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Pogk pogo transposable element derived with KRAB domain [ Rattus norvegicus (Norway rat) ]

Gene ID: 304941, updated on 27-Nov-2024

Summary

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Official Symbol
Pogkprovided by RGD
Official Full Name
pogo transposable element derived with KRAB domainprovided by RGD
Primary source
RGD:1308951
See related
EnsemblRapid:ENSRNOG00000032058 AllianceGenome:RGD:1308951
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. Predicted to be involved in regulation of DNA-templated transcription. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. Orthologous to human POGK (pogo transposable element derived with KRAB domain). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Lung (RPKM 118.1), Adrenal (RPKM 72.6) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Pogk in Genome Data Viewer
Location:
13q23
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 13 NC_086031.1 (81180410..81196326, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 13 NC_051348.1 (78647447..78663363, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 13 NC_005112.4 (84603126..84619042, complement)

Chromosome 13 - NC_086031.1Genomic Context describing neighboring genes Neighboring gene cold shock domain-containing protein E1-like Neighboring gene maelstrom spermatogenic transposon silencer Neighboring gene immunoglobulin-like domain containing receptor 2 Neighboring gene uncharacterized LOC120096307 Neighboring gene uncharacterized LOC120096308 Neighboring gene transcriptional adaptor 1 Neighboring gene flavin-containing monooxygenase 13 Neighboring gene flavin containing dimethylaniline monoxygenase like

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. 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 IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
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
  

General protein information

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Preferred Names
pogo transposable element with KRAB 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_001107194.2 → NP_001100664.2  pogo transposable element with KRAB domain

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000013
    UniProtKB/TrEMBL
    D3ZV46
    Related
    ENSRNOP00000051209.2, ENSRNOT00000045056.5
    Conserved Domains (5) summary
    cd07765
    Location:68 → 105
    KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
    smart00674
    Location:275 → 342
    CENPB; Putative DNA-binding domain in centromere protein B, mouse jerky and transposases
    smart00349
    Location:68 → 123
    KRAB; krueppel associated box
    pfam03184
    Location:414 → 586
    DDE_1; DDE superfamily endonuclease
    pfam09607
    Location:214 → 266
    BrkDBD; Brinker DNA-binding 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_086031.1 Reference GRCr8

    Range
    81180410..81196326 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017598827.3 → XP_017454316.1  pogo transposable element with KRAB domain isoform X1

    UniProtKB/TrEMBL
    A0A8I6A8F7, A6IDK2
    Related
    ENSRNOP00000088020.1, ENSRNOT00000100051.2
    Conserved Domains (5) summary
    cd07765
    Location:56 → 93
    KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
    smart00674
    Location:263 → 330
    CENPB; Putative DNA-binding domain in centromere protein B, mouse jerky and transposases
    smart00349
    Location:56 → 111
    KRAB; krueppel associated box
    pfam03184
    Location:402 → 574
    DDE_1; DDE superfamily endonuclease
    pfam09607
    Location:202 → 254
    BrkDBD; Brinker DNA-binding domain

  2. XM_017598828.3 → XP_017454317.1  pogo transposable element with KRAB domain isoform X2

    Conserved Domains (5) summary
    cd07765
    Location:49 → 86
    KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
    smart00674
    Location:256 → 323
    CENPB; Putative DNA-binding domain in centromere protein B, mouse jerky and transposases
    smart00349
    Location:49 → 104
    KRAB; krueppel associated box
    pfam03184
    Location:395 → 567
    DDE_1; DDE superfamily endonuclease
    pfam09607
    Location:195 → 247
    BrkDBD; Brinker DNA-binding domain

  3. XM_039090789.2 → XP_038946717.1  pogo transposable element with KRAB domain isoform X3

    UniProtKB/TrEMBL
    A6IDK3
    Conserved Domains (3) summary
    smart00674
    Location:122 → 189
    CENPB; Putative DNA-binding domain in centromere protein B, mouse jerky and transposases
    pfam03184
    Location:261 → 433
    DDE_1; DDE superfamily endonuclease
    pfam09607
    Location:61 → 113
    BrkDBD; Brinker DNA-binding domain
Nucleotide Protein Strain
Heading Accession and Version

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