Aliases for RRN3 Gene

Aliases for RRN3 Gene

  • RRN3 Homolog, RNA Polymerase I Transcription Factor 2 3 5
  • Transcription Initiation Factor IA 2 3 4
  • RNA Polymerase I-Specific Transcription Initiation Factor RRN3 3 4
  • TIF-IA 3 4
  • TIFIA 3 4
  • RRN3 RNA Polymerase I Transcription Factor Homolog (S. Cerevisiae) 2
  • RRN3 RNA Polymerase I Transcription Factor Homolog (Yeast) 2
  • RRN3 RNA Polymerase I Transcription Factor Homolog 3
  • Transcription Initiation Factor TIF-IA 3
  • A-270G1.2 3

External Ids for RRN3 Gene

Previous GeneCards Identifiers for RRN3 Gene

  • GC16M016636
  • GC16P020093
  • GC16M015081
  • GC16M015120
  • GC16M015061
  • GC16M015153
  • GC16M014799

Summaries for RRN3 Gene

GeneCards Summary for RRN3 Gene

RRN3 (RRN3 Homolog, RNA Polymerase I Transcription Factor) is a Protein Coding gene. Diseases associated with RRN3 include Noonan Syndrome 1. Among its related pathways are Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 and RNA Polymerase I Promoter Escape. Gene Ontology (GO) annotations related to this gene include binding and RNA polymerase binding.

UniProtKB/Swiss-Prot Summary for RRN3 Gene

  • Required for efficient transcription initiation by RNA polymerase I. Required for the formation of the competent preinitiation complex (PIC). Dissociates from pol I as a consequence of transcription. In vitro, cannot activate transcription in a subsequent transcription reaction (By similarity).

Gene Wiki entry for RRN3 Gene

Additional gene information for RRN3 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RRN3 Gene

Genomics for RRN3 Gene

GeneHancer (GH) Regulatory Elements for RRN3 Gene

Promoters and enhancers for RRN3 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RRN3 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RRN3

Top Transcription factor binding sites by QIAGEN in the RRN3 gene promoter:
  • AP-1
  • AP-4
  • ATF-2
  • c-Jun
  • FOXO1
  • FOXO1a
  • HNF-1
  • HNF-1A

Genomic Locations for RRN3 Gene

Genomic Locations for RRN3 Gene
chr16:15,060,022-15,094,335
(GRCh38/hg38)
Size:
34,314 bases
Orientation:
Minus strand
chr16:15,153,879-15,188,174
(GRCh37/hg19)
Size:
34,296 bases
Orientation:
Minus strand

Genomic View for RRN3 Gene

Genes around RRN3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RRN3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RRN3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RRN3 Gene

Proteins for RRN3 Gene

  • Protein details for RRN3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NYV6-RRN3_HUMAN
    Recommended name:
    RNA polymerase I-specific transcription initiation factor RRN3
    Protein Accession:
    Q9NYV6
    Secondary Accessions:
    • A2RTY9
    • B4E0J7
    • B4E3T2
    • Q3MHU9
    • Q6IPL4
    • Q9H4F0

    Protein attributes for RRN3 Gene

    Size:
    651 amino acids
    Molecular mass:
    74107 Da
    Quaternary structure:
    • Interacts with TWISTNB, EIF3L, TAF1B and TAF1C.

    Alternative splice isoforms for RRN3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RRN3 Gene

Post-translational modifications for RRN3 Gene

  • Phosphorylation is required for participation in rDNA transcription (By similarity). Phosphorylated at Thr-200 by MAPK9/JNK2, which abrogates initiation complex formation.
  • Ubiquitination at Lys568
  • Modification sites at PhosphoSitePlus

Other Protein References for RRN3 Gene

No data available for DME Specific Peptides for RRN3 Gene

Domains & Families for RRN3 Gene

Gene Families for RRN3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for RRN3 Gene

Blocks:
  • RNA polymerase I specific transcription initiation factor RRN3
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for RRN3 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ52380, highly similar to RNA polymerase I-specific transcriptioninitiation factor RRN3 (B4E0J7_HUMAN)
  • cDNA FLJ53965, highly similar to RNA polymerase I-specific transcription initiation factor RRN3 (B4E3T2_HUMAN)
  • RRN3 protein (Q3MHU9_HUMAN)
  • Transcription initiation factor IA (RRN3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9NYV6

UniProtKB/Swiss-Prot:

RRN3_HUMAN :
  • Belongs to the RRN3 family.
Family:
  • Belongs to the RRN3 family.
genes like me logo Genes that share domains with RRN3: view

Function for RRN3 Gene

Molecular function for RRN3 Gene

UniProtKB/Swiss-Prot Function:
Required for efficient transcription initiation by RNA polymerase I. Required for the formation of the competent preinitiation complex (PIC). Dissociates from pol I as a consequence of transcription. In vitro, cannot activate transcription in a subsequent transcription reaction (By similarity).

Phenotypes From GWAS Catalog for RRN3 Gene

Gene Ontology (GO) - Molecular Function for RRN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001042 RNA polymerase I core binding IBA 21873635
GO:0001164 RNA polymerase I CORE element sequence-specific DNA binding IDA 22368283
GO:0001181 RNA polymerase I general transcription initiation factor activity IBA 21873635
GO:0070063 RNA polymerase binding IEA --
genes like me logo Genes that share ontologies with RRN3: view
genes like me logo Genes that share phenotypes with RRN3: view

Animal Models for RRN3 Gene

MGI Knock Outs for RRN3:
  • Rrn3 Rrn3<tm1.2Igt>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RRN3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RRN3 Gene

Localization for RRN3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RRN3 Gene

Nucleus, nucleolus.

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 RRN3 gene
Compartment Confidence
nucleus 5
mitochondrion 2
cytosol 2
plasma membrane 1
extracellular 1
cytoskeleton 1
endoplasmic reticulum 1
lysosome 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for RRN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA 21873635
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IDA,IEA --
genes like me logo Genes that share ontologies with RRN3: view

Pathways & Interactions for RRN3 Gene

genes like me logo Genes that share pathways with RRN3: view

SIGNOR curated interactions for RRN3 Gene

Is activated by:
Is inactivated by:

Gene Ontology (GO) - Biological Process for RRN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001188 RNA polymerase I preinitiation complex assembly IEA --
GO:0001701 in utero embryonic development IEA --
GO:0006352 DNA-templated transcription, initiation IEA --
GO:0006361 transcription initiation from RNA polymerase I promoter TAS,IBA --
GO:0007000 nucleolus organization IEA --
genes like me logo Genes that share ontologies with RRN3: view

Drugs & Compounds for RRN3 Gene

No Compound Related Data Available

Transcripts for RRN3 Gene

mRNA/cDNA for RRN3 Gene

2 REFSEQ mRNAs :
20 NCBI additional mRNA sequence :
6 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RRN3

Alternative Splicing Database (ASD) splice patterns (SP) for RRN3 Gene

No ASD Table

Relevant External Links for RRN3 Gene

GeneLoc Exon Structure for
RRN3

Expression for RRN3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RRN3 Gene

Protein differential expression in normal tissues from HIPED for RRN3 Gene

This gene is overexpressed in Bone (39.0) and Adrenal (30.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RRN3 Gene



Protein tissue co-expression partners for RRN3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RRN3

SOURCE GeneReport for Unigene cluster for RRN3 Gene:

Hs.460078

Evidence on tissue expression from TISSUES for RRN3 Gene

  • Nervous system(4.7)
  • Kidney(4.2)
  • Spleen(4.2)
genes like me logo Genes that share expression patterns with RRN3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RRN3 Gene

Orthologs for RRN3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for RRN3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RRN3 31 30
  • 99.58 (n)
OneToOne
dog
(Canis familiaris)
Mammalia RRN3 31 30
  • 89.08 (n)
OneToOne
cow
(Bos Taurus)
Mammalia RRN3 31 30
  • 88.87 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Rrn3 17 31 30
  • 86.28 (n)
rat
(Rattus norvegicus)
Mammalia Rrn3 30
  • 85.97 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia RRN3 31
  • 80 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia RRN3 31
  • 80 (a)
OneToOne
chicken
(Gallus gallus)
Aves RRN3 31 30
  • 74.06 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RRN3 31
  • 65 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rrn3 30
  • 68.8 (n)
Str.15752 30
zebrafish
(Danio rerio)
Actinopterygii rrn3 31 30
  • 64.63 (n)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.3554 30
fruit fly
(Drosophila melanogaster)
Insecta Tif-IA 31 32 30
  • 47.58 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009024 30
  • 45.74 (n)
worm
(Caenorhabditis elegans)
Secernentea C36E8.1 31 32 30
  • 45.47 (n)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RRN3 33 31
  • 23 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT2G39240 30
  • 43.49 (n)
rice
(Oryza sativa)
Liliopsida Os06g0688100 30
  • 44.68 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes rrn3 30
  • 44.25 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU09247 30
  • 42.1 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.2045 31
  • 37 (a)
OneToOne
Species where no ortholog for RRN3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • 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)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • 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)

Evolution for RRN3 Gene

ENSEMBL:
Gene Tree for RRN3 (if available)
TreeFam:
Gene Tree for RRN3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RRN3: view image

Paralogs for RRN3 Gene

(3) SIMAP similar genes for RRN3 Gene using alignment to 6 proteins:

  • RRN3_HUMAN
  • B4E0J7_HUMAN
  • B4E3T2_HUMAN
  • F5H148_HUMAN
  • H3BMT1_HUMAN
  • Q3MHU9_HUMAN
genes like me logo Genes that share paralogs with RRN3: view

No data available for Paralogs for RRN3 Gene

Variants for RRN3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RRN3 Gene

SNP ID Clinical significance and condition Chr 16 pos Variation AA Info Type
rs2941256 - p.Ile348Met

Additional dbSNP identifiers (rs#s) for RRN3 Gene

Structural Variations from Database of Genomic Variants (DGV) for RRN3 Gene

Variant ID Type Subtype PubMed ID
dgv2755n100 CNV gain 25217958
dgv2765n100 CNV gain 25217958
dgv2770n100 CNV loss 25217958
dgv344n27 CNV loss 19166990
dgv4922n54 CNV loss 21841781
esv2758632 CNV gain+loss 17122850
esv2762254 CNV gain+loss 21179565
esv3366485 CNV insertion 20981092
esv3570354 CNV gain 25503493
esv3582039 CNV loss 25503493
esv3638020 CNV loss 21293372
esv3638021 CNV gain 21293372
esv3892796 CNV loss 25118596
esv3892797 CNV gain 25118596
nsv1036298 CNV gain 25217958
nsv1038955 CNV loss 25217958
nsv1042130 CNV gain 25217958
nsv1050325 CNV loss 25217958
nsv1053467 CNV loss 25217958
nsv457426 CNV gain 19166990
nsv509598 CNV insertion 20534489
nsv511045 OTHER complex 20534489
nsv571527 CNV gain+loss 21841781
nsv7277 OTHER inversion 18451855
nsv977910 CNV duplication 23825009
nsv984266 CNV duplication 23825009

Variation tolerance for RRN3 Gene

Residual Variation Intolerance Score: 84.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.91; 67.73% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RRN3 Gene

Human Gene Mutation Database (HGMD)
RRN3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RRN3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RRN3 Gene

Disorders for RRN3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for RRN3 Gene - From: DISEASES

Disorder Aliases PubMed IDs
noonan syndrome 1
  • ns1
- elite association - COSMIC cancer census association via MalaCards
Search RRN3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RRN3

genes like me logo Genes that share disorders with RRN3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RRN3 Gene

Publications for RRN3 Gene

  1. RNA polymerase I transcription factor Rrn3 is functionally conserved between yeast and human. (PMID: 10758157) Moorefield B … Reeder RH (Proceedings of the National Academy of Sciences of the United States of America 2000) 2 3 4 23 54
  2. Multiple interactions between RNA polymerase I, TIF-IA and TAF(I) subunits regulate preinitiation complex assembly at the ribosomal gene promoter. (PMID: 12393749) Yuan X … Grummt I (EMBO reports 2002) 3 4 23 54
  3. hRRN3 is essential in the SL1-mediated recruitment of RNA Polymerase I to rRNA gene promoters. (PMID: 11250903) Miller G … Zomerdijk JC (The EMBO journal 2001) 2 3 4 54
  4. The nucleolus as a stress sensor: JNK2 inactivates the transcription factor TIF-IA and down-regulates rRNA synthesis. (PMID: 15805466) Mayer C … Grummt I (Genes & development 2005) 4 23 54
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 54

Products for RRN3 Gene

Sources for RRN3 Gene