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    PGBD1 piggyBac transposable element derived 1 [ Homo sapiens (human) ]

    Gene ID: 84547, updated on 28-Oct-2024

    Summary

    Official Symbol
    PGBD1provided by HGNC
    Official Full Name
    piggyBac transposable element derived 1provided by HGNC
    Primary source
    HGNC:HGNC:19398
    See related
    Ensembl:ENSG00000137338 AllianceGenome:HGNC:19398
    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
    Also known as
    SCAND4; HUCEP-4; dJ874C20.4
    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. This gene product is specifically expressed in the brain, however, its exact function is not known. Alternative splicing results in multiple transcript variants encoding the same protein.[provided by RefSeq, May 2010]
    Expression
    Ubiquitous expression in brain (RPKM 2.1), endometrium (RPKM 1.7) and 25 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See PGBD1 in Genome Data Viewer
    Location:
    6p22.1
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (28281572..28302549)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (28153313..28174278)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (28249349..28270326)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17043 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24352 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:28234963-28235527 Neighboring gene NFKB activating protein like Neighboring gene zinc finger and SCAN domain containing 26 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17044 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:28249721-28249897 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:28251848-28252055 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:28278749-28279250 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:28279251-28279750 Neighboring gene SMIM15 pseudogene 2 Neighboring gene zinc finger and SCAN domain containing 31 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24353 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24354 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:28321865-28322364 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24355 Neighboring gene zinc finger with KRAB and SCAN domains 3

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Process Evidence Code Pubs
    involved_in regulation of transcription by RNA polymerase II NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    piggyBac transposable element-derived protein 1
    Names
    cerebral protein 4

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001184743.2NP_001171672.1  piggyBac transposable element-derived protein 1

      See identical proteins and their annotated locations for NP_001171672.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AL021997
      Consensus CDS
      CCDS4648.1
      UniProtKB/Swiss-Prot
      Q53F43, Q6NTF5, Q8WWS4, Q96JS3
      UniProtKB/TrEMBL
      A8K5B3
      Related
      ENSP00000259883.3, ENST00000259883.3
      Conserved Domains (2) summary
      smart00431
      Location:40142
      SCAN; leucine rich region
      pfam13843
      Location:418775
      DDE_Tnp_1_7; Transposase IS4
    2. NM_001386059.1NP_001372988.1  piggyBac transposable element-derived protein 1

      Status: VALIDATED

      Source sequence(s)
      AL021997
      Consensus CDS
      CCDS4648.1
      UniProtKB/Swiss-Prot
      Q53F43, Q6NTF5, Q8WWS4, Q96JS3
      UniProtKB/TrEMBL
      A8K5B3
      Conserved Domains (2) summary
      smart00431
      Location:40142
      SCAN; leucine rich region
      pfam13843
      Location:418775
      DDE_Tnp_1_7; Transposase IS4
    3. NM_032507.4NP_115896.1  piggyBac transposable element-derived protein 1

      See identical proteins and their annotated locations for NP_115896.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AL021997
      Consensus CDS
      CCDS4648.1
      UniProtKB/Swiss-Prot
      Q53F43, Q6NTF5, Q8WWS4, Q96JS3
      UniProtKB/TrEMBL
      A8K5B3
      Related
      ENSP00000506997.1, ENST00000682144.1
      Conserved Domains (2) summary
      smart00431
      Location:40142
      SCAN; leucine rich region
      pfam13843
      Location:418775
      DDE_Tnp_1_7; Transposase IS4

    RNA

    1. NR_169855.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL021997
    2. NR_169856.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL021997
    3. NR_169857.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL021997
    4. NR_169858.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL021997
    5. NR_169859.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL021997
    6. NR_169860.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL021997

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      28281572..28302549
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      28153313..28174278
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)