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    PGBD2 piggyBac transposable element derived 2 [ Homo sapiens (human) ]

    Gene ID: 267002, updated on 10-Dec-2024

    Summary

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    Official Symbol
    PGBD2provided by HGNC
    Official Full Name
    piggyBac transposable element derived 2provided by HGNC
    Primary source
    HGNC:HGNC:19399
    See related
    Ensembl:ENSG00000185220 AllianceGenome:HGNC:19399
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    The piggyBac family of proteins, found in diverse animals, are transposases related to the transposase of the canonical piggyBac transposon from the moth, Trichoplusia ni. This family also includes genes in several genomes, including human, that appear to have been derived from the piggyBac transposons. This gene belongs to the subfamily of piggyBac transposable element derived (PGBD) genes. The PGBD proteins appear to be novel, with no obvious relationship to other transposases, or other known protein families. The exact function of this gene is not known. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in testis (RPKM 3.5), thyroid (RPKM 2.7) and 25 other tissues See more
    Orthologs
    all
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    Genomic context

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    See PGBD2 in Genome Data Viewer
    Location:
    1q44
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (248872851..248930191)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (248311348..248368818)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (249200434..249213345)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2882 Neighboring gene zinc finger protein 692 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2883 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2884 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2051 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2885 Neighboring gene ZNF692 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2886 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2887 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:249166437-249167278 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:249167279-249168120 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2053 Neighboring gene tRNA-Leu (anticodon CAA) 4-1 Neighboring gene tRNA-Glu (anticodon CTC) 2-1 Neighboring gene CRISPRi-validated cis-regulatory element chr1.12988 Neighboring gene CRISPRi-validated cis-regulatory element chr1.12989 Neighboring gene Sharpr-MPRA regulatory region 4184 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:249190071-249190253 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:249200064-249200985 Neighboring gene RNA, U6 small nuclear 1205, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2056 Neighboring gene ribosomal protein L23a pseudogene 25

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. A sequence-ready map of the human chromosome 1q telomere. Xiang Z, et al. Genomics, 2001 Feb 15. PMID 11247672
    2. Molecular evolutionary analysis of the widespread piggyBac transposon family and related "domesticated" sequences. Sarkar A, et al. Mol Genet Genomics, 2003 Nov. PMID 12955498
    3. Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets. Mihalič F, et al. Nat Commun, 2023 Sep 13. PMID 37704626, Free PMC Article
    4. Architecture of the human interactome defines protein communities and disease networks. Huttlin EL, et al. Nature, 2017 May 25. PMID 28514442, Free PMC Article
    5. Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Huttlin EL, et al. Cell, 2021 May 27. PMID 33961781, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    piggyBac transposable element-derived protein 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_001017434.2 → NP_001017434.1  piggyBac transposable element-derived protein 2 isoform b

      See identical proteins and their annotated locations for NP_001017434.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a.
      Source sequence(s)
      AI038307, AK123219, AL672183
      Consensus CDS
      CCDS31129.1
      Related
      ENSP00000355424.3, ENST00000355360.8
      Conserved Domains (1) summary
      pfam13843
      Location:1 → 248
      DDE_Tnp_1_7; Transposase IS4

    2. NM_170725.3 → NP_733843.1  piggyBac transposable element-derived protein 2 isoform a

      See identical proteins and their annotated locations for NP_733843.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
      Source sequence(s)
      AI038307, AK123219, AL672183, BC063785
      Consensus CDS
      CCDS31128.1
      UniProtKB/Swiss-Prot
      B3KVR8, Q6MZF8, Q6P3X8
      UniProtKB/TrEMBL
      B4DPA1
      Related
      ENSP00000331643.5, ENST00000329291.6
      Conserved Domains (1) summary
      pfam13843
      Location:140 → 499
      DDE_Tnp_1_7; Transposase IS4

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    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
      248872851..248930191
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011544161.4 → XP_011542463.1  piggyBac transposable element-derived protein 2 isoform X1

      See identical proteins and their annotated locations for XP_011542463.1

      UniProtKB/Swiss-Prot
      B3KVR8, Q6MZF8, Q6P3X8
      UniProtKB/TrEMBL
      B4DPA1
      Conserved Domains (1) summary
      pfam13843
      Location:140 → 499
      DDE_Tnp_1_7; Transposase IS4

    2. XM_047417845.1 → XP_047273801.1  piggyBac transposable element-derived protein 2 isoform X4

    3. XM_047417849.1 → XP_047273805.1  piggyBac transposable element-derived protein 2 isoform X5

    4. XM_011544159.3 → XP_011542461.1  piggyBac transposable element-derived protein 2 isoform X1

      See identical proteins and their annotated locations for XP_011542461.1

      UniProtKB/Swiss-Prot
      B3KVR8, Q6MZF8, Q6P3X8
      UniProtKB/TrEMBL
      B4DPA1
      Conserved Domains (1) summary
      pfam13843
      Location:140 → 499
      DDE_Tnp_1_7; Transposase IS4

    5. XM_047417844.1 → XP_047273800.1  piggyBac transposable element-derived protein 2 isoform X3

    6. XM_047417842.1 → XP_047273798.1  piggyBac transposable element-derived protein 2 isoform X2

      UniProtKB/TrEMBL
      B4DPA1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      248311348..248368818
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054335973.1 → XP_054191948.1  piggyBac transposable element-derived protein 2 isoform X1

      UniProtKB/Swiss-Prot
      B3KVR8, Q6MZF8, Q6P3X8
      UniProtKB/TrEMBL
      B4DPA1

    2. XM_054335975.1 → XP_054191950.1  piggyBac transposable element-derived protein 2 isoform X4

    3. XM_054335976.1 → XP_054191951.1  piggyBac transposable element-derived protein 2 isoform X5

    4. XM_054335972.1 → XP_054191947.1  piggyBac transposable element-derived protein 2 isoform X1

      UniProtKB/Swiss-Prot
      B3KVR8, Q6MZF8, Q6P3X8
      UniProtKB/TrEMBL
      B4DPA1

    5. XM_054335974.1 → XP_054191949.1  piggyBac transposable element-derived protein 2 isoform X2

      UniProtKB/TrEMBL
      B4DPA1
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6P3X8.1 GenPept UniProtKB/Swiss-Prot:Q6P3X8

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