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

    Gene ID: 310658, updated on 2-Oct-2018

    Summary

    Official Symbol
    Pogzprovided by RGD
    Official Full Name
    pogo transposable element derived with ZNF domainprovided by RGD
    Primary source
    RGD:1309980
    See related
    Ensembl:ENSRNOG00000053599
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Expression
    Biased expression in Thymus (RPKM 102.0), Adrenal (RPKM 91.1) and 9 other tissues See more
    Orthologs

    Genomic context

    See Pogz in Genome Data Viewer
    Location:
    2q34
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    106 current Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (195995322..196041500)
    104 previous assembly Rnor_5.0 (GCF_000001895.4) 2 NC_005101.3 (215507126..215534827)

    Chromosome 2 - NC_005101.4Genomic Context describing neighboring genes Neighboring gene cingulin Neighboring gene rCG31129-like Neighboring gene high mobility group protein B1 pseudogene Neighboring gene uncharacterized LOC108350065 Neighboring gene proteasome 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

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    kinetochore assembly IEA
    Inferred from Electronic Annotation
    more info
     
    kinetochore assembly ISO
    Inferred from Sequence Orthology
    more info
     
    mitotic sister chromatid cohesion IEA
    Inferred from Electronic Annotation
    more info
     
    mitotic sister chromatid cohesion ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    cytosol ISO
    Inferred from Sequence Orthology
    more info
     
    nuclear chromatin IEA
    Inferred from Electronic Annotation
    more info
     
    nuclear chromatin ISO
    Inferred from Sequence Orthology
    more info
     
    nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    nucleus ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    pogo transposable element with ZNF domain

    NCBI Reference Sequences (RefSeq)

    RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

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

    Reference Rnor_6.0 Primary Assembly

    Genomic

    1. NC_005101.4 Reference Rnor_6.0 Primary Assembly

      Range
      195995322..196041500
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

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

      UniProtKB/TrEMBL
      A0A0G2JY58
      Conserved Domains (4) summary
      smart00674
      Location:10181079
      CENPB; Putative DNA-binding domain in centromere protein B, mouse jerky and transposases
      sd00017
      Location:529550
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00020
      Location:493526
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cl21549
      Location:11531277
      rve; Integrase core domain
    2. XM_008761295.2XP_008759517.1  pogo transposable element with ZNF domain isoform X1

      UniProtKB/TrEMBL
      A0A0G2JY58
      Related
      ENSRNOP00000070527.1, ENSRNOT00000082849.1
      Conserved Domains (4) summary
      smart00674
      Location:10181079
      CENPB; Putative DNA-binding domain in centromere protein B, mouse jerky and transposases
      sd00017
      Location:529550
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00020
      Location:493526
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cl21549
      Location:11531277
      rve; Integrase core domain
    3. XM_008761296.2XP_008759518.1  pogo transposable element with ZNF domain isoform X2

      See identical proteins and their annotated locations for XP_008759518.1

      Conserved Domains (5) summary
      smart00674
      Location:10091070
      CENPB; Putative DNA-binding domain in centromere protein B, mouse jerky and transposases
      sd00017
      Location:520541
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00020
      Location:484517
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam15273
      Location:403440
      NHS; NHS-like
      cl21549
      Location:11441268
      rve; Integrase core domain
    4. XM_008761299.2XP_008759521.1  pogo transposable element with ZNF domain isoform X5

      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
    5. XM_008761297.2XP_008759519.1  pogo transposable element with ZNF domain isoform X3

      See identical proteins and their annotated locations for XP_008759519.1

      UniProtKB/TrEMBL
      D3ZV33
      Conserved Domains (5) summary
      smart00674
      Location:9651026
      CENPB; Putative DNA-binding domain in centromere protein B, mouse jerky and transposases
      sd00017
      Location:476497
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00020
      Location:440473
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam15273
      Location:359396
      NHS; NHS-like
      cl21549
      Location:11001224
      rve; Integrase core domain
    6. XM_008761298.2XP_008759520.1  pogo transposable element with ZNF domain isoform X4

      Conserved Domains (5) summary
      smart00674
      Location:9561017
      CENPB; Putative DNA-binding domain in centromere protein B, mouse jerky and transposases
      sd00017
      Location:467488
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00020
      Location:431464
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam15273
      Location:350387
      NHS; NHS-like
      cl21549
      Location:10911215
      rve; Integrase core domain
    7. NM_001107693.1NP_001101163.1  

      Conserved Domains (5) summary
      smart00674
      Location:9651026
      CENPB; Putative DNA-binding domain in centromere protein B, mouse jerky and transposases
      sd00017
      Location:476497
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00020
      Location:440473
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam15273
      Location:359396
      NHS; NHS-like
      cl21549
      Location:11001224
      rve; Integrase core domain

    Alternate Rn_Celera

    Genomic

    1. AC_000070.1 Alternate Rn_Celera

      Range
      174957108..174984012
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001107693.1NP_001101163.1  

      Conserved Domains (5) summary
      smart00674
      Location:9651026
      CENPB; Putative DNA-binding domain in centromere protein B, mouse jerky and transposases
      sd00017
      Location:476497
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00020
      Location:440473
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam15273
      Location:359396
      NHS; NHS-like
      cl21549
      Location:11001224
      rve; Integrase core domain

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001107693.1: Suppressed sequence

      Description
      NM_001107693.1: This RefSeq was suppressed temporarily based on the calculation that the encoded protein was shorter than proteins from the putative ortholog from zebrafish: pogzb (GeneID:561483).
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