Human Gene RPAP1 (uc001zod.3) Description and Page Index
  Description: Homo sapiens RNA polymerase II associated protein 1 (RPAP1), mRNA.
RefSeq Summary (NM_015540): This protein forms part of the RNA polymerase II (RNAPII) enzyme complex and may recruit RNAPII to chromatin through its interaction with acetylated histones. [provided by RefSeq, Jul 2012]. ##Evidence-Data-START## Transcript exon combination :: BC000246.1, SRR1803615.29460.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA1965299, SAMEA1966682 [ECO:0000350] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000304330.9/ ENSP00000306123.4 RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr15:41,809,375-41,836,464 Size: 27,090 Total Exon Count: 25 Strand: -
Coding Region
   Position: hg19 chr15:41,809,740-41,829,323 Size: 19,584 Coding Exon Count: 24 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr15:41,809,375-41,836,464)mRNA (may differ from genome)Protein (1393 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
OMIMPubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=RNA polymerase II-associated protein 1;
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. Required for interaction of the RNA polymerase II complex with acetylated histone H3.
SUBUNIT: Part of a RNA polymerase II complex that contains POLR2A, POLR2B, POLR2C, POLR2D, POLR2E, POLR2F, POLR2G, POLR2H, POLR2I, POLR2J, POLR2K, POLR2L, RPAP1, FCP1 plus the general transcription factors TFIIB and TFIIF.
SUBCELLULAR LOCATION: Nucleus (By similarity).
SIMILARITY: Belongs to the RPAP1 family.
SEQUENCE CAUTION: Sequence=BAA92641.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): RPAP1
CDC HuGE Published Literature: RPAP1

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 7.83 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 258.03 RPKM

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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -36.60124-0.295 Picture PostScript Text
3' UTR -119.05365-0.326 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
IPR013929 - RNA_pol_II_AP1_C
IPR013930 - RNA_pol_II_AP1_N

Pfam Domains:
PF08620 - RPAP1-like, C-terminal
PF08621 - RPAP1-like, N-terminal

ModBase Predicted Comparative 3D Structure on Q9BWH6
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 orthologGenome BrowserGenome BrowserGenome BrowserNo orthologGenome Browser
Gene DetailsGene Details Gene Details Gene Details
Gene SorterGene Sorter Gene Sorter Gene Sorter
 RGDEnsemblFlyBase SGD
 Protein SequenceProtein SequenceProtein Sequence Protein Sequence
 AlignmentAlignmentAlignment Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0005515 protein binding
GO:0016740 transferase activity
GO:0016779 nucleotidyltransferase activity

Biological Process:
GO:0006366 transcription from RNA polymerase II promoter

Cellular Component:
GO:0005634 nucleus

-  Descriptions from all associated GenBank mRNAs
  LF205848 - JP 2014500723-A/13351: Polycomb-Associated Non-Coding RNAs.
AL157487 - Homo sapiens mRNA; cDNA DKFZp434E1120 (from clone DKFZp434E1120).
AL117479 - Homo sapiens mRNA; cDNA DKFZp727M111 (from clone DKFZp727M111).
BC000246 - Homo sapiens RNA polymerase II associated protein 1, mRNA (cDNA clone MGC:858 IMAGE:3357380), complete cds.
AB037824 - Homo sapiens mRNA for KIAA1403 protein, partial cds.
AK022794 - Homo sapiens cDNA FLJ12732 fis, clone NT2RP2000175.
EU832337 - Synthetic construct Homo sapiens clone HAIB:100067366; DKFZo008F1227 RNA polymerase II associated protein 1 protein (RPAP1) gene, encodes complete protein.
EU832422 - Synthetic construct Homo sapiens clone HAIB:100067451; DKFZo004F1228 RNA polymerase II associated protein 1 protein (RPAP1) gene, encodes complete protein.
AB527440 - Synthetic construct DNA, clone: pF1KE1031, Homo sapiens RPAP1 gene for RNA polymerase II associated protein 1, without stop codon, in Flexi system.
MA441425 - JP 2018138019-A/13351: Polycomb-Associated Non-Coding RNAs.
JD120734 - Sequence 101758 from Patent EP1572962.
LF348852 - JP 2014500723-A/156355: Polycomb-Associated Non-Coding RNAs.
JD170704 - Sequence 151728 from Patent EP1572962.
JD239654 - Sequence 220678 from Patent EP1572962.
JD176889 - Sequence 157913 from Patent EP1572962.
JD382292 - Sequence 363316 from Patent EP1572962.
LF348853 - JP 2014500723-A/156356: Polycomb-Associated Non-Coding RNAs.
MA584429 - JP 2018138019-A/156355: Polycomb-Associated Non-Coding RNAs.
MA584430 - JP 2018138019-A/156356: Polycomb-Associated Non-Coding RNAs.
AK290224 - Homo sapiens cDNA FLJ77037 partial cds, highly similar to Homo sapiens RNA polymerase II associated protein 1, mRNA.
LF348855 - JP 2014500723-A/156358: Polycomb-Associated Non-Coding RNAs.
AK308884 - Homo sapiens cDNA, FLJ98925.
LF348857 - JP 2014500723-A/156360: Polycomb-Associated Non-Coding RNAs.
JD097723 - Sequence 78747 from Patent EP1572962.
CU674098 - Synthetic construct Homo sapiens gateway clone IMAGE:100023252 5' read RPAP1 mRNA.
JD108349 - Sequence 89373 from Patent EP1572962.
JD215799 - Sequence 196823 from Patent EP1572962.
JD474918 - Sequence 455942 from Patent EP1572962.
JD241300 - Sequence 222324 from Patent EP1572962.
JD257413 - Sequence 238437 from Patent EP1572962.
JD227894 - Sequence 208918 from Patent EP1572962.
JD060236 - Sequence 41260 from Patent EP1572962.
JD318177 - Sequence 299201 from Patent EP1572962.
MA584432 - JP 2018138019-A/156358: Polycomb-Associated Non-Coding RNAs.
MA584434 - JP 2018138019-A/156360: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: KIAA1403, NM_015540, NP_056355, Q9BWH6, Q9H9I2, Q9NSQ5, Q9P2E4, Q9UFS7, RPAP1_HUMAN
UCSC ID: uc001zod.3
RefSeq Accession: NM_015540
Protein: Q9BWH6 (aka RPAP1_HUMAN)
CCDS: CCDS10079.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_015540.2
exon count: 25CDS single in 3' UTR: no RNA size: 4698
ORF size: 4182CDS single in intron: no Alignment % ID: 99.98
txCdsPredict score: 8492.00frame shift in genome: no % Coverage: 99.43
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.