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

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; 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: mouse all
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Genomic context

Location:: 16q22.1

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (69132649..69169021)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (74928956..74965636)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (69166552..69202924)

Chromosome 16 - NC_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.

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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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH104264 (e-PCR)
- UniSTS:98589

D16S2538E (e-PCR)
- UniSTS:41278

SHGC-61081 (e-PCR)
- UniSTS:41824

RH65345 (e-PCR)
- UniSTS:43126

G65582 (e-PCR)
- UniSTS:225516

SHGC-60702 (e-PCR)
- UniSTS:80891

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	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	IEA Inferred from Electronic Annotation 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

NG_008278.1 RefSeqGene

Range

5054..41426

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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 ...
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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000016.10 Reference GRCh38.p14 Primary Assembly

Range

69132649..69169021

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

NW_003315946.1 Reference GRCh38.p14 ALT_REF_LOCI_1

Range

60815..86658 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060940.1 Alternate T2T-CHM13v2.0

Range

74928956..74965636

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054314209.1 → XP_054170184.1 U3 small nucleolar RNA-associated protein 4 homolog isoform X2
XM_054314208.1 → XP_054170183.1 U3 small nucleolar RNA-associated protein 4 homolog isoform X1