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POGK pogo transposable element derived with KRAB domain [ Homo sapiens (human) ]

Gene ID: 57645, updated on 3-Apr-2024

Summary

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Official Symbol
POGKprovided by HGNC
Official Full Name
pogo transposable element derived with KRAB domainprovided by HGNC
Primary source
HGNC:HGNC:18800
See related
Ensembl:ENSG00000143157 MIM:620039; AllianceGenome:HGNC:18800
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
BASS2; KRBOX2; LST003
Summary
The exact function of the protein encoded by this gene is not known. However, this gene product contains a KRAB domain (which is involved in protein-protein interactions) at the N-terminus, and a transposase domain at the C-terminus, suggesting that it may belong to the family of DNA-mediated transposons in human. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in brain (RPKM 8.9), lung (RPKM 8.9) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
1q24.1
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (166839475..166856359)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (166185193..166202191)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (166808712..166825596)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene flavin containing dimethylaniline monoxygenase 11, pseudogene Neighboring gene MPRA-validated peak440 silencer Neighboring gene calponin 2 pseudogene 10 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1511 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1512 Neighboring gene transcriptional adaptor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1513 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1514 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2027 Neighboring gene deoxyuridine triphosphatase pseudogene 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:166852951-166853452 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:166853453-166853952 Neighboring gene uncharacterized LOC124904450

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. A selection system for human apoptosis inhibitors using yeast. Greenhalf W, et al. Yeast, 1999 Sep 30. PMID 10509013
  2. Genomic predictors of combat stress vulnerability and resilience in U.S. Marines: A genome-wide association study across multiple ancestries implicates PRTFDC1 as a potential PTSD gene. Nievergelt CM, et al. Psychoneuroendocrinology, 2015 Jan. PMID 25456346
  3. Pre-B-cell leukemia homeobox 1 (PBX1) shows functional and possible genetic association with bone mineral density variation. Cheung CL, et al. Hum Mol Genet, 2009 Feb 15. PMID 19064610
  4. Follow-up of a major linkage peak on chromosome 1 reveals suggestive QTLs associated with essential hypertension: GenNet study. Ehret GB, et al. Eur J Hum Genet, 2009 Dec. PMID 19536175, Free PMC Article
  5. Prediction of the coding sequences of unidentified human genes. XVII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. Nagase T, et al. DNA Res, 2000 Apr 28. PMID 10819331

See all (28) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Observational study of gene-disease association. (HuGE Navigator)
    Title: Follow-up of a major linkage peak on chromosome 1 reveals suggestive QTLs associated with essential hypertension: GenNet study.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genomic predictors of combat stress vulnerability and resilience in U.S. Marines: A genome-wide association study across multiple ancestries implicates PRTFDC1 as a potential PTSD gene.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA1513, KIAA15131

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
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 IDA
Inferred from Direct Assay
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
Names
KRAB box domain containing 2

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_001314014.2 → NP_001300943.1  pogo transposable element with KRAB domain isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and lacks two consecutive exons in the coding region which results in the use of an alternate start codon compared to variant 1. The encoded isoform (2) is shorter and has a distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AK293946, AL008639, DB049597
    UniProtKB/TrEMBL
    B4DF62
    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

  2. NM_017542.5 → NP_060012.3  pogo transposable element with KRAB domain isoform 1

    See identical proteins and their annotated locations for NP_060012.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AB040946, AL008639, DB049597
    Consensus CDS
    CCDS1254.1
    UniProtKB/Swiss-Prot
    Q5TIJ1, Q8TE07, Q9P215
    UniProtKB/TrEMBL
    B4DS22
    Related
    ENSP00000356850.4, ENST00000367876.9
    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 → 107
    KRAB; krueppel associated box
    pfam03184
    Location:395 → 567
    DDE_1; DDE superfamily endonuclease
    pfam09607
    Location:195 → 247
    BrkDBD; Brinker DNA-binding domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    166839475..166856359
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005245370.5 → XP_005245427.1  pogo transposable element with KRAB domain isoform X1

    See identical proteins and their annotated locations for XP_005245427.1

    UniProtKB/Swiss-Prot
    Q5TIJ1, Q8TE07, Q9P215
    UniProtKB/TrEMBL
    B4DS22
    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 → 107
    KRAB; krueppel associated box
    pfam03184
    Location:395 → 567
    DDE_1; DDE superfamily endonuclease
    pfam09607
    Location:195 → 247
    BrkDBD; Brinker DNA-binding domain

  2. XM_017001915.2 → XP_016857404.1  pogo transposable element with KRAB domain isoform X3

    UniProtKB/TrEMBL
    B4DF62
    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_011509815.3 → XP_011508117.1  pogo transposable element with KRAB domain isoform X2

    UniProtKB/TrEMBL
    B4DS22
    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 → 107
    KRAB; krueppel associated box
    pfam03184
    Location:386 → 549
    DDE_1; DDE superfamily endonuclease
    pfam09607
    Location:195 → 247
    BrkDBD; Brinker DNA-binding domain

  4. XM_047426196.1 → XP_047282152.1  pogo transposable element with KRAB domain isoform X1

    UniProtKB/Swiss-Prot
    Q5TIJ1, Q8TE07, Q9P215

  5. XM_017001914.3 → XP_016857403.1  pogo transposable element with KRAB domain isoform X1

    UniProtKB/Swiss-Prot
    Q5TIJ1, Q8TE07, Q9P215
    UniProtKB/TrEMBL
    B4DS22
    Related
    ENSP00000356849.1, ENST00000367875.1
    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 → 107
    KRAB; krueppel associated box
    pfam03184
    Location:395 → 567
    DDE_1; DDE superfamily endonuclease
    pfam09607
    Location:195 → 247
    BrkDBD; Brinker DNA-binding domain

  6. XM_011509814.3 → XP_011508116.1  pogo transposable element with KRAB domain isoform X1

    See identical proteins and their annotated locations for XP_011508116.1

    UniProtKB/Swiss-Prot
    Q5TIJ1, Q8TE07, Q9P215
    UniProtKB/TrEMBL
    B4DS22
    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 → 107
    KRAB; krueppel associated box
    pfam03184
    Location:395 → 567
    DDE_1; DDE superfamily endonuclease
    pfam09607
    Location:195 → 247
    BrkDBD; Brinker DNA-binding domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    166185193..166202191
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054337893.1 → XP_054193868.1  pogo transposable element with KRAB domain isoform X1

    UniProtKB/Swiss-Prot
    Q5TIJ1, Q8TE07, Q9P215

  2. XM_054337895.1 → XP_054193870.1  pogo transposable element with KRAB domain isoform X1

    UniProtKB/Swiss-Prot
    Q5TIJ1, Q8TE07, Q9P215

  3. XM_054337898.1 → XP_054193873.1  pogo transposable element with KRAB domain isoform X3

  4. XM_054337897.1 → XP_054193872.1  pogo transposable element with KRAB domain isoform X2

  5. XM_054337896.1 → XP_054193871.1  pogo transposable element with KRAB domain isoform X1

    UniProtKB/Swiss-Prot
    Q5TIJ1, Q8TE07, Q9P215

  6. XM_054337894.1 → XP_054193869.1  pogo transposable element with KRAB domain isoform X1

    UniProtKB/Swiss-Prot
    Q5TIJ1, Q8TE07, Q9P215
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9P215.2 GenPept UniProtKB/Swiss-Prot:Q9P215

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