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Pbx4 PBX homeobox 4 [ Rattus norvegicus (Norway rat) ]

Gene ID: 361131, updated on 17-Aug-2024

Summary

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Official Symbol
Pbx4provided by RGD
Official Full Name
PBX homeobox 4provided by RGD
Primary source
RGD:1305100
See related
EnsemblRapid:ENSRNOG00000010736 AllianceGenome:RGD:1305100
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
Edg4
Summary
Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in animal organ development; neuron development; and regulation of transcription by RNA polymerase II. Predicted to be located in XY body. Orthologous to human PBX4 (PBX homeobox 4). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Testes (RPKM 43.7), Adrenal (RPKM 38.9) and 3 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Pbx4 in Genome Data Viewer
Location:
16p14
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 16 NC_086034.1 (19588998..19624016, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 16 NC_051351.1 (19555089..19590054, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 16 NC_005115.4 (21303117..21338771, complement)

Chromosome 16 - NC_086034.1Genomic Context describing neighboring genes Neighboring gene YjeF N-terminal domain containing 3 Neighboring gene cartilage intermediate layer protein 2 Neighboring gene lysophosphatidic acid receptor 2 Neighboring gene Gem-interacting protein

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. In vivo analysis of developmentally and evolutionarily dynamic protein-DNA interactions regulating transcription of the Pgk2 gene during mammalian spermatogenesis. Yoshioka H, et al. Mol Cell Biol, 2007 Nov. PMID 17875925, Free PMC Article
  2. Pbx4, a new Pbx family member on mouse chromosome 8, is expressed during spermatogenesis. Wagner K, et al. Mech Dev, 2001 May. PMID 11335119
  3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

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Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
involved_in animal organ morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in brain development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in embryonic organ development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in eye development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in neuron development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in XY body ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
pre-B-cell leukemia transcription factor 4
Names
endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor 4
pre-B-cell leukemia homeobox 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_001108399.1 → NP_001101869.1  pre-B-cell leukemia transcription factor 4

    See identical proteins and their annotated locations for NP_001101869.1

    Status: PROVISIONAL

    Source sequence(s)
    CH474031
    UniProtKB/TrEMBL
    A6KAA9, D4AA41
    Related
    ENSRNOP00000014265.5, ENSRNOT00000014265.7
    Conserved Domains (2) summary
    cd00086
    Location:217 → 277
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
    pfam03792
    Location:25 → 215
    PBC; PBC domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

  1. NC_086034.1 Reference GRCr8

    Range
    19588998..19624016 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006252909.5 → XP_006252971.1  pre-B-cell leukemia transcription factor 4 isoform X2

    See identical proteins and their annotated locations for XP_006252971.1

    Conserved Domains (2) summary
    cd00086
    Location:161 → 221
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
    pfam03792
    Location:1 → 159
    PBC; PBC domain

  2. XM_063275511.1 → XP_063131581.1  pre-B-cell leukemia transcription factor 4 isoform X3

    UniProtKB/TrEMBL
    A6KAB0

  3. XM_063275510.1 → XP_063131580.1  pre-B-cell leukemia transcription factor 4 isoform X2

  4. XM_063275509.1 → XP_063131579.1  pre-B-cell leukemia transcription factor 4 isoform X1

Nucleotide Protein Strain
Heading Accession and Version

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