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

Gene ID: 310658, updated on 2-Nov-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 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
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 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 nucleic acid 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
  
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
  
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
    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
    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
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