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Aliases for UTP4 Gene

Aliases for UTP4 Gene

  • UTP4, Small Subunit Processome Component 2 3 5
  • Cirrhosis, Autosomal Recessive 1A (Cirhin) 2 3
  • CIRHIN 3 4
  • CIRH1A 3 4
  • UTP4, Small Subunit (SSU) Processome Component, Homolog (Yeast) 2
  • UTP4, Small Subunit (SSU) Processome Component, Homolog 3
  • U3 Small Nucleolar RNA-Associated Protein 4 Homolog 3
  • UTP4 Small Subunit (SSU) Processome Component 3
  • UTP4 Small Subunit Processome Component 4
  • Testis Expressed Gene 292 3
  • KIAA1988 4
  • CPERP-E 4
  • TEX292 3
  • NAIC 3

External Ids for UTP4 Gene

Previous HGNC Symbols for UTP4 Gene

  • CIRH1A

Summaries for UTP4 Gene

Entrez Gene Summary for UTP4 Gene

  • 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]

GeneCards Summary for UTP4 Gene

UTP4 (UTP4, Small Subunit Processome Component) is a Protein Coding gene. Diseases associated with UTP4 include Cirrhosis, North American Indian Childhood Type and Intrahepatic Cholestasis. Among its related pathways are rRNA processing in the nucleus and cytosol and Gene Expression.

UniProtKB/Swiss-Prot for UTP4 Gene

  • May be a transcriptional regulator. Acts as a positive regulator of HIVEP1 which specifically binds to the DNA sequence 5-GGGACTTTCC-3 found in enhancer elements of numerous viral promoters such as those of HIV-1, SV40, or CMV. Ribosome biogenesis factor involved in small subunit (SSU) pre-rRNA processing at sites A, A0, 1 and 2b.

Gene Wiki entry for UTP4 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for UTP4 Gene

Genomics for UTP4 Gene

Regulatory Elements for UTP4 Gene

Enhancers for UTP4 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH16G069393 1.9 FANTOM5 Ensembl ENCODE dbSUPER 19.7 +266.1 266053 7.4 HNRNPUL1 PKNOX1 FOXA2 MLX ZFP64 ARID4B SIN3A DMAP1 FEZF1 ZNF2 UTP4 CYB5B NIP7 TERF2 MIR1538 NFAT5 NQO1 LOC400541 GC16M069451
GH16G069325 1.2 Ensembl ENCODE 29.2 +195.6 195603 2.3 ARID4B DMAP1 ZNF48 YY1 ZNF121 SLC30A9 ZHX2 MXD4 MIER2 KAT8 UTP4 TMED6 NIP7 CHTF8 PIR46379 PIR53878
GH16G069402 2 FANTOM5 Ensembl ENCODE dbSUPER 15.6 +276.9 276887 11.5 PKNOX1 FOXA2 MLX ZFP64 ARID4B FEZF1 DMAP1 YY1 SLC30A9 ZNF302 PDPR LOC400541 NONOP1 TMED6 LOC100506083 UTP4 TERF2 MIR1538 NFAT5 NIP7
GH16G069384 1.4 ENCODE dbSUPER 20 +254.1 254077 2.5 HDGF MLX CREB3L1 ARNT ARID4B SIN3A DMAP1 YBX1 ZNF2 YY1 NIP7 UTP4 NONOP1 CHTF8 PDXDC2P-NPIPB14P PDXDC2P EXOSC6 PDPR NPIPB14P NOB1
GH16G069310 1.4 FANTOM5 ENCODE 19.9 +180.2 180150 2.3 PKNOX1 FOXA2 ARNT CREB3L1 AGO1 ZFP64 ARID4B SIN3A YY1 SLC30A9 UTP4 SNTB2 LOC400541 PDPR VPS4A PIR42936
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around UTP4 on UCSC Golden Path with GeneCards custom track

Promoters for UTP4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000087374 1109 2401 HDGF PKNOX1 MLX CREB3L1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B

Genomic Location for UTP4 Gene

Chromosome:
16
Start:
69,131,291 bp from pter
End:
69,231,130 bp from pter
Size:
99,840 bases
Orientation:
Plus strand

Genomic View for UTP4 Gene

Genes around UTP4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
UTP4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for UTP4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for UTP4 Gene

Proteins for UTP4 Gene

  • Protein details for UTP4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q969X6-UTP4_HUMAN
    Recommended name:
    U3 small nucleolar RNA-associated protein 4 homolog
    Protein Accession:
    Q969X6
    Secondary Accessions:
    • Q8NCD9
    • Q8TF14
    • Q96SP0
    • Q96SR9
    • Q96SZ9
    • Q96T13
    • Q9BWK6

    Protein attributes for UTP4 Gene

    Size:
    686 amino acids
    Molecular mass:
    76890 Da
    Quaternary structure:
    • Interacts with HIVEP1 (PubMed:19732766). Forms a complex with NOL11, UTP15, WDR43 and WDR75; within this complex, directly interacts with NOL11, UTP15 and WDR43 (PubMed:22916032, PubMed:24219289).
    SequenceCaution:
    • Sequence=BAB55100.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAB55116.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAB55212.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAB85574.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for UTP4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for UTP4 Gene

Post-translational modifications for UTP4 Gene

  • May be phosphorylated during mitosis; may control the association of this protein with WRD43 and UTP15.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for UTP4 Gene

Domains & Families for UTP4 Gene

Gene Families for UTP4 Gene

Protein Domains for UTP4 Gene

Suggested Antigen Peptide Sequences for UTP4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with UTP4: view

No data available for UniProtKB/Swiss-Prot for UTP4 Gene

Function for UTP4 Gene

Molecular function for UTP4 Gene

UniProtKB/Swiss-Prot Function:
May be a transcriptional regulator. Acts as a positive regulator of HIVEP1 which specifically binds to the DNA sequence 5-GGGACTTTCC-3 found in enhancer elements of numerous viral promoters such as those of HIV-1, SV40, or CMV. Ribosome biogenesis factor involved in small subunit (SSU) pre-rRNA processing at sites A, A0, 1 and 2b.

Gene Ontology (GO) - Molecular Function for UTP4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IDA 22658674
GO:0005515 protein binding IPI 19732766
genes like me logo Genes that share ontologies with UTP4: view
genes like me logo Genes that share phenotypes with UTP4: view

Human Phenotype Ontology for UTP4 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

miRNA for UTP4 Gene

miRTarBase miRNAs that target UTP4

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for UTP4 Gene

Localization for UTP4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for UTP4 Gene

Nucleus, nucleolus. Chromosome. Note=Found predominantly at the fibrillar center. {ECO:0000269 PubMed:24219289}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for UTP4 gene
Compartment Confidence
nucleus 5
mitochondrion 2
peroxisome 2
cytosol 2

Gene Ontology (GO) - Cellular Components for UTP4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001650 fibrillar center IDA 24219289
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005694 chromosome IDA,IEA 20813266
GO:0005730 nucleolus IEA,IDA 16225863
genes like me logo Genes that share ontologies with UTP4: view

Pathways & Interactions for UTP4 Gene

genes like me logo Genes that share pathways with UTP4: view

Gene Ontology (GO) - Biological Process for UTP4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA,IDA 19732766
GO:0006364 rRNA processing TAS --
GO:0030490 maturation of SSU-rRNA IMP 22916032
genes like me logo Genes that share ontologies with UTP4: view

No data available for SIGNOR curated interactions for UTP4 Gene

Drugs & Compounds for UTP4 Gene

No Compound Related Data Available

Transcripts for UTP4 Gene

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for UTP4 Gene

No ASD Table

Relevant External Links for UTP4 Gene

GeneLoc Exon Structure for
UTP4
ECgene alternative splicing isoforms for
UTP4

Expression for UTP4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

NURSA nuclear receptor signaling pathways regulating expression of UTP4 Gene:

UTP4

Evidence on tissue expression from TISSUES for UTP4 Gene

  • Nervous system(4.8)
  • Muscle(4.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for UTP4 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • integumentary
  • lymphatic
  • nervous
Organs:
Head and neck:
  • eye
  • head
  • mouth
Abdomen:
  • biliary tract
  • liver
  • spleen
General:
  • blood
  • blood vessel
  • coagulation system
  • skin
genes like me logo Genes that share expression patterns with UTP4: view

Primer Products

No data available for mRNA expression in normal human tissues , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for UTP4 Gene

Orthologs for UTP4 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for UTP4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CIRH1A 35 34
  • 99.76 (n)
OneToOne
dog
(Canis familiaris)
Mammalia -- 35
  • 98 (a)
OneToMany
CIRH1A 34
  • 90.52 (n)
-- 35
  • 90 (a)
OneToMany
cow
(Bos Taurus)
Mammalia CIRH1A 35 34
  • 89.21 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Cirh1a 34
  • 88.39 (n)
mouse
(Mus musculus)
Mammalia Cirh1a 35 34
  • 87.9 (n)
OneToOne
Utp4 16
oppossum
(Monodelphis domestica)
Mammalia CIRH1A 35
  • 77 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 69 (a)
OneToMany
-- 35
  • 66 (a)
OneToMany
chicken
(Gallus gallus)
Aves CIRH1A 34 35
  • 63.8 (n)
lizard
(Anolis carolinensis)
Reptilia CIRH1A 35
  • 61 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia cirh1a 34
  • 60.11 (n)
Str.8218 34
African clawed frog
(Xenopus laevis)
Amphibia MGC52698 34
zebrafish
(Danio rerio)
Actinopterygii cirh1a 35 34
  • 58.35 (n)
OneToOne
wufi09g10 34
fruit fly
(Drosophila melanogaster)
Insecta l(3)72Dn 35 34
  • 41.5 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006092 34
  • 40.82 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes UTP4 34 35 37
  • 41.14 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AGR367C 34
  • 40.99 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0D13222g 34
  • 40.46 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT4G07410 34
  • 41.72 (n)
rice
(Oryza sativa)
Liliopsida Os03g0735100 34
  • 42.82 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes utp4 34
  • 43.38 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 31 (a)
OneToOne
Species where no ortholog for UTP4 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for UTP4 Gene

ENSEMBL:
Gene Tree for UTP4 (if available)
TreeFam:
Gene Tree for UTP4 (if available)

Paralogs for UTP4 Gene

No data available for Paralogs for UTP4 Gene

Variants for UTP4 Gene

Sequence variations from dbSNP and Humsavar for UTP4 Gene

SNP ID Clin Chr 16 pos Sequence Context AA Info Type
rs1000307099 -- 69,135,385(+) CTGTC(A/C)GTGAC intron-variant
rs1000537458 -- 69,130,925(+) GGTAA(C/T)TTCTC intron-variant, upstream-variant-2KB
rs1000915406 -- 69,134,408(+) GACCA(C/G)TGGGA intron-variant, upstream-variant-2KB
rs1001543133 -- 69,139,510(+) GGCAG(A/G)TGCCT intron-variant
rs1001743305 -- 69,135,038(+) AACAG(C/T)CATGG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for UTP4 Gene

Variant ID Type Subtype PubMed ID
nsv1070354 CNV deletion 25765185
nsv1850 CNV deletion 18451855
nsv1851 CNV insertion 18451855
nsv472861 CNV novel sequence insertion 20440878
nsv481633 CNV novel sequence insertion 20440878

Variation tolerance for UTP4 Gene

Residual Variation Intolerance Score: 14.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.31; 53.34% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for UTP4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
UTP4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for UTP4 Gene

Disorders for UTP4 Gene

MalaCards: The human disease database

(3) MalaCards diseases for UTP4 Gene - From: OMIM, GeneTests, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
cirrhosis, north american indian childhood type
  • north american indian childhood cirrhosis
intrahepatic cholestasis
  • intrahepatic cholestasis of pregnancy
cholestasis
  • bile occlusion
- elite association - COSMIC cancer census association via MalaCards
Search UTP4 in MalaCards View complete list of genes associated with diseases

Relevant External Links for UTP4

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
UTP4
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
UTP4
genes like me logo Genes that share disorders with UTP4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for UTP4 Gene

Publications for UTP4 Gene

  1. Cirhin up-regulates a canonical NF-kappaB element through strong interaction with Cirip/HIVEP1. (PMID: 19732766) Yu B. … Richter A. (Exp. Cell Res. 2009) 3 4 22 64
  2. Nucleolar localization of cirhin, the protein mutated in North American Indian childhood cirrhosis. (PMID: 16225863) Yu B. … Richter A. (Exp. Cell Res. 2005) 3 4 22 64
  3. A missense mutation (R565W) in cirhin (FLJ14728) in North American Indian childhood cirrhosis. (PMID: 12417987) Chagnon P. … Richter A. (Am. J. Hum. Genet. 2002) 3 4 22 64
  4. Interaction, mobility, and phosphorylation of human orthologues of WD repeat-containing components of the yeast SSU processome t-UTP sub- complex. (PMID: 24219289) Sato M. … Horigome T. (Biochem. Cell Biol. 2013) 3 4 64
  5. NOL11, implicated in the pathogenesis of North American Indian childhood cirrhosis, is required for pre-rRNA transcription and processing. (PMID: 22916032) Freed E.F. … Baserga S.J. (PLoS Genet. 2012) 3 4 64

Products for UTP4 Gene

Sources for UTP4 Gene

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