Utp4 UTP4 small subunit processome component [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Utp4provided by RGD
Official Full Name: UTP4 small subunit processome componentprovided by RGD
Primary source: RGD:1311341
See related: EnsemblRapid:ENSRNOG00000020333 AllianceGenome:RGD:1311341
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Naic; Cirh1a; Cirhin; Tex292; Teg-292
Summary: Predicted to be involved in maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) and regulation of DNA-templated transcription. Predicted to be located in chromosome and fibrillar center. Predicted to be part of small-subunit processome and t-UTP complex. Human ortholog(s) of this gene implicated in cholestasis and primary biliary cholangitis. Orthologous to human UTP4 (UTP4 small subunit processome component). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Thymus (RPKM 107.5), Kidney (RPKM 94.2) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 19q12

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	19	NC_086037.1 (51696437..51730323)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	19	NC_051354.1 (34790962..34820558)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	19	NC_005118.4 (39087995..39116124)

Chromosome 19 - NC_086037.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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Gene Ontology Provided by RGD

Process	Evidence Code	Pubs
involved_in biological_process	ND No biological Data available more info
involved_in maturation of SSU-rRNA	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
involved_in ribosomal small subunit biogenesis	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in chromosome	ISO Inferred from Sequence Orthology more info
located_in fibrillar center	ISO Inferred from Sequence Orthology more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleolus	ISS Inferred from Sequence or Structural Similarity more info
part_of small-subunit processome	IBA Inferred from Biological aspect of Ancestor more info
part_of small-subunit processome	ISO Inferred from Sequence Orthology more info
part_of t-UTP complex	IBA Inferred from Biological aspect of Ancestor more info
part_of t-UTP complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: U3 small nucleolar RNA-associated protein 4 homolog

Names: UTP4 small subunit (SSU) processome component; 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.

mRNA and Protein(s)

NM_001009640.1 → NP_001009640.1 U3 small nucleolar RNA-associated protein 4 homolog

See identical proteins and their annotated locations for NP_001009640.1

Status: PROVISIONAL

Source sequence(s)

BC088461

UniProtKB/TrEMBL

A6IYY1, Q5I0C9

Related

ENSRNOP00000112370.1, ENSRNOT00000166964.1

Conserved Domains (2) summary

sd00039
Location:21 → 57

7WD40; WD40 repeat [structural motif]

cl29593
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_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086037.1 Reference GRCr8

Range

51696437..51730323

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006255563.5 → XP_006255625.1 U3 small nucleolar RNA-associated protein 4 homolog isoform X1

See identical proteins and their annotated locations for XP_006255625.1

UniProtKB/TrEMBL

A6IYY1, Q5I0C9

Conserved Domains (2) summary

sd00039
Location:21 → 57

7WD40; WD40 repeat [structural motif]

cl29593
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 ...
XM_006255562.3 → XP_006255624.1 U3 small nucleolar RNA-associated protein 4 homolog isoform X1

See identical proteins and their annotated locations for XP_006255624.1

UniProtKB/TrEMBL

A6IYY1, Q5I0C9

Conserved Domains (2) summary

sd00039
Location:21 → 57

7WD40; WD40 repeat [structural motif]

cl29593
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 ...