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

    Gene ID: 84916, updated on 3-Nov-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
    mouse all
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    Genomic context

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    See UTP4 in Genome Data Viewer
    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_000016.10Genomic 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 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. 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
    3. North American Indian cirrhosis in children: a review of 30 cases. Drouin E, et al. J Pediatr Gastroenterol Nutr, 2000 Oct. PMID 11045837
    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 (91) 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
    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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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