PBX4 PBX homeobox 4 [Homo sapiens (human)] - Gene

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: mouse all
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Genomic context

Location:: 19p13.11

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (19561713..19618687, complement)
RS_2023_10	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_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Identifying the Potential Roles of PBX4 in Human Cancers Based on Integrative Analysis.
Title: Identifying the Potential Roles of PBX4 in Human Cancers Based on Integrative Analysis.
up-regulation of PREP1 and PBX genes could be implicated in the modulation of the cellular response to chemotherapeutic-induced apoptosis.
Title: MEIS1, PREP1, and PBX4 are differentially expressed in acute lymphoblastic leukemia: association of MEIS1 expression with higher proliferation and chemotherapy resistance.
Sex (male)-specific association of rs16996148 SNP in the NCAN/CILP2/PBX4 and serum lipid levels is observed both the Mulao and Han ethnic groups.
Title: Sex-specific association of rs16996148 SNP in the NCAN/CILP2/PBX4 and serum lipid levels in the Mulao and Han populations.
Observational study of gene-disease association. (HuGE Navigator)
Title: Pharmacogenetic analysis of lipid responses to rosuvastatin in Chinese patients.
Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
Title: Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans.

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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

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

PBX4_2885 (e-PCR)
- UniSTS:462385

SHGC-58358 (e-PCR)
- UniSTS:41597

NoName (e-PCR)
- UniSTS:480898

NoName (e-PCR)
- UniSTS:485630

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
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	ISS Inferred from Sequence or Structural Similarity more info	PubMed

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 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

Component	Evidence Code	Pubs
located_in XY body	IEA Inferred from Electronic Annotation more info
part_of chromatin	ISA Inferred from Sequence Alignment more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IC Inferred by Curator more info	PubMed

General protein information

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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)

NM_025245.3 → NP_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

A5D8Y0, B3KUK9, Q9BYU1

Related

ENSP00000251203.5, ENST00000251203.14

Conserved Domains (2) summary

cd00086
Location:211 → 272

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:18 → 209

PBC; PBC domain

RNA

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: 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

NC_000019.10 Reference GRCh38.p14 Primary Assembly

Range

19561713..19618687 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047439471.1 → XP_047295427.1 pre-B-cell leukemia transcription factor 4 isoform X2
XM_006722911.4 → XP_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:125 → 186

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 → 123

PBC; PBC domain
XM_011528320.4 → XP_011526622.1 pre-B-cell leukemia transcription factor 4 isoform X1

Conserved Domains (2) summary

cd00086
Location:228 → 289

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:18 → 226

PBC; PBC domain
XM_011528322.2 → XP_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:125 → 186

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 → 123

PBC; PBC domain
XM_017027329.3 → XP_016882818.1 pre-B-cell leukemia transcription factor 4 isoform X4
XM_047439472.1 → XP_047295428.1 pre-B-cell leukemia transcription factor 4 isoform X3

Alternate T2T-CHM13v2.0

Genomic

NC_060943.1 Alternate T2T-CHM13v2.0

Range

19699203..19756196 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054322237.1 → XP_054178212.1 pre-B-cell leukemia transcription factor 4 isoform X2
XM_054322236.1 → XP_054178211.1 pre-B-cell leukemia transcription factor 4 isoform X2
XM_054322234.1 → XP_054178209.1 pre-B-cell leukemia transcription factor 4 isoform X1
XM_054322235.1 → XP_054178210.1 pre-B-cell leukemia transcription factor 4 isoform X2
XM_054322239.1 → XP_054178214.1 pre-B-cell leukemia transcription factor 4 isoform X4
XM_054322238.1 → XP_054178213.1 pre-B-cell leukemia transcription factor 4 isoform X3