Human Gene RPAP3 (ENST00000005386.8_7) from GENCODE V47lift37
  Description: RNA polymerase II associated protein 3, transcript variant 1 (from RefSeq NM_024604.3)
Gencode Transcript: ENST00000005386.8_7
Gencode Gene: ENSG00000005175.10_10
Transcript (Including UTRs)
   Position: hg19 chr12:48,055,032-48,099,813 Size: 44,782 Total Exon Count: 17 Strand: -
Coding Region
   Position: hg19 chr12:48,057,288-48,096,623 Size: 39,336 Coding Exon Count: 16 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:48,055,032-48,099,813)mRNA (may differ from genome)Protein (665 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RPAP3_HUMAN
DESCRIPTION: RecName: Full=RNA polymerase II-associated protein 3;
FUNCTION: Forms an interface between the RNA polymerase II enzyme and chaperone/scaffolding protein, suggesting that it is required to connect RNA polymerase II to regulators of protein complex formation.
SUBUNIT: Tightly associated with the RNA polymerase II complex.
SIMILARITY: Belongs to the RPAP3 family.
SIMILARITY: Contains 7 TPR repeats.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 12.77 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 296.44 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -40.7085-0.479 Picture PostScript Text
3' UTR -529.902256-0.235 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR025986 - RPAP3-like_C
IPR001440 - TPR-1
IPR013026 - TPR-contain_dom
IPR011990 - TPR-like_helical
IPR019734 - TPR_repeat

Pfam Domains:
PF00515 - Tetratricopeptide repeat
PF07719 - Tetratricopeptide repeat
PF13176 - Tetratricopeptide repeat
PF13181 - Tetratricopeptide repeat
PF13414 - TPR repeat
PF13877 - Potential Monad-binding region of RPAP3

SCOP Domains:
81901 - HCP-like
48439 - Protein prenylyltransferase
48452 - TPR-like
116846 - MIT domain
140361 - MIT domain-like

ModBase Predicted Comparative 3D Structure on Q9H6T3
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Cellular Component:
GO:0005829 cytosol
GO:0097255 R2TP complex


-  Descriptions from all associated GenBank mRNAs
  AK025561 - Homo sapiens cDNA: FLJ21908 fis, clone HEP03830.
AK299465 - Homo sapiens cDNA FLJ50185 complete cds, weakly similar to Homo sapiens translocase of outer mitochondrial membrane 34 (TOMM34), mRNA.
BC056415 - Homo sapiens RNA polymerase II associated protein 3, mRNA (cDNA clone MGC:64954 IMAGE:5218249), complete cds.
JD339287 - Sequence 320311 from Patent EP1572962.
KJ894707 - Synthetic construct Homo sapiens clone ccsbBroadEn_04101 RPAP3 gene, encodes complete protein.
BC003680 - Homo sapiens, clone IMAGE:3949956, mRNA.

-  Other Names for This Gene
  Alternate Gene Symbols: B4DRW9, ENST00000005386.1, ENST00000005386.2, ENST00000005386.3, ENST00000005386.4, ENST00000005386.5, ENST00000005386.6, ENST00000005386.7, NM_024604, Q6PHR5, Q9H6T3, RPAP3_HUMAN, uc317bvv.1, uc317bvv.2
UCSC ID: ENST00000005386.8_7
RefSeq Accession: NM_024604.3
Protein: Q9H6T3 (aka RPAP3_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.