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

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

    Summary

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    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 DNA binding activity and metal ion binding activity. Predicted to be involved in kinetochore assembly; mitotic sister chromatid cohesion; and positive regulation of transcription by RNA polymerase II. 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. Predicted to be active in nucleus. 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, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 102.0), Adrenal (RPKM 91.1) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    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

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

    Bibliography

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    Related articles in PubMed

    1. Hepatoma-derived growth factor-related protein 2 promotes DNA repair by homologous recombination. Baude A, et al. Nucleic Acids Res, 2016 Mar 18. PMID 26721387, Free PMC Article
    2. Human POGZ modulates dissociation of HP1alpha from mitotic chromosome arms through Aurora B activation. Nozawa RS, et al. Nat Cell Biol, 2010 Jul. PMID 20562864
    3. Normalization and subtraction: two approaches to facilitate gene discovery. Bonaldo MF, et al. Genome Res, 1996 Sep. PMID 8889548
    4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    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
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within_positive_effect double-strand break repair via homologous recombination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in kinetochore assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in mitotic sister chromatid cohesion ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    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

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    Preferred Names
    pogo transposable element with ZNF domain

    NCBI Reference Sequences (RefSeq)

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    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_001107693.2 → NP_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:819 → 876
      tatB; Sec-independent protein translocase subunit TatB
      smart00674
      Location:965 → 1026
      CENPB; Putative DNA-binding domain in centromere protein B, mouse jerky and transposases
      PHA03247
      Location:211 → 405
      PHA03247; large tegument protein UL36; Provisional
      sd00017
      Location:476 → 497
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00020
      Location:440 → 473
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cl21549
      Location:1106 → 1217
      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_063281872.1 → XP_063137942.1  pogo transposable element with ZNF domain isoform X2

      UniProtKB/TrEMBL
      A6K2T0, A6K2T1, D3ZV33

    2. XM_017590895.3 → XP_017446384.1  pogo transposable element with ZNF domain isoform X1

      UniProtKB/TrEMBL
      A0A0G2JY58, A6K2T0
      Conserved Domains (6) summary
      PRK00404
      Location:872 → 929
      tatB; Sec-independent protein translocase subunit TatB
      smart00674
      Location:1018 → 1079
      CENPB; Putative DNA-binding domain in centromere protein B, mouse jerky and transposases
      PHA03247
      Location:264 → 458
      PHA03247; large tegument protein UL36; Provisional
      sd00017
      Location:529 → 550
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00020
      Location:493 → 526
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cl21549
      Location:1159 → 1270
      rve; Integrase core domain

    3. XM_063281871.1 → XP_063137941.1  pogo transposable element with ZNF domain isoform X2

      UniProtKB/TrEMBL
      A6K2T0, A6K2T1, D3ZV33

    4. XM_008761295.4 → XP_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:872 → 929
      tatB; Sec-independent protein translocase subunit TatB
      smart00674
      Location:1018 → 1079
      CENPB; Putative DNA-binding domain in centromere protein B, mouse jerky and transposases
      PHA03247
      Location:264 → 458
      PHA03247; large tegument protein UL36; Provisional
      sd00017
      Location:529 → 550
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00020
      Location:493 → 526
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cl21549
      Location:1159 → 1270
      rve; Integrase core domain

    5. XM_008761297.4 → XP_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:819 → 876
      tatB; Sec-independent protein translocase subunit TatB
      smart00674
      Location:965 → 1026
      CENPB; Putative DNA-binding domain in centromere protein B, mouse jerky and transposases
      PHA03247
      Location:211 → 405
      PHA03247; large tegument protein UL36; Provisional
      sd00017
      Location:476 → 497
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00020
      Location:440 → 473
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cl21549
      Location:1106 → 1217
      rve; Integrase core domain

    6. XM_008761299.4 → XP_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:912 → 973
      CENPB; Putative DNA-binding domain in centromere protein B, mouse jerky and transposases
      sd00017
      Location:423 → 444
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00020
      Location:387 → 420
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam15273
      Location:306 → 343
      NHS; NHS-like
      cl21549
      Location:1047 → 1171
      rve; Integrase core domain

    7. XM_039102346.2 → XP_038958274.1  pogo transposable element with ZNF domain isoform X4

      UniProtKB/TrEMBL
      A0A8I5ZSI0
      Conserved Domains (5) summary
      PRK00404
      Location:713 → 770
      tatB; Sec-independent protein translocase subunit TatB
      smart00674
      Location:859 → 920
      CENPB; Putative DNA-binding domain in centromere protein B, mouse jerky and transposases
      sd00017
      Location:370 → 391
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00020
      Location:334 → 367
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cl21549
      Location:1000 → 1111
      rve; Integrase core domain
    Nucleotide Protein Strain
    Heading Accession and Version

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