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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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    See POGK in Genome Data Viewer
    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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