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

Gene ID: 84547, updated on 26-Oct-2022

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
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Genomic context

See PGBD1 in Genome Data Viewer
Location:
6p22.1
Exon count:
8
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (28281572..28302549)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (28153313..28174278)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (28249349..28270326)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene NFKB activating protein like Neighboring gene zinc finger and SCAN domain containing 26 Neighboring gene SMIM15 pseudogene 2 Neighboring gene zinc finger and SCAN domain containing 31 Neighboring gene zinc finger with KRAB and SCAN domains 3

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
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 scavenger receptor activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in endocytosis IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
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)

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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_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
    Q8WWS4, Q96JS3
    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
    Q8WWS4
    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
    Q8WWS4, Q96JS3
    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: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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)