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Pogk pogo transposable element with KRAB domain [ Mus musculus (house mouse) ]

Gene ID: 71592, updated on 26-Sep-2022

Summary

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Official Symbol
Pogkprovided by MGI
Official Full Name
pogo transposable element with KRAB domainprovided by MGI
Primary source
MGI:MGI:1918842
See related
Ensembl:ENSMUSG00000040596 AllianceGenome:MGI:1918842
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
BASS2; mKIAA1513; 9130401E23Rik
Summary
Predicted to enable DNA binding activity. Predicted to be involved in regulation of transcription, DNA-templated. 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, Apr 2022]
Expression
Ubiquitous expression in CNS E11.5 (RPKM 2.2), CNS E14 (RPKM 2.1) and 24 other tissues See more
Orthologs
human all
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Genomic context

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See Pogk in Genome Data Viewer
Location:
1; 1 H2.3
Exon count:
6
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (166217895..166237427, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (166393610..166409853, complement)

Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene maelstrom spermatogenic transposon silencer Neighboring gene immunoglobulin-like domain containing receptor 2 Neighboring gene transcriptional adaptor 1 Neighboring gene ubiquinol-cytochrome c reductase subunit pseudogene Neighboring gene predicted gene, 39694

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Prediction of the coding sequences of mouse homologues of KIAA gene: II. The complete nucleotide sequences of 400 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries. Okazaki N, et al. DNA Res, 2003 Feb 28. PMID 12693553
  2. A systems approach reveals that the myogenesis genome network is regulated by the transcriptional repressor RP58. Yokoyama S, et al. Dev Cell, 2009 Dec. PMID 20059953, Free PMC Article
  3. Normalization and subtraction: two approaches to facilitate gene discovery. Bonaldo MF, et al. Genome Res, 1996 Sep. PMID 8889548
  4. Antisense transcription in the mammalian transcriptome. Katayama S, et al. Science, 2005 Sep 2. PMID 16141073
  5. High-efficiency full-length cDNA cloning. Carninci P, et al. Methods Enzymol, 1999. PMID 10349636

See all (12) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into Functions

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (1) 

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
enables molecular_function ND
No biological Data available
more info
  
enables nucleic acid binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
acts_upstream_of_or_within multicellular organism development IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 

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_001142948.2 → NP_001136420.1  pogo transposable element with KRAB domain isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon in the 5' end. The resulting isoform (2) has a longer and distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AC161807
    Consensus CDS
    CCDS48432.1
    UniProtKB/Swiss-Prot
    Q80TC5
    UniProtKB/TrEMBL
    E9Q3B2, Q6GQW2
    Related
    ENSMUSP00000127395.2, ENSMUST00000169324.8
    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

  2. NM_001405162.1 → NP_001392091.1  pogo transposable element with KRAB domain isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC161807

  3. NM_001405163.1 → NP_001392092.1  pogo transposable element with KRAB domain isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC161807

  4. NM_001405164.1 → NP_001392093.1  pogo transposable element with KRAB domain isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC161807

  5. NM_001405165.1 → NP_001392094.1  pogo transposable element with KRAB domain isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC161807

  6. NM_175170.5 → NP_780379.2  pogo transposable element with KRAB domain isoform 1

    See identical proteins and their annotated locations for NP_780379.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript but encodes the shorter isoform (1).
    Source sequence(s)
    AC161807
    Consensus CDS
    CCDS35762.1
    UniProtKB/Swiss-Prot
    Q80TC5
    UniProtKB/TrEMBL
    A0A0R4J1T0
    Related
    ENSMUSP00000118270.3, ENSMUST00000128861.3
    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

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000067.7 Reference GRCm39 C57BL/6J

    Range
    166217895..166237427 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017312357.3 → XP_017167846.1  pogo transposable element with KRAB domain isoform X1

    Conserved Domains (4) summary
    smart00674
    Location:242 → 309
    CENPB; Putative DNA-binding domain in centromere protein B, mouse jerky and transposases
    pfam09607
    Location:181 → 233
    BrkDBD; Brinker DNA-binding domain
    pfam01352
    Location:68 → 105
    KRAB; KRAB box
    pfam03184
    Location:381 → 553
    DDE_1; DDE superfamily endonuclease

  2. XM_036153687.1 → XP_036009580.1  pogo transposable element with KRAB domain isoform X3

    Conserved Domains (3) summary
    smart00674
    Location:138 → 205
    CENPB; Putative DNA-binding domain in centromere protein B, mouse jerky and transposases
    pfam03184
    Location:277 → 449
    DDE_1; DDE superfamily endonuclease
    pfam09607
    Location:77 → 129
    BrkDBD; Brinker DNA-binding domain

  3. XM_036153686.1 → XP_036009579.1  pogo transposable element with KRAB domain isoform X2

    Conserved Domains (4) summary
    smart00674
    Location:230 → 297
    CENPB; Putative DNA-binding domain in centromere protein B, mouse jerky and transposases
    pfam03184
    Location:369 → 541
    DDE_1; DDE superfamily endonuclease
    pfam01352
    Location:56 → 93
    KRAB; KRAB box
    pfam09607
    Location:169 → 221
    BrkDBD; Brinker DNA-binding domain

  4. XM_011238869.4 → XP_011237171.1  pogo transposable element with KRAB domain isoform X3

    Conserved Domains (3) summary
    smart00674
    Location:138 → 205
    CENPB; Putative DNA-binding domain in centromere protein B, mouse jerky and transposases
    pfam03184
    Location:277 → 449
    DDE_1; DDE superfamily endonuclease
    pfam09607
    Location:77 → 129
    BrkDBD; Brinker DNA-binding domain
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q80TC5.2 GenPept UniProtKB/Swiss-Prot:Q80TC5

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