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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
  • TIF-IA 3 4
  • TIFIA 3 4
  • RRN3 RNA Polymerase I Transcription Factor Homolog (S. Cerevisiae) 2
  • RNA Polymerase I-Specific Transcription Initiation Factor RRN3 3
  • 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. Among its related pathways are Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 and RNA Polymerase I Promoter Escape. GO annotations related to this gene include binding and RNA polymerase binding.

UniProtKB/Swiss-Prot 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

No data available for Entrez Gene Summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RRN3 Gene

Genomics for RRN3 Gene

Regulatory Elements for RRN3 Gene

Enhancers for RRN3 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
GH16F014095 1.1 Ensembl ENCODE 32 +997.4 997428 3.8 ZFP64 ZNF493 ZNF133 FEZF1 FOS ZNF202 ZHX2 REST PPARG ZNF518A LOC100505915 ENSG00000183458 RRN3 BFAR NPIPA3 ENSG00000207425 ENSG00000261819 MKL2 ENSG00000276564
GH16F015588 1.8 FANTOM5 Ensembl ENCODE 24.9 -497.0 -496988 5.4 MLX FEZF1 DMAP1 YY1 SLC30A9 ZNF548 ZNF263 SP3 TBX21 MEF2D BFAR ENSG00000263335 LOC100505915 RRN3 PKD1P6 RPL17P40 ENSG00000270734 LOC105371095 ENSG00000263029 NDE1
GH16F015057 0.4 ENCODE 22.1 +36.4 36427 1.2 NR2F1 ARID4B MXD4 RARA GATA3 CEBPA CUX1 NR2F6 SMAD4 THAP11 RRN3 PDXDC1 NPIPP1 NTAN1
GH16F015071 0.5 Ensembl 21.2 +22.1 22107 0.9 CTCF ZNF654 RAD21 LOC100505915 RRN3 NPIPA2 NTAN1
GH16F015054 1 ENCODE 20.7 +38.6 38596 1.8 CREB3L1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF207 ZNF143 KLF13 ENSG00000183458 LOC100505915 BFAR NPIPA3 NPIPA5 RRN3 ENSG00000270734 LOC105371095 ENSG00000207425 ENSG00000261819
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around RRN3 on UCSC Golden Path with GeneCards custom track

Promoters for RRN3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001503883 534 2400 CREB3L1 MLX ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 ZNF143 SP3

Genomic Location for RRN3 Gene

Chromosome:
16
Start:
15,060,022 bp from pter
End:
15,094,335 bp from pter
Size:
34,314 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 Lys 568
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for RRN3 Gene

Domains & Families for RRN3 Gene

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

No data available for Gene Families for RRN3 Gene

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).

Gene Ontology (GO) - Molecular Function for RRN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001042 RNA polymerase I core binding IBA --
GO:0001164 RNA polymerase I CORE element sequence-specific DNA binding IDA 22368283
GO:0001181 transcription factor activity, core RNA polymerase I binding IBA --
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:

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

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
Jensen Localization Image for RRN3 Gene COMPARTMENTS Subcellular localization image for RRN3 gene
Compartment Confidence
nucleus 5
cytosol 2
mitochondrion 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for RRN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IDA --
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:0001180 transcription initiation from RNA polymerase I promoter for nuclear large rRNA transcript IBA --
GO:0001701 in utero embryonic development IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006352 DNA-templated transcription, initiation IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with RRN3: view

Transcripts for RRN3 Gene

Unigene Clusters for RRN3 Gene

RRN3 RNA polymerase I transcription factor homolog (S. cerevisiae):
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

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

No ASD Table

Relevant External Links for RRN3 Gene

GeneLoc Exon Structure for
RRN3
ECgene alternative splicing isoforms 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, PaxDb, MaxQB, and MOPED for RRN3 Gene



Protein tissue co-expression partners for RRN3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RRN3 Gene:

RRN3

SOURCE GeneReport for Unigene cluster for RRN3 Gene:

Hs.460078
genes like me logo Genes that share expression patterns with RRN3: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt 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 34 35
  • 99.58 (n)
dog
(Canis familiaris)
Mammalia RRN3 34 35
  • 89.08 (n)
cow
(Bos Taurus)
Mammalia RRN3 34 35
  • 88.87 (n)
mouse
(Mus musculus)
Mammalia Rrn3 34 16 35
  • 86.28 (n)
rat
(Rattus norvegicus)
Mammalia Rrn3 34
  • 85.97 (n)
oppossum
(Monodelphis domestica)
Mammalia RRN3 35
  • 80 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia RRN3 35
  • 80 (a)
OneToOne
chicken
(Gallus gallus)
Aves RRN3 34 35
  • 74.06 (n)
lizard
(Anolis carolinensis)
Reptilia RRN3 35
  • 65 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rrn3 34
  • 68.8 (n)
Str.15752 34
zebrafish
(Danio rerio)
Actinopterygii rrn3 34 35
  • 64.63 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.3554 34
fruit fly
(Drosophila melanogaster)
Insecta Tif-IA 36 34 35
  • 47.58 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009024 34
  • 45.74 (n)
worm
(Caenorhabditis elegans)
Secernentea C36E8.1 36 34 35
  • 45.47 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RRN3 35 37
  • 23 (a)
OneToOne
thale cress
(Arabidopsis thaliana)
eudicotyledons AT2G39240 34
  • 43.49 (n)
rice
(Oryza sativa)
Liliopsida Os06g0688100 34
  • 44.68 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes rrn3 34
  • 44.25 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU09247 34
  • 42.1 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.2045 35
  • 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)

Paralogs for RRN3 Gene

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

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 from dbSNP and Humsavar for RRN3 Gene

SNP ID Clin Chr 16 pos Sequence Context AA Info Type
rs10153160 -- 15,079,148(+) ACACC(A/G)AGATT intron-variant
rs10153173 -- 15,079,016(+) catgt(A/T)agcca intron-variant
rs10664930 -- 15,063,722(+) AAAAA(-/A)GAAAA intron-variant
rs10852374 -- 15,093,947(+) ACATA(C/G)TCACT intron-variant, upstream-variant-2KB
rs11075254 -- 15,068,494(+) AGCTT(C/G)TCTAA intron-variant

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)

Relevant External Links for RRN3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RRN3

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

Disorders for RRN3 Gene

Relevant External Links for RRN3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RRN3

No disorders were found for RRN3 Gene.

No data available for MalaCards , 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 R.H. (Proc. Natl. Acad. Sci. U.S.A. 2000) 2 3 4 22 64
  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 Rep. 2002) 3 4 22 64
  3. hRRN3 is essential in the SL1-mediated recruitment of RNA polymerase I to rRNA gene promoters. (PMID: 11250903) Miller G. … Zomerdijk J.C.B.M. (EMBO J. 2001) 2 3 4 64
  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 Dev. 2005) 4 22 64
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64

Products for RRN3 Gene

Sources for RRN3 Gene

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