U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

    Gene ID: 231571, updated on 2-Nov-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 PERK-mediated unfolded protein response and snRNA transcription. Predicted to be located in cytosol and nucleolus. Predicted to be part of transcription preinitiation complex. Predicted to be active in cytoplasm and nucleus. Orthologous to human RPAP2 (RNA polymerase II associated protein 2). [provided by Alliance of Genome Resources, Nov 2024]
    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
    See Rpap2 in Genome Data Viewer
    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 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. Mouse screen reveals multiple new genes underlying mouse and human hearing loss. Ingham NJ, et al. PLoS Biol, 2019 Apr. PMID 30973865, Free PMC Article
    2. Database resources of the National Center for Biotechnology Information. Wheeler DL, et al. Nucleic Acids Res, 2001 Jan 1. PMID 11125038, Free PMC Article
    3. 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
    4. Genetic determinants of micronucleus formation in vivo. Adams DJ, et al. Nature, 2024 Mar. PMID 38355793, Free PMC Article
    5. 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

    See all (17) 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 II CTD heptapeptide repeat phosphatase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables RNA polymerase core enzyme binding 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 protein serine/threonine phosphatase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein serine/threonine phosphatase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in PERK-mediated unfolded protein response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in PERK-mediated unfolded protein response ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in snRNA transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in snRNA transcription ISS
    Inferred from Sequence or Structural Similarity
    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 cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleolus IEA
    Inferred from Electronic Annotation
    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
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    part_of transcription preinitiation complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of transcription preinitiation complex ISS
    Inferred from Sequence or Structural Similarity
    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