U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Rpap2 RNA polymerase II associated protein 2 [ Mus musculus (house mouse) ]

Gene ID: 231571, updated on 5-Mar-2024

Summary

Go to the top of the page Help
Official Symbol
Rpap2provided by MGI
Official Full Name
RNA polymerase II associated protein 2provided by MGI
Primary source
MGI:MGI:2141142
See related
Ensembl:ENSMUSG00000033773 AllianceGenome:MGI:2141142
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Summary
Predicted to enable RNA polymerase II CTD heptapeptide repeat phosphatase activity. Predicted to be involved in dephosphorylation of RNA polymerase II C-terminal domain and snRNA transcription. Predicted to be located in cytosol and nucleolus. Predicted to be part of RNA polymerase II, holoenzyme. Predicted to be active in cytoplasm and nucleus. Orthologous to human RPAP2 (RNA polymerase II associated protein 2). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in bladder adult (RPKM 2.6), testis adult (RPKM 2.6) and 26 other tissues See more
Orthologs
human all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
5 F; 5 52.23 cM
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (107745239..107809719)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (107597373..107661853)

Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene BTB domain containing 8 Neighboring gene LSM12 homolog pseudogene Neighboring gene RIKEN cDNA 1700028K03 gene Neighboring gene glomulin, FKBP associated protein Neighboring gene STARR-seq mESC enhancer starr_13890 Neighboring gene STARR-positive B cell enhancer ABC_E1683 Neighboring gene RIKEN cDNA A930041C12 gene Neighboring gene Gfi1 +35 kb enhancer Neighboring gene RIKEN cDNA 4930428O21 gene Neighboring gene +19.5 kb enhancer downstream of Gfi1 Neighboring gene Gfi1 +5.8 kb enhancer Neighboring gene Gfi1 promoter regions Neighboring gene growth factor independent 1 transcription repressor

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. Database resources of the National Center for Biotechnology Information. Wheeler DL, et al. Nucleic Acids Res, 2001 Jan 1. PMID 11125038, Free PMC Article
  2. Genome-wide expression profiling of mid-gestation placenta and embryo using a 15,000 mouse developmental cDNA microarray. Tanaka TS, et al. Proc Natl Acad Sci U S A, 2000 Aug 1. PMID 10922068, Free PMC Article
  3. A conditional knockout resource for the genome-wide study of mouse gene function. Skarnes WC, et al. Nature, 2011 Jun 15. PMID 21677750, Free PMC Article
  4. Normalization and subtraction: two approaches to facilitate gene discovery. Bonaldo MF, et al. Genome Res, 1996 Sep. PMID 8889548
  5. Wnk1 kinase deficiency lowers blood pressure in mice: a gene-trap screen to identify potential targets for therapeutic intervention. Zambrowicz BP, et al. Proc Natl Acad Sci U S A, 2003 Nov 25. PMID 14610273, Free PMC Article

See all (15) citations in PubMed

GeneRIFs: Gene References Into Functions

Variation

Go to the top of the page Help

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (1) 

Pathways from PubChem

Go to the top of the page

General gene information

Go to the top of the page Help

Markers

Homology

Clone Names

  • MGC27814

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables RNA polymerase II CTD heptapeptide repeat phosphatase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II CTD heptapeptide repeat phosphatase activity ISO
Inferred from Sequence Orthology
more info
  
enables RNA polymerase core enzyme binding IEA
Inferred from Electronic Annotation
more info
  
enables hydrolase activity IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables myosin phosphatase activity IEA
Inferred from Electronic Annotation
more info
  
enables phosphoprotein phosphatase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein serine/threonine phosphatase activity ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
involved_in PERK-mediated unfolded protein response ISO
Inferred from Sequence Orthology
more info
  
involved_in snRNA transcription ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
  
located_in cytosol ISO
Inferred from Sequence Orthology
more info
  
located_in nucleolus ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  
part_of transcription preinitiation complex ISO
Inferred from Sequence Orthology
more info
  

General protein information

Go to the top of the page Help
Preferred Names
putative RNA polymerase II subunit B1 CTD phosphatase Rpap2
NP_001156933.1
NP_001156934.1
NP_001276498.1
NP_001276499.1
NP_001346845.1
NP_001346846.1
NP_001346847.1
NP_659160.2
XP_006534963.1
XP_006534966.1
XP_030110267.1
XP_030110268.1
XP_036020968.1
XP_036020969.1
XP_036020970.1

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001163461.2 → NP_001156933.1  putative RNA polymerase II subunit B1 CTD phosphatase Rpap2 isoform B

    See identical proteins and their annotated locations for NP_001156933.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks multiple 3' exons and contains an alternate 3' terminal exon, resulting in a different 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (B) has a shorter C-terminus than isoform A.
    Source sequence(s)
    AC117574, AK161901
    Consensus CDS
    CCDS51588.1
    UniProtKB/Swiss-Prot
    Q8VC34
    Related
    ENSMUSP00000108273.2, ENSMUST00000112654.8
    Conserved Domains (1) summary
    pfam04181
    Location:81 → 152
    RPAP2_Rtr1; Rtr1/RPAP2 family

  2. NM_001163462.2 → NP_001156934.1  putative RNA polymerase II subunit B1 CTD phosphatase Rpap2 isoform C

    See identical proteins and their annotated locations for NP_001156934.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in both the 5' and 3' coding regions and UTRs, compared to variant 1. The encoded isoform (C) has shorter N- and C- termini compared to isoform A.
    Source sequence(s)
    AC117574, AK049889
    Consensus CDS
    CCDS51589.1
    UniProtKB/Swiss-Prot
    Q8VC34
    Related
    ENSMUSP00000108269.2, ENSMUST00000112650.8
    Conserved Domains (1) summary
    pfam04181
    Location:2 → 73
    RPAP2_Rtr1; Rtr1/RPAP2 family

  3. NM_001289569.1 → NP_001276498.1  putative RNA polymerase II subunit B1 CTD phosphatase Rpap2 isoform D

    See identical proteins and their annotated locations for NP_001276498.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses an alternate splice site in the 5' coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (D) has a distinct N-terminus and is shorter than isoform A.
    Source sequence(s)
    AC117574, AK034418, AV221546
    Consensus CDS
    CCDS71631.1
    UniProtKB/Swiss-Prot
    Q8VC34
    Related
    ENSMUSP00000108270.2, ENSMUST00000112651.8
    Conserved Domains (1) summary
    pfam04181
    Location:4 → 75
    RPAP2_Rtr1; Rtr1/RPAP2 family

  4. NM_001289570.1 → NP_001276499.1  putative RNA polymerase II subunit B1 CTD phosphatase Rpap2 isoform E

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) lacks multiple 3' exons and contains an alternate 3' terminal exon, resulting in a different 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (E) has a distinct C-terminus and is shorter than isoform A.
    Source sequence(s)
    AC117574, AK166574
    Consensus CDS
    CCDS71630.1
    UniProtKB/Swiss-Prot
    Q8VC34
    Related
    ENSMUSP00000108274.2, ENSMUST00000112655.8
    Conserved Domains (1) summary
    pfam04181
    Location:81 → 152
    RPAP2_Rtr1; Rtr1/RPAP2 family

  5. NM_001359916.1 → NP_001346845.1  putative RNA polymerase II subunit B1 CTD phosphatase Rpap2 isoform F

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (F) has a shorter and distinct N-terminus compared to isoform A.
    Source sequence(s)
    AC117574
    Conserved Domains (1) summary
    pfam04181
    Location:72 → 143
    RPAP2_Rtr1; Rtr1/RPAP2 family

  6. NM_001359917.1 → NP_001346846.1  putative RNA polymerase II subunit B1 CTD phosphatase Rpap2 isoform G

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (G) is shorter at the N-terminus compared to isoform A. Variants 7 and 8 both encode the same isoform (G).
    Source sequence(s)
    AC117574
    Conserved Domains (1) summary
    pfam04181
    Location:2 → 73
    RPAP2_Rtr1; Rtr1/RPAP2 family

  7. NM_001359918.1 → NP_001346847.1  putative RNA polymerase II subunit B1 CTD phosphatase Rpap2 isoform G

    Status: VALIDATED

    Description
    Transcript Variant: This variant (8) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (G) is shorter at the N-terminus compared to isoform A. Variants 7 and 8 both encode the same isoform (G).
    Source sequence(s)
    AC117574
    Conserved Domains (1) summary
    pfam04181
    Location:2 → 73
    RPAP2_Rtr1; Rtr1/RPAP2 family

  8. NM_144911.3 → NP_659160.2  putative RNA polymerase II subunit B1 CTD phosphatase Rpap2 isoform A

    See identical proteins and their annotated locations for NP_659160.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (A).
    Source sequence(s)
    AC117574, AK034418, AK145830, AV221546
    Consensus CDS
    CCDS19506.1
    UniProtKB/Swiss-Prot
    Q3TLC8, Q3TSP8, Q3UKX0, Q8C7M5, Q8CBW8, Q8VC34
    Related
    ENSMUSP00000070209.6, ENSMUST00000065422.12
    Conserved Domains (1) summary
    pfam04181
    Location:81 → 152
    RPAP2_Rtr1; Rtr1/RPAP2 family

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000071.7 Reference GRCm39 C57BL/6J

    Range
    107745239..107809719
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006534900.3 → XP_006534963.1  putative RNA polymerase II subunit B1 CTD phosphatase Rpap2 isoform X2

    See identical proteins and their annotated locations for XP_006534963.1

    UniProtKB/Swiss-Prot
    Q8VC34
    Conserved Domains (1) summary
    pfam04181
    Location:4 → 75
    RPAP2_Rtr1; Rtr1/RPAP2 family

  2. XM_030254408.1 → XP_030110268.1  putative RNA polymerase II subunit B1 CTD phosphatase Rpap2 isoform X3

    Conserved Domains (1) summary
    pfam04181
    Location:2 → 73
    RPAP2_Rtr1; Rtr1/RPAP2 family

  3. XM_036165076.1 → XP_036020969.1  putative RNA polymerase II subunit B1 CTD phosphatase Rpap2 isoform X3

    Conserved Domains (1) summary
    pfam04181
    Location:2 → 73
    RPAP2_Rtr1; Rtr1/RPAP2 family

  4. XM_036165075.1 → XP_036020968.1  putative RNA polymerase II subunit B1 CTD phosphatase Rpap2 isoform X2

    Conserved Domains (1) summary
    pfam04181
    Location:4 → 75
    RPAP2_Rtr1; Rtr1/RPAP2 family

  5. XM_006534903.4 → XP_006534966.1  putative RNA polymerase II subunit B1 CTD phosphatase Rpap2 isoform X3

    See identical proteins and their annotated locations for XP_006534966.1

    Conserved Domains (1) summary
    pfam04181
    Location:2 → 73
    RPAP2_Rtr1; Rtr1/RPAP2 family

  6. XM_030254407.2 → XP_030110267.1  putative RNA polymerase II subunit B1 CTD phosphatase Rpap2 isoform X1

    Conserved Domains (1) summary
    pfam04181
    Location:72 → 143
    RPAP2_Rtr1; Rtr1/RPAP2 family

  7. XM_036165077.1 → XP_036020970.1  putative RNA polymerase II subunit B1 CTD phosphatase Rpap2 isoform X3

    Conserved Domains (1) summary
    pfam04181
    Location:2 → 73
    RPAP2_Rtr1; Rtr1/RPAP2 family
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8VC34.2 GenPept UniProtKB/Swiss-Prot:Q8VC34

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous