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    Pogz pogo transposable element derived with ZNF domain [ Rattus norvegicus (Norway rat) ]

    Gene ID: 310658, updated on 27-Nov-2024

    Summary

    Official Symbol
    Pogzprovided by RGD
    Official Full Name
    pogo transposable element derived with ZNF domainprovided by RGD
    Primary source
    RGD:1309980
    See related
    EnsemblRapid:ENSRNOG00000053599 AllianceGenome:RGD:1309980
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable nucleic acid binding activity. Predicted to be involved in kinetochore assembly and mitotic sister chromatid cohesion. Predicted to act upstream of or within with a positive effect on double-strand break repair via homologous recombination. Predicted to be located in chromatin; cytosol; and nucleoplasm. Human ortholog(s) of this gene implicated in White-Sutton syndrome. Orthologous to human POGZ (pogo transposable element derived with ZNF domain). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Thymus (RPKM 102.0), Adrenal (RPKM 91.1) and 9 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Pogz in Genome Data Viewer
    Location:
    2q34
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 2 NC_086020.1 (185069492..185129741)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 2 NC_051337.1 (182394269..182440711)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (195995322..196041500)

    Chromosome 2 - NC_086020.1Genomic Context describing neighboring genes Neighboring gene cingulin Neighboring gene uncharacterized LOC134485648 Neighboring gene NADH:ubiquinone oxidoreductase subunit S5, pseudogene 2 Neighboring gene high mobility group protein B1 pseudogene Neighboring gene small nucleolar RNA U89 Neighboring gene proteasome 20S subunit beta 4

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    General gene information

    Markers

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in chromatin ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleoplasm 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
     

    General protein information

    Preferred Names
    pogo transposable element with ZNF domain

    NCBI Reference Sequences (RefSeq)

    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_001107693.2NP_001101163.1  pogo transposable element with ZNF domain

      See identical proteins and their annotated locations for NP_001101163.1

      Status: VALIDATED

      Source sequence(s)
      CA504014, JAXUCZ010000002
      UniProtKB/TrEMBL
      A6K2T0, A6K2T1, D3ZV33
      Conserved Domains (6) summary
      PRK00404
      Location:819876
      tatB; Sec-independent protein translocase subunit TatB
      smart00674
      Location:9651026
      CENPB; Putative DNA-binding domain in centromere protein B, mouse jerky and transposases
      PHA03247
      Location:211405
      PHA03247; large tegument protein UL36; Provisional
      sd00017
      Location:476497
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00020
      Location:440473
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cl21549
      Location:11061217
      rve; Integrase core domain

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086020.1 Reference GRCr8

      Range
      185069492..185129741
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063281872.1XP_063137942.1  pogo transposable element with ZNF domain isoform X2

      UniProtKB/TrEMBL
      A6K2T1, D3ZV33
    2. XM_017590895.3XP_017446384.1  pogo transposable element with ZNF domain isoform X1

      UniProtKB/TrEMBL
      A0A0G2JY58, A6K2T0
      Conserved Domains (6) summary
      PRK00404
      Location:872929
      tatB; Sec-independent protein translocase subunit TatB
      smart00674
      Location:10181079
      CENPB; Putative DNA-binding domain in centromere protein B, mouse jerky and transposases
      PHA03247
      Location:264458
      PHA03247; large tegument protein UL36; Provisional
      sd00017
      Location:529550
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00020
      Location:493526
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cl21549
      Location:11591270
      rve; Integrase core domain
    3. XM_063281871.1XP_063137941.1  pogo transposable element with ZNF domain isoform X2

      UniProtKB/TrEMBL
      A6K2T1, D3ZV33
    4. XM_008761295.4XP_008759517.1  pogo transposable element with ZNF domain isoform X1

      UniProtKB/TrEMBL
      A0A0G2JY58, A6K2T0
      Related
      ENSRNOP00000070527.2, ENSRNOT00000082849.3
      Conserved Domains (6) summary
      PRK00404
      Location:872929
      tatB; Sec-independent protein translocase subunit TatB
      smart00674
      Location:10181079
      CENPB; Putative DNA-binding domain in centromere protein B, mouse jerky and transposases
      PHA03247
      Location:264458
      PHA03247; large tegument protein UL36; Provisional
      sd00017
      Location:529550
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00020
      Location:493526
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cl21549
      Location:11591270
      rve; Integrase core domain
    5. XM_008761297.4XP_008759519.1  pogo transposable element with ZNF domain isoform X2

      See identical proteins and their annotated locations for XP_008759519.1

      UniProtKB/TrEMBL
      A6K2T0, A6K2T1, D3ZV33
      Related
      ENSRNOP00000070100.1, ENSRNOT00000084023.3
      Conserved Domains (6) summary
      PRK00404
      Location:819876
      tatB; Sec-independent protein translocase subunit TatB
      smart00674
      Location:9651026
      CENPB; Putative DNA-binding domain in centromere protein B, mouse jerky and transposases
      PHA03247
      Location:211405
      PHA03247; large tegument protein UL36; Provisional
      sd00017
      Location:476497
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00020
      Location:440473
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cl21549
      Location:11061217
      rve; Integrase core domain
    6. XM_008761299.4XP_008759521.1  pogo transposable element with ZNF domain isoform X3

      UniProtKB/TrEMBL
      A0A8I6A9K5, A6K2T0
      Related
      ENSRNOP00000090463.1, ENSRNOT00000094202.2
      Conserved Domains (5) summary
      smart00674
      Location:912973
      CENPB; Putative DNA-binding domain in centromere protein B, mouse jerky and transposases
      sd00017
      Location:423444
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00020
      Location:387420
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam15273
      Location:306343
      NHS; NHS-like
      cl21549
      Location:10471171
      rve; Integrase core domain
    7. XM_039102346.2XP_038958274.1  pogo transposable element with ZNF domain isoform X4

      UniProtKB/TrEMBL
      A0A8I5ZSI0
      Conserved Domains (5) summary
      PRK00404
      Location:713770
      tatB; Sec-independent protein translocase subunit TatB
      smart00674
      Location:859920
      CENPB; Putative DNA-binding domain in centromere protein B, mouse jerky and transposases
      sd00017
      Location:370391
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00020
      Location:334367
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cl21549
      Location:10001111
      rve; Integrase core domain