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

Gene ID: 84135, updated on 3-Apr-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 and positive regulation of transcription by RNA polymerase I. Located in endoplasmic reticulum and fibrillar center. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in bone marrow (RPKM 3.2), thyroid (RPKM 2.7) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
5q13.2
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (73565741..73583380)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (74047053..74064689)
105.20220307 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 RNA, U7 small nuclear 196 pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

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 (63) 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)

Genotypes

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_2023_10

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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