RRN3 RRN3 homolog, RNA polymerase I transcription factor [Homo sapiens (human)] - Gene

Summary

Official Symbol: RRN3provided by HGNC
Official Full Name: RRN3 homolog, RNA polymerase I transcription factorprovided by HGNC
Primary source: HGNC:HGNC:30346
See related: Ensembl:ENSG00000085721 MIM:605121; AllianceGenome:HGNC:30346
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: TIFIA; A-270G1.2
Summary: Enables RNA polymerase I core promoter sequence-specific DNA binding activity. Predicted to be involved in transcription initiation from RNA polymerase I promoter. Predicted to act upstream of or within several processes, including DNA-templated transcription, initiation; negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator; and regulation of transcription, DNA-templated. Located in nucleolus. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in bone marrow (RPKM 15.3), thyroid (RPKM 14.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 16p13.11

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (15060022..15094335, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (15061074..15095386, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (15153879..15188192, complement)

Chromosome 16 - NC_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

High RRN3 expression is associated with malignant characteristics and poor prognosis in pancreatic cancer.
Title: High RRN3 expression is associated with malignant characteristics and poor prognosis in pancreatic cancer.
Depletion of Ebp1 expression in primary colon cancer cells inhibits cell proliferation, colony forming, and invasion in vitro as well as tumor formation in vivo and enhances cell sensitivity to irradiation. We further demonstrated that Ebp1 interacts with TIF-90, a splice variant of transcription initiation factor IA (TIF-IA) of the RNA polymerase I complex.
Title: Ebp1 p48 promotes oncogenic activities in human colon cancer cells through regulation of TIF-90-mediated ribosomal RNA synthesis.
Specific stress stimuli of NF-kappaB induce degradation of a critical component of the PolI complex, TIF-IA. This degradation precedes activation of NF-kappaB and is associated with increased nucleolar size.
Title: Identification of a novel TIF-IA-NF-κB nucleolar stress response pathway.
These data support a model in which activated Akt enhances rRNA synthesis both by preventing TIF-IA degradation and phosphorylating CK2alpha, which in turn phosphorylates TIF-IA.
Title: Akt activation enhances ribosomal RNA synthesis through casein kinase II and TIF-IA.
DNA binding by the ribosomal DNA transcription factor rrn3 is essential for ribosomal DNA transcription
Title: DNA binding by the ribosomal DNA transcription factor rrn3 is essential for ribosomal DNA transcription.
reveals the molecular basis of Rrn3-regulated Pol I initiation and cell growth
Title: Molecular basis of Rrn3-regulated RNA polymerase I initiation and cell growth.
CK2 phosphorylates the transcription initiation factor TIF-IA at serines 170 and 172 (Ser170/172), and this phosphorylation triggers the release of TIF-IA from Pol I after transcription initiation.
Title: Phosphorylation by casein kinase 2 facilitates rRNA gene transcription by promoting dissociation of TIF-IA from elongating RNA polymerase I.
The definition of the Alu element within the TIF-IA gene as an exon is restricted to certain types of cancers; the element is not exonized in normal human cells.
Title: Biased exonization of transposed elements in duplicated genes: A lesson from the TIF-IA gene.
Phosphorylation of S44 activates and S199 inactivates TIF-IA.
Title: mTOR-dependent activation of the transcription factor TIF-IA links rRNA synthesis to nutrient availability.
ERK-dependent phosphorylation of the transcription initiation factor TIF-IA is required for RNA polymerase I transcription and cell growth.
Title: ERK-dependent phosphorylation of the transcription initiation factor TIF-IA is required for RNA polymerase I transcription and cell growth.

Submit: New GeneRIF Correction See all GeneRIFs (11)

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

EBI GWAS Catalog

Description
Genome-wide association study of plasma N6 polyunsaturated fatty acids within the cohorts for heart and aging research in genomic epidemiology consortium. EBI GWAS Catalog EBI GWAS CatalogPubMed

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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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA polymerase I core binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase I core promoter sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase I general transcription initiation factor activity	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase I general transcription initiation factor activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA polymerase I preinitiation complex assembly	IEA Inferred from Electronic Annotation more info
involved_in cytoplasm organization	IEA Inferred from Electronic Annotation more info
involved_in fibroblast proliferation	IEA Inferred from Electronic Annotation more info
involved_in homeostasis of number of cells	IEA Inferred from Electronic Annotation more info
involved_in in utero embryonic development	IEA Inferred from Electronic Annotation more info
involved_in intrinsic apoptotic signaling pathway by p53 class mediator	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator	IEA Inferred from Electronic Annotation more info
involved_in nucleolus organization	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of DNA-templated transcription initiation	IEA Inferred from Electronic Annotation more info
involved_in ribosome biogenesis	IEA Inferred from Electronic Annotation more info
involved_in transcription initiation at RNA polymerase I promoter	IBA Inferred from Biological aspect of Ancestor more info
involved_in transcription initiation at RNA polymerase I promoter	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: RNA polymerase I-specific transcription initiation factor RRN3

Names: RRN3 RNA polymerase I transcription factor homolog; TIF-IA; transcription initiation factor IA; transcription initiation factor TIF-IA

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_001301064.1 → NP_001287993.1 RNA polymerase I-specific transcription initiation factor RRN3 isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. It encodes isoform 2 which is shorter than isoform 1.

Source sequence(s)

AK316520, BC036182, CK906270, DA764092, DC376629

Consensus CDS

CCDS73833.1

UniProtKB/TrEMBL

B4DTK6, F5H148

Related

ENSP00000402027.2, ENST00000429751.6

Conserved Domains (1) summary

pfam05327
Location:85 → 555

RRN3; RNA polymerase I specific transcription initiation factor RRN3
NM_018427.5 → NP_060897.3 RNA polymerase I-specific transcription initiation factor RRN3 isoform 1

See identical proteins and their annotated locations for NP_060897.3

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AK225662, BC036182, BC132688

Consensus CDS

CCDS10559.1

UniProtKB/Swiss-Prot

A2RTY9, B4E0J7, B4E3T2, Q3MHU9, Q6IPL4, Q9H4F0, Q9NYV6

UniProtKB/TrEMBL

H3BMT1

Related

ENSP00000198767.7, ENST00000198767.11

Conserved Domains (1) summary

pfam05327
Location:64 → 585

RRN3; RNA polymerase I specific transcription initiation factor RRN3