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UTP4 UTP4 small subunit processome component [ Homo sapiens (human) ]

Gene ID: 84916, updated on 17-Jun-2019

Summary

Official Symbol
UTP4provided by HGNC
Official Full Name
UTP4 small subunit processome componentprovided by HGNC
Primary source
HGNC:HGNC:1983
See related
Ensembl:ENSG00000141076 MIM:607456
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NAIC; CIRH1A; CIRHIN; TEX292
Summary
This gene encodes a WD40-repeat-containing protein that is localized to the nucleolus. Mutation of this gene causes North American Indian childhood cirrhosis, a severe intrahepatic cholestasis that results in transient neonatal jaundice, and progresses to periportal fibrosis and cirrhosis in childhood and adolescence. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
Expression
Ubiquitous expression in kidney (RPKM 22.9), testis (RPKM 21.3) and 25 other tissues See more
Orthologs

Genomic context

See UTP4 in Genome Data Viewer
Location:
16q22.1
Exon count:
18
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (69132596..69169034)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (69166499..69202937)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene transport and golgi organization 6 homolog Neighboring gene ribosomal protein S2 pseudogene 45 Neighboring gene hyaluronan synthase 3 Neighboring gene DERPC proline and glycine rich nuclear protein Neighboring gene chromosome transmission fidelity factor 8 Neighboring gene Sharpr-MPRA regulatory region 12307 Neighboring gene RNA, U6 small nuclear 22, pseudogene

Genomic regions, transcripts, and products

Expression

  • 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

Pathways from BioSystems

  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Major pathway of rRNA processing in the nucleolus and cytosol, organism-specific biosystem (from REACTOME)
    Major pathway of rRNA processing in the nucleolus and cytosol, organism-specific biosystemIn humans, a 47S precursor rRNA (pre-rRNA) is transcribed by RNA polymerase I from rRNA-encoding genes (rDNA) at the boundary of the fibrillar center and the dense fibrillar components of the nucleol...
  • Ribosome biogenesis in eukaryotes, organism-specific biosystem (from KEGG)
    Ribosome biogenesis in eukaryotes, organism-specific biosystemRibosomes are the cellular factories responsible for making proteins. In eukaryotes, ribosome biogenesis involves the production and correct assembly of four rRNAs and about 80 ribosomal proteins. It...
  • Ribosome biogenesis in eukaryotes, conserved biosystem (from KEGG)
    Ribosome biogenesis in eukaryotes, conserved biosystemRibosomes are the cellular factories responsible for making proteins. In eukaryotes, ribosome biogenesis involves the production and correct assembly of four rRNAs and about 80 ribosomal proteins. It...
  • rRNA modification in the nucleus and cytosol, organism-specific biosystem (from REACTOME)
    rRNA modification in the nucleus and cytosol, organism-specific biosystemHuman ribosomal RNAs (rRNAs) contain about 200 residues that are enzymatically modified after transcription in the nucleolus (Maden and Khan 1977, Maden 1988, Maden and Hughes 1997, reviewed in Herna...
  • rRNA processing, organism-specific biosystem (from REACTOME)
    rRNA processing, organism-specific biosystemEach eukaryotic cytosolic ribosome contains 4 molecules of RNA: 28S rRNA (25S rRNA in yeast), 5.8S rRNA, and 5S rRNA in the 60S subunit and 18S rRNA in the 40S subunit. The 18S rRNA, 5.8S rRNA, and 2...
  • rRNA processing in the nucleus and cytosol, organism-specific biosystem (from REACTOME)
    rRNA processing in the nucleus and cytosol, organism-specific biosystemEach eukaryotic cytosolic ribosome contains 4 molecules of RNA: 28S rRNA (25S rRNA in yeast), 5.8S rRNA, and 5S rRNA in the 60S subunit and 18S rRNA in the 40S subunit. The 18S rRNA, 5.8S rRNA, and 2...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ14728, FLJ17146, KIAA1988

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
maturation of SSU-rRNA IMP
Inferred from Mutant Phenotype
more info
PubMed 
maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
rRNA processing TAS
Traceable Author Statement
more info
 
regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
90S preribosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chromosome IDA
Inferred from Direct Assay
more info
PubMed 
fibrillar center IDA
Inferred from Direct Assay
more info
PubMed 
nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
small-subunit processome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
t-UTP complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
t-UTP complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
U3 small nucleolar RNA-associated protein 4 homolog
Names
UTP4 small subunit (SSU) processome component
UTP4, small subunit (SSU) processome component, homolog
cirrhosis, autosomal recessive 1A (cirhin)
testis expressed gene 292

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_008278.1 RefSeqGene

    Range
    5001..41439
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001318391.1NP_001305320.1  U3 small nucleolar RNA-associated protein 4 homolog isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. It encodes isoform 2, which has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    BX647265, CA430627, DC368305
    Related
    ENSP00000456709.1, ENST00000562237.5
    Conserved Domains (3) summary
    COG2319
    Location:11436
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:2260
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:3223
    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 ...
  2. NM_032830.3NP_116219.2  U3 small nucleolar RNA-associated protein 4 homolog isoform 1

    See identical proteins and their annotated locations for NP_116219.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    BC009348, DA277545
    Consensus CDS
    CCDS10872.1
    UniProtKB/Swiss-Prot
    Q969X6
    Related
    ENSP00000327179.7, ENST00000314423.12
    Conserved Domains (3) summary
    COG2319
    Location:238547
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:2057
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:16306
    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 ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p13 Primary Assembly

    Range
    69132596..69169034
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005256205.3XP_005256262.2  U3 small nucleolar RNA-associated protein 4 homolog isoform X1

    Conserved Domains (3) summary
    COG2319
    Location:58380
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:304340
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:59411
    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 ...

RNA

  1. XR_001752011.2 RNA Sequence

Reference GRCh38.p13 ALT_REF_LOCI_1

Genomic

  1. NW_003315946.1 Reference GRCh38.p13 ALT_REF_LOCI_1

    Range
    60802..86658 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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