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

Gene ID: 84916, updated on 3-Apr-2024

Summary

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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; AllianceGenome:HGNC:1983
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
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Genomic context

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Location:
16q22.1
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (69132649..69169021)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (74928956..74965636)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (69166552..69202924)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene transport and golgi organization 6 homolog Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11034 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:69096798-69097616 Neighboring gene ribosomal protein S2 pseudogene 45 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:69105561-69106280 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:69106281-69106998 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:69106999-69107717 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:69107718-69108435 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:69111819-69112338 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:69122977-69123854 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:69131715-69132540 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:69133965-69134466 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr16:69139221-69139769 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7651 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:69143266-69144235 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7652 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7653 Neighboring gene hyaluronan synthase 3 Neighboring gene chromosome transmission fidelity factor 8 Neighboring gene DERPC proline and glycine rich nuclear protein Neighboring gene Sharpr-MPRA regulatory region 12307 Neighboring gene RNA, U6 small nuclear 22, pseudogene Neighboring gene syntrophin beta 2 Neighboring gene zinc finger CCHC-type and RNA binding motif containing 1 pseudogene

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. CIRH1A augments the proliferation of RKO colorectal cancer cells. Guo F, et al. Oncol Rep, 2017 Apr. PMID 28350096
  2. North American Indian cirrhosis in children: a review of 30 cases. Drouin E, et al. J Pediatr Gastroenterol Nutr, 2000 Oct. PMID 11045837
  3. Localization of a recessive gene for North American Indian childhood cirrhosis to chromosome region 16q22-and identification of a shared haplotype. Bétard C, et al. Am J Hum Genet, 2000 Jul. PMID 10820129, Free PMC Article
  4. Nucleolar localization of cirhin, the protein mutated in North American Indian childhood cirrhosis. Yu B, et al. Exp Cell Res, 2005 Dec 10. PMID 16225863
  5. Molecular basis of intrahepatic cholestasis. Carlton VE, et al. Ann Med, 2004. PMID 15768832

See all (80) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Results show that CIRH1A was highly expressed in carcinoma samples and colorectal cancer cells and suggest that CIRH1A plays a critical role in the proliferation, cell cycle distribution, and apoptosis of human malignant colorectal cells.
    Title: CIRH1A augments the proliferation of RKO colorectal cancer cells.
  2. Cirhin is a transcriptional regulatory factor of this NF-kappaB sequence and could be a participant in the regulation of other genes with NF-kappaB responsive elements.
    Title: Cirhin up-regulates a canonical NF-kappaB element through strong interaction with Cirip/HIVEP1.
  3. A missense mutation (R565W) in cirhin (FLJ14728) in North American Indian childhood cirrhosis
    Title: A missense mutation (R565W) in cirhin (FLJ14728) in North American Indian childhood cirrhosis.
  4. Cirhin is a nucleolar protein and the R565W mutation, for which all North American Indian childhood cirrhosis patients are homozygous, has no effect on subcellular localization.
    Title: Nucleolar localization of cirhin, the protein mutated in North American Indian childhood cirrhosis.
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

  • FLJ14728, FLJ17146, KIAA1988

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 maturation of SSU-rRNA 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 regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in ribosomal small subunit biogenesis IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
part_of 90S preribosome IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in chromosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in fibrillar center IDA
Inferred from Direct Assay
more info
 PubMed 
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
  
part_of small-subunit processome IDA
Inferred from Direct Assay
more info
 PubMed 
part_of t-UTP complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of t-UTP complex IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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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)

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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.

Genomic

  1. NG_008278.1 RefSeqGene

    Range
    5054..41426
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001318391.2 → NP_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
    UniProtKB/TrEMBL
    H3BSH7
    Related
    ENSP00000456709.1, ENST00000562237.5
    Conserved Domains (3) summary
    COG2319
    Location:11 → 436
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:22 → 60
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:3 → 223
    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_032830.3 → NP_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
    Q8NCD9, Q8TF14, Q969X6, Q96SP0, Q96SR9, Q96SZ9, Q96T13, Q9BWK6
    UniProtKB/TrEMBL
    H3BSH7
    Related
    ENSP00000327179.7, ENST00000314423.12
    Conserved Domains (3) summary
    COG2319
    Location:238 → 547
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:20 → 57
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:16 → 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 ...

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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    69132649..69169021
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047434817.1 → XP_047290773.1  U3 small nucleolar RNA-associated protein 4 homolog isoform X2

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

    UniProtKB/TrEMBL
    A0A0J9YWM9
    Conserved Domains (3) summary
    COG2319
    Location:58 → 380
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:304 → 340
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:59 → 411
    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 ...

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NW_003315946.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    60815..86658 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    74928956..74965636
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054314209.1 → XP_054170184.1  U3 small nucleolar RNA-associated protein 4 homolog isoform X2

  2. XM_054314208.1 → XP_054170183.1  U3 small nucleolar RNA-associated protein 4 homolog isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q969X6.1 GenPept UniProtKB/Swiss-Prot:Q969X6

Gene LinkOut

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