Aliases for RPAP2 Gene

Aliases for RPAP2 Gene

  • RNA Polymerase II Associated Protein 2 2 3 5
  • Putative RNA Polymerase II Subunit B1 CTD Phosphatase RPAP2 3 4
  • C1orf82 3 4
  • Rtr1 2 3
  • RNA Polymerase II-Associated Protein 2 4
  • Chromosome 1 Open Reading Frame 82 2
  • EC 3.1.3.16 4
  • FLJ13150 2
  • RPAP2 5

External Ids for RPAP2 Gene

Previous HGNC Symbols for RPAP2 Gene

  • C1orf82

Previous GeneCards Identifiers for RPAP2 Gene

  • GC01P092537
  • GC01P092764
  • GC01P090884

Summaries for RPAP2 Gene

GeneCards Summary for RPAP2 Gene

RPAP2 (RNA Polymerase II Associated Protein 2) is a Protein Coding gene. Among its related pathways are Tat-mediated elongation of the HIV-1 transcript and Gene Expression. Gene Ontology (GO) annotations related to this gene include RNA polymerase II CTD heptapeptide repeat phosphatase activity.

UniProtKB/Swiss-Prot Summary for RPAP2 Gene

  • Protein phosphatase that displays CTD phosphatase activity and regulates transcription of snRNA genes. Recognizes and binds phosphorylated 'Ser-7' of the C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit POLR2A, and mediates dephosphorylation of 'Ser-5' of the CTD, thereby promoting transcription of snRNA genes.

Gene Wiki entry for RPAP2 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RPAP2 Gene

Genomics for RPAP2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for RPAP2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J092297 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 250.7 -0.3 -349 3.8 ZNF207 MYC ZNF600 ZNF580 POLR2A ZSCAN16 ZIC2 ZBTB10 YY1 MXD4 RPAP2 lnc-GLMN-1 GLMN DIPK1A EVI5 piR-31758 C1orf146
GH01J092079 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 250.1 -218.3 -218349 2.2 ZNF600 POLR2A ZIC2 ZBTB10 YY1 NONO SMAD5 MBD2 ZNF341 MNT BTBD8 RPAP2 SNORA66 SNORD21 RPL5 GAPDHP46 C1orf146
GH01J093078 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 31 +781.4 781448 4.6 BCLAF1 SP1 ZNF207 ZNF654 MYC IKZF1 ZNF600 JUND ZNF580 ZNF592 MTF2 NONHSAG002079.2 lnc-TMED5-6 CCDC18-AS1 SNORA66 SNORD21 GLMN RPAP2 RPL5 DNTTIP2
GH01J091882 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 22.3 -414.0 -414011 4.4 ZNF654 MYC IKZF1 ZNF600 ZNF580 ZMYM3 CEBPA ZNF10 ZSCAN16 NFIC TGFBR3 lnc-SETSIP-3 RPAP2 HFM1 SNORA66 SNORD21 RPL5 GLMN BTBD8 ZNF644
GH01J092831 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 19.4 +534.4 534379 4.2 BCLAF1 SP1 ZNF207 NCOR1 IKZF1 MYC ZNF600 SSRP1 ZNF580 ATF2 RPL5 HSALNG0005218 SNORD21 SNORA66 MTF2 CCDC18-AS1 GLMN DR1 RPAP2 BTBD8
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RPAP2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RPAP2

Top Transcription factor binding sites by QIAGEN in the RPAP2 gene promoter:
  • AhR
  • AML1a
  • Arnt
  • Nkx3-1
  • Nkx3-1 v1
  • Nkx3-1 v2
  • Nkx3-1 v3
  • Nkx3-1 v4
  • Pax-2
  • Pax-2a

Genomic Locations for RPAP2 Gene

Latest Assembly
chr1:92,299,050-92,402,056
(GRCh38/hg38)
Size:
103,007 bases
Orientation:
Plus strand

Previous Assembly
chr1:92,764,616-92,867,613
(GRCh37/hg19 by Entrez Gene)
Size:
102,998 bases
Orientation:
Plus strand

chr1:92,764,522-92,867,613
(GRCh37/hg19 by Ensembl)
Size:
103,092 bases
Orientation:
Plus strand

Genomic View for RPAP2 Gene

Genes around RPAP2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RPAP2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RPAP2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RPAP2 Gene

Proteins for RPAP2 Gene

  • Protein details for RPAP2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8IXW5-RPAP2_HUMAN
    Recommended name:
    Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2
    Protein Accession:
    Q8IXW5
    Secondary Accessions:
    • C9JKB5
    • Q49AS7
    • Q9H8Y2

    Protein attributes for RPAP2 Gene

    Size:
    612 amino acids
    Molecular mass:
    69509 Da
    Quaternary structure:
    • Associates with the RNA polymerase II complex. Interacts with transcribing RNA polymerase II phosphorylated on 'Ser-7' on CTD.

    Alternative splice isoforms for RPAP2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RPAP2 Gene

Post-translational modifications for RPAP2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RPAP2 Gene

No data available for DME Specific Peptides for RPAP2 Gene

Domains & Families for RPAP2 Gene

Gene Families for RPAP2 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted membrane proteins

Protein Domains for RPAP2 Gene

Suggested Antigen Peptide Sequences for RPAP2 Gene

GenScript: Design optimal peptide antigens:
  • RNA polymerase II-associated protein 2 (RPAP2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8IXW5

UniProtKB/Swiss-Prot:

RPAP2_HUMAN :
  • The RTR1-type zinc finger mediates interactions with RNA polymerase II complex subunits.
  • Belongs to the RPAP2 family.
Domain:
  • The RTR1-type zinc finger mediates interactions with RNA polymerase II complex subunits.
Family:
  • Belongs to the RPAP2 family.
genes like me logo Genes that share domains with RPAP2: view

Function for RPAP2 Gene

Molecular function for RPAP2 Gene

UniProtKB/Swiss-Prot Function:
Protein phosphatase that displays CTD phosphatase activity and regulates transcription of snRNA genes. Recognizes and binds phosphorylated 'Ser-7' of the C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit POLR2A, and mediates dephosphorylation of 'Ser-5' of the CTD, thereby promoting transcription of snRNA genes.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=H2O + O-phospho-L-seryl-[protein] = L-seryl-[protein] + phosphate; Xref=Rhea:RHEA:20629, Rhea:RHEA-COMP:9863, Rhea:RHEA-COMP:11604, ChEBI:CHEBI:15377, ChEBI:CHEBI:29999, ChEBI:CHEBI:43474, ChEBI:CHEBI:83421; EC=3.1.3.16;.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=H2O + O-phospho-L-threonyl-[protein] = L-threonyl-[protein] + phosphate; Xref=Rhea:RHEA:47004, Rhea:RHEA-COMP:11060, Rhea:RHEA-COMP:11605, ChEBI:CHEBI:15377, ChEBI:CHEBI:30013, ChEBI:CHEBI:43474, ChEBI:CHEBI:61977; EC=3.1.3.16;.

Enzyme Numbers (IUBMB) for RPAP2 Gene

Phenotypes From GWAS Catalog for RPAP2 Gene

Gene Ontology (GO) - Molecular Function for RPAP2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004721 phosphoprotein phosphatase activity IEA --
GO:0004722 protein serine/threonine phosphatase activity EXP 22137580
GO:0005515 protein binding IPI 24656813
GO:0008420 RNA polymerase II CTD heptapeptide repeat phosphatase activity IBA,IMP 22137580
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with RPAP2: view
genes like me logo Genes that share phenotypes with RPAP2: view

Animal Models for RPAP2 Gene

MGI Knock Outs for RPAP2:
  • Rpap2 Rpap2<tm1a(KOMP)Wtsi>

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RPAP2

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RPAP2 Gene

Localization for RPAP2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RPAP2 Gene

Cytoplasm. Nucleus. Note=Shuttles between the cytoplasm and the nucleus in a CRM1-dependent manner.

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 RPAP2 gene
Compartment Confidence
nucleus 5
cytosol 5
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nucleoli (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RPAP2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA,IDA 22137580
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IDA --
GO:0005737 cytoplasm IBA,IDA 22137580
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with RPAP2: view

Pathways & Interactions for RPAP2 Gene

genes like me logo Genes that share pathways with RPAP2: view

Pathways by source for RPAP2 Gene

2 Reactome pathways for RPAP2 Gene

SIGNOR curated interactions for RPAP2 Gene

Activates:

Gene Ontology (GO) - Biological Process for RPAP2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0009301 snRNA transcription IMP 22137580
GO:0042795 snRNA transcription by RNA polymerase II TAS --
GO:0070940 dephosphorylation of RNA polymerase II C-terminal domain IBA,IMP 22137580
genes like me logo Genes that share ontologies with RPAP2: view

Drugs & Compounds for RPAP2 Gene

(2) Drugs for RPAP2 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Water Approved Pharma 0
Phosphate Experimental Pharma 0
genes like me logo Genes that share compounds with RPAP2: view

Transcripts for RPAP2 Gene

mRNA/cDNA for RPAP2 Gene

1 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RPAP2

Alternative Splicing Database (ASD) splice patterns (SP) for RPAP2 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14
SP1: -
SP2: -
SP3:
SP4:

Relevant External Links for RPAP2 Gene

GeneLoc Exon Structure for
RPAP2

Expression for RPAP2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RPAP2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for RPAP2 Gene

This gene is overexpressed in Testis (25.8), CD8 Tcells (23.6), and Blymphocyte (7.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RPAP2 Gene



Protein tissue co-expression partners for RPAP2 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RPAP2

SOURCE GeneReport for Unigene cluster for RPAP2 Gene:

Hs.444421

Evidence on tissue expression from TISSUES for RPAP2 Gene

  • Nervous system(4.3)
genes like me logo Genes that share expression patterns with RPAP2: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RPAP2 Gene

Orthologs for RPAP2 Gene

This gene was present in the common ancestor of animals.

Orthologs for RPAP2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia RPAP2 29 30
  • 99.56 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia RPAP2 29
  • 89.55 (n)
-- 30
  • 85 (a)
OneToMany
-- 30
  • 80 (a)
OneToMany
Cow
(Bos Taurus)
Mammalia RPAP2 29 30
  • 88.45 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Rpap2 29
  • 77.83 (n)
Mouse
(Mus musculus)
Mammalia Rpap2 29 16 30
  • 77.65 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia RPAP2 30
  • 61 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia RPAP2 30
  • 52 (a)
OneToOne
Chicken
(Gallus gallus)
Aves RPAP2 29 30
  • 64.34 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia RPAP2 30
  • 47 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia rpap2 29
  • 58.47 (n)
Str.16031 29
Zebrafish
(Danio rerio)
Actinopterygii rpap2 29 30
  • 54.36 (n)
OneToOne
Dr.25701 29
Fruit Fly
(Drosophila melanogaster)
Insecta CG34183 30
  • 50 (a)
OneToOne
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 35 (a)
OneToOne
Species where no ortholog for RPAP2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • Fission Yeast (Schizosaccharomyces pombe)
  • 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)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for RPAP2 Gene

ENSEMBL:
Gene Tree for RPAP2 (if available)
TreeFam:
Gene Tree for RPAP2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RPAP2: view image
Alliance of Genome Resources:
Additional Orthologs for RPAP2

Paralogs for RPAP2 Gene

Pseudogenes.org Pseudogenes for RPAP2 Gene

genes like me logo Genes that share paralogs with RPAP2: view

No data available for Paralogs for RPAP2 Gene

Variants for RPAP2 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for RPAP2 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for RPAP2 Gene

Variant ID Type Subtype PubMed ID
esv2714684 CNV deletion 23290073
esv3346260 CNV insertion 20981092
nsv1133878 CNV deletion 24896259
nsv477492 CNV novel sequence insertion 20440878
nsv830592 CNV gain 17160897

Variation tolerance for RPAP2 Gene

Residual Variation Intolerance Score: 30.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.56; 44.49% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RPAP2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RPAP2
Leiden Open Variation Database (LOVD)
RPAP2

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RPAP2 Gene

Disorders for RPAP2 Gene

Additional Disease Information for RPAP2

No disorders were found for RPAP2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RPAP2 Gene

Publications for RPAP2 Gene

  1. Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme. (PMID: 17643375) Jeronimo C … Coulombe B (Molecular cell 2007) 2 3 4
  2. RPRD1A and RPRD1B are human RNA polymerase II C-terminal domain scaffolds for Ser5 dephosphorylation. (PMID: 24997600) Ni Z … Greenblatt JF (Nature structural & molecular biology 2014) 3 4
  3. Ser7 phosphorylation of the CTD recruits the RPAP2 Ser5 phosphatase to snRNA genes. (PMID: 22137580) Egloff S … Murphy S (Molecular cell 2012) 3 4
  4. The yeast regulator of transcription protein Rtr1 lacks an active site and phosphatase activity. (PMID: 22781759) Xiang K … Tong L (Nature communications 2012) 2 3
  5. Control of the RNA polymerase II phosphorylation state in promoter regions by CTD interaction domain-containing proteins RPRD1A and RPRD1B. (PMID: 22231121) Ni Z … Greenblatt JF (Transcription 2011) 3 4

Products for RPAP2 Gene

Sources for RPAP2 Gene