107986423 Neighboring gene Rho guanine nucleotide exchange factor 28 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:72989307-72989931 Neighboring gene NANOG hESC enhancer GRCh37_chr5:73042994-73043575 Neighboring gene Sharpr-MPRA regulatory region 14272 Neighboring gene Sharpr-MPRA regulatory region 14554 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:73091866-73093065 Neighboring gene ATP5PF pseudogene 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. The perichromosomal layer. Van Hooser AA, et al. Chromosoma, 2005 Dec. PMID 16136320
    2. Dynamics of WD-repeat containing proteins in SSU processome components. Wada K, et al. Biochem Cell Biol, 2014 Jun. PMID 24754225
    3. Interaction, mobility, and phosphorylation of human orthologues of WD repeat-containing components of the yeast SSU processome t-UTP sub-complex. Sato M, et al. Biochem Cell Biol, 2013 Dec. PMID 24219289
    4. NOL11, implicated in the pathogenesis of North American Indian childhood cirrhosis, is required for pre-rRNA transcription and processing. Freed EF, et al. PLoS Genet, 2012. PMID 22916032, Free PMC Article
    5. Recruitment of factors linking transcription and processing of pre-rRNA to NOR chromatin is UBF-dependent and occurs independent of transcription in human cells. Prieto JL, et al. Genes Dev, 2007 Aug 15. PMID 17699751, Free PMC Article

    See all (73) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat Expression of HIV-1 Tat downregulates the abundance of UTP15, U3 small nucleolar ribonucleoprotein (UTP15) in the nucleoli of Jurkat T-cells PubMed

    Go to the HIV-1, Human Interaction Database

    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

    • FLJ12787

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in positive regulation of rRNA processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase I IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase I IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in rRNA processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ribosomal small subunit biogenesis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		  
    located_in fibrillar center IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    U3 small nucleolar RNA-associated protein 15 homolog
    Names
    Src-associated protein SAW
    UTP15 SSU processome component
    UTP15, U3 small nucleolar ribonucleoprotein, 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_001284430.1 → NP_001271359.1  U3 small nucleolar RNA-associated protein 15 homolog isoform 2

      See identical proteins and their annotated locations for NP_001271359.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame acceptor splice site in the 5' coding region compared to variant 1. The resulting shorter isoform (2) lacks an internal protein segment compared to isoform 1.
      Source sequence(s)
      AC010279, AK022849, AK302021, AL520195, BP872156
      Consensus CDS
      CCDS68893.1
      UniProtKB/TrEMBL
      H0Y8P4
      Related
      ENSP00000424609.1, ENST00000508491.1
      Conserved Domains (4) summary
      COG2319
      Location:75 → 291
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:53 → 296
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
      pfam09384
      Location:324 → 468
      UTP15_C; UTP15 C terminal
      sd00039
      Location:65 → 101
      7WD40; WD40 repeat [structural motif]

    2. NM_001284431.1 → NP_001271360.1  U3 small nucleolar RNA-associated protein 15 homolog isoform 3

      See identical proteins and their annotated locations for NP_001271360.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an exon in the 5' coding region and initiates translation from an in-frame downstream start codon compared to variant 1. The resulting isoform (3) has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AC010279, AK022849, AK300525, AL520195, BP872156
      Consensus CDS
      CCDS68894.1
      UniProtKB/Swiss-Prot
      Q8TED0
      Related
      ENSP00000440796.1, ENST00000543251.5
      Conserved Domains (4) summary
      COG2319
      Location:2 → 120
      WD40; WD40 repeat [General function prediction only]
      pfam09384
      Location:153 → 297
      UTP15_C; UTP15 C terminal
      sd00039
      Location:19 → 54
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:1 → 125
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    3. NM_032175.4 → NP_115551.2  U3 small nucleolar RNA-associated protein 15 homolog isoform 1

      See identical proteins and their annotated locations for NP_115551.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1)
      Source sequence(s)
      AC010279, AK022849, AL520195, AL831972, BC150197, BP872156
      Consensus CDS
      CCDS34186.1
      UniProtKB/Swiss-Prot
      B4DU75, B4DXK8, Q6IA60, Q8TED0, Q96E08, Q9H9F8
      UniProtKB/TrEMBL
      H0Y8P4
      Related
      ENSP00000296792.4, ENST00000296792.9
      Conserved Domains (4) summary
      COG2319
      Location:28 → 310
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:39 → 306
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
      pfam09384
      Location:343 → 487
      UTP15_C; UTP15 C terminal
      sd00039
      Location:41 → 79
      7WD40; WD40 repeat [structural motif]

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      73565741..73583380
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011543680.3 → XP_011541982.1  U3 small nucleolar RNA-associated protein 15 homolog isoform X1

      See identical proteins and their annotated locations for XP_011541982.1

      UniProtKB/Swiss-Prot
      B4DU75, B4DXK8, Q6IA60, Q8TED0, Q96E08, Q9H9F8
      UniProtKB/TrEMBL
      H0Y8P4
      Conserved Domains (4) summary
      COG2319
      Location:28 → 310
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:39 → 306
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
      pfam09384
      Location:343 → 487
      UTP15_C; UTP15 C terminal
      sd00039
      Location:41 → 79
      7WD40; WD40 repeat [structural motif]

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      74047053..74064689
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054353681.1 → XP_054209656.1  U3 small nucleolar RNA-associated protein 15 homolog isoform X1

      UniProtKB/Swiss-Prot
      B4DU75, B4DXK8, Q6IA60, Q8TED0, Q96E08, Q9H9F8
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8TED0.3 GenPept UniProtKB/Swiss-Prot:Q8TED0

    Gene LinkOut

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