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PBX4 PBX homeobox 4 [ Homo sapiens (human) ]

Gene ID: 80714, updated on 5-Aug-2022

Summary

Official Symbol
PBX4provided by HGNC
Official Full Name
PBX homeobox 4provided by HGNC
Primary source
HGNC:HGNC:13403
See related
Ensembl:ENSG00000105717 MIM:608127; AllianceGenome:HGNC:13403
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This gene encodes a member of the pre-B cell leukemia transcription factor family. These proteins are homeobox proteins that play critical roles in embryonic development and cellular differentiation both as Hox cofactors and through Hox-independent pathways. The encoded protein contains a homeobox DNA-binding domain, but specific functions of the protein have not been determined. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, May 2011]
Expression
Broad expression in thyroid (RPKM 3.9), testis (RPKM 2.5) and 18 other tissues See more
Orthologs
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Genomic context

See PBX4 in Genome Data Viewer
Location:
19p13.11
Exon count:
9
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (19561713..19618687, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (19699203..19756196, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (19672522..19729496, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene YjeF N-terminal domain containing 3 Neighboring gene Sharpr-MPRA regulatory region 4095 Neighboring gene cartilage intermediate layer protein 2 Neighboring gene PHD finger protein 5C pseudogene Neighboring gene lysophosphatidic acid receptor 2 Neighboring gene GEM interacting protein

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?

Phenotypes

EBI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci.
EBI GWAS Catalog
Biological, clinical and population relevance of 95 loci for blood lipids.
EBI GWAS Catalog
Common variants at 30 loci contribute to polygenic dyslipidemia.
EBI GWAS Catalog
Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
EBI GWAS Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS Catalog
Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans.
EBI GWAS Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in animal organ morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in brain development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in embryonic organ development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in eye development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in neuron development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in positive regulation of DNA-templated transcription IC
Inferred by Curator
more info
PubMed 
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 XY body IEA
Inferred from Electronic Annotation
more info
 
located_in chromatin ISA
Inferred from Sequence Alignment
more info
 
located_in nucleus IC
Inferred by Curator
more info
PubMed 

General protein information

Preferred Names
pre-B-cell leukemia transcription factor 4
Names
homeobox protein PBX4
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_025245.3NP_079521.1  pre-B-cell leukemia transcription factor 4

    See identical proteins and their annotated locations for NP_079521.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and is protein-coding.
    Source sequence(s)
    BC141859
    Consensus CDS
    CCDS12406.1
    UniProtKB/Swiss-Prot
    B3KUK9, Q9BYU1
    Related
    ENSP00000251203.5, ENST00000251203.14
    Conserved Domains (2) summary
    cd00086
    Location:211272
    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:18209
    PBC; PBC domain

RNA

  1. NR_038198.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK097427, BC143588, CK300861
    Related
    ENST00000557978.6

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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    19561713..19618687 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047439471.1XP_047295427.1  pre-B-cell leukemia transcription factor 4 isoform X2

  2. XM_006722911.4XP_006722974.1  pre-B-cell leukemia transcription factor 4 isoform X2

    See identical proteins and their annotated locations for XP_006722974.1

    Conserved Domains (2) summary
    cd00086
    Location:125186
    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:1123
    PBC; PBC domain
  3. XM_011528320.4XP_011526622.1  pre-B-cell leukemia transcription factor 4 isoform X1

    Conserved Domains (2) summary
    cd00086
    Location:228289
    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:18226
    PBC; PBC domain
  4. XM_011528322.2XP_011526624.1  pre-B-cell leukemia transcription factor 4 isoform X2

    See identical proteins and their annotated locations for XP_011526624.1

    Conserved Domains (2) summary
    cd00086
    Location:125186
    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:1123
    PBC; PBC domain
  5. XM_017027329.3XP_016882818.1  pre-B-cell leukemia transcription factor 4 isoform X4

  6. XM_047439472.1XP_047295428.1  pre-B-cell leukemia transcription factor 4 isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    19699203..19756196 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)