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

Gene ID: 267002, updated on 3-Apr-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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Location:
1q44
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (248872851..248930191)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (248311348..248368818)
105.20220307 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: 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 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. Architecture of the human interactome defines protein communities and disease networks. Huttlin EL, et al. Nature, 2017 May 25. PMID 28514442, Free PMC Article
  4. 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
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

See all (6) 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)

Genotypes

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_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
    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

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

  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

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

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

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