Human Gene RPAP2 (ENST00000610020.2_4) from GENCODE V47lift37

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Description: RNA polymerase II associated protein 2 (from RefSeq NM_024813.3)
Gencode Transcript: ENST00000610020.2_4
Gencode Gene: ENSG00000122484.9_7
Transcript (Including UTRs)
Position: hg19 chr1:92,764,616-92,867,613 Size: 102,998 Total Exon Count: 13 Strand: +
Coding Region
Position: hg19 chr1:92,764,631-92,852,568 Size: 87,938 Coding Exon Count: 13

Page Index	Sequence and Links	UniProtKB Comments	Primers	CTD	Gene Alleles
RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species	GO Annotations
mRNA Descriptions	Pathways	Other Names	Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr1:92,764,616-92,867,613)			mRNA (may differ from genome)		Protein (612 aa)
Gene Sorter	Genome Browser	Other Species FASTA	VisiGene	Gene interactions	Table Schema
AlphaFold	BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards
HGNC	MGI	OMIM	PubMed	Reactome	UniProtKB
Wikipedia	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: RPAP2_HUMAN DESCRIPTION: RecName: Full=Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2; EC=3.1.3.16; AltName: Full=RNA polymerase II-associated protein 2; 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. CATALYTIC ACTIVITY: A phosphoprotein + H(2)O = a protein + phosphate. SUBUNIT: Associates with the RNA polymerase II complex. Interacts with transcribing RNA polymerase II phosphorylated on 'Ser-7' on CTD. SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Note=Shuttles between the cytoplasm and the nucleus in a CRM1-dependent manner. DOMAIN: The RTR1-type zinc finger mediates interactions with RNA polymerase II complex subunits (PubMed:22137580). SIMILARITY: Belongs to the RPAP2 family. SIMILARITY: Contains 1 RTR1-type zinc finger.

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 C006780 bisphenol A D001564 Benzo(a)pyrene D013749 Tetrachlorodibenzodioxin C044887 beta-methylcholine

Common Gene Haplotype Alleles


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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 4.72 RPKM in Brain - Cerebellum Total median expression: 65.11 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

Region	Fold Energy	Bases	Energy/Base	Display As
3' UTR	-4356.78	15045	-0.290	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
IPR007308 - DUF408

Pfam Domains:
PF04181 - Rtr1/RPAP2 family

ModBase Predicted Comparative 3D Structure on Q8IXW5


Front	Top	Side

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.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	No ortholog	Genome Browser
Gene Details	Gene Details		Gene Details		Gene Details
Gene Sorter	Gene Sorter		Gene Sorter		Gene Sorter
	RGD	Ensembl			SGD
					Protein Sequence
					Alignment

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0004721 phosphoprotein phosphatase activity GO:0004722 protein serine/threonine phosphatase activity GO:0005515 protein binding GO:0008420 CTD phosphatase activity GO:0016787 hydrolase activity GO:0046872 metal ion binding Biological Process: GO:0006351 transcription, DNA-templated GO:0006355 regulation of transcription, DNA-templated GO:0009301 snRNA transcription GO:0042795 snRNA transcription from RNA polymerase II promoter GO:0070940 dephosphorylation of RNA polymerase II C-terminal domain Cellular Component: GO:0005634 nucleus GO:0005654 nucleoplasm GO:0005730 nucleolus GO:0005737 cytoplasm GO:0005829 cytosol GO:0016591 DNA-directed RNA polymerase II, holoenzyme

Descriptions from all associated GenBank mRNAs


	BC039014 - Homo sapiens RNA polymerase II associated protein 2, mRNA (cDNA clone MGC:47579 IMAGE:5744281), complete cds. AK023212 - Homo sapiens cDNA FLJ13150 fis, clone NT2RP3003353, weakly similar to HYPOTHETICAL 26.2 KD PROTEIN IN GDI1-COX15 INTERGENIC REGION. BC031070 - Homo sapiens RNA polymerase II associated protein 2, mRNA (cDNA clone MGC:33693 IMAGE:5313284), complete cds. AK225054 - Homo sapiens mRNA for hypothetical protein LOC79871 variant, clone: adSE01679. JF432356 - Synthetic construct Homo sapiens clone IMAGE:100073548 RNA polymerase II associated protein 2 (RPAP2) gene, encodes complete protein. CU691638 - Synthetic construct Homo sapiens gateway clone IMAGE:100020983 5' read RPAP2 mRNA. JD509983 - Sequence 491007 from Patent EP1572962. JD347399 - Sequence 328423 from Patent EP1572962. JD332621 - Sequence 313645 from Patent EP1572962. JD285922 - Sequence 266946 from Patent EP1572962. JD284271 - Sequence 265295 from Patent EP1572962. JD454279 - Sequence 435303 from Patent EP1572962. JD482132 - Sequence 463156 from Patent EP1572962. JD204235 - Sequence 185259 from Patent EP1572962. JD374933 - Sequence 355957 from Patent EP1572962. JD428595 - Sequence 409619 from Patent EP1572962. JD564836 - Sequence 545860 from Patent EP1572962. JD248505 - Sequence 229529 from Patent EP1572962. JD045852 - Sequence 26876 from Patent EP1572962. JD512316 - Sequence 493340 from Patent EP1572962. JD171323 - Sequence 152347 from Patent EP1572962. JD241464 - Sequence 222488 from Patent EP1572962. JD030111 - Sequence 11135 from Patent EP1572962. JD092947 - Sequence 73971 from Patent EP1572962. JD350621 - Sequence 331645 from Patent EP1572962. JD085130 - Sequence 66154 from Patent EP1572962. JD249598 - Sequence 230622 from Patent EP1572962. JD269993 - Sequence 251017 from Patent EP1572962. JD354121 - Sequence 335145 from Patent EP1572962. JD378054 - Sequence 359078 from Patent EP1572962. JD516832 - Sequence 497856 from Patent EP1572962. JD256512 - Sequence 237536 from Patent EP1572962. JD560660 - Sequence 541684 from Patent EP1572962. JD476672 - Sequence 457696 from Patent EP1572962. JD246248 - Sequence 227272 from Patent EP1572962. JD306793 - Sequence 287817 from Patent EP1572962. JD414695 - Sequence 395719 from Patent EP1572962. JD488093 - Sequence 469117 from Patent EP1572962. JD414697 - Sequence 395721 from Patent EP1572962. JD120467 - Sequence 101491 from Patent EP1572962. JD405541 - Sequence 386565 from Patent EP1572962. JD379489 - Sequence 360513 from Patent EP1572962. JD360948 - Sequence 341972 from Patent EP1572962. JD043146 - Sequence 24170 from Patent EP1572962. JD043145 - Sequence 24169 from Patent EP1572962. JD043144 - Sequence 24168 from Patent EP1572962. JD313430 - Sequence 294454 from Patent EP1572962. JD434364 - Sequence 415388 from Patent EP1572962. JD117099 - Sequence 98123 from Patent EP1572962. JD277612 - Sequence 258636 from Patent EP1572962. JD482660 - Sequence 463684 from Patent EP1572962. AK124503 - Homo sapiens cDNA FLJ42512 fis, clone BRACE2045954.

Biochemical and Signaling Pathways


	Reactome (by CSHL, EBI, and GO) Protein Q8IXW5 (Reactome details) participates in the following event(s): R-HSA-6810235 RPAP2 binds RNA polymerase II phosphorylated at serine-7 residues of heptad repeats in the C-terminal domain R-HSA-6814885 CBCAP complex binds 7-methylguanosine cap of snRNA R-HSA-6807505 RNA polymerase II transcribes snRNA genes R-HSA-73857 RNA Polymerase II Transcription R-HSA-74160 Gene expression (Transcription)

Other Names for This Gene


	Alternate Gene Symbols: C1orf82, C9JKB5, ENST00000610020.1, NM_024813, Q49AS7, Q8IXW5, Q9H8Y2, RPAP2_HUMAN, uc327mmb.1, uc327mmb.2 UCSC ID: ENST00000610020.2_4 RefSeq Accession: NM_024813.3 Protein: Q8IXW5 (aka RPAP2_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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