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    PBX3 PBX homeobox 3 [ Homo sapiens (human) ]

    Gene ID: 5090, updated on 2-Nov-2024

    Summary

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    Official Symbol
    PBX3provided by HGNC
    Official Full Name
    PBX homeobox 3provided by HGNC
    Primary source
    HGNC:HGNC:8634
    See related
    Ensembl:ENSG00000167081 MIM:176312; AllianceGenome:HGNC:8634
    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
    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 several processes, including eye development; nervous system development; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including adult locomotory behavior; dorsal spinal cord development; and regulation of respiratory gaseous exchange by nervous system process. Predicted to be located in chromatin. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Biomarker of esophagus squamous cell carcinoma. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in adrenal (RPKM 28.9), ovary (RPKM 26.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PBX3 in Genome Data Viewer
    Location:
    9q33.3
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (125747373..125967377)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (137947324..138172756)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (128509652..128729656)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene MAPK associated protein 1 Neighboring gene uncharacterized LOC124902358 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:128458383-128459122 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20278 Neighboring gene Sharpr-MPRA regulatory region 13831 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29014 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20280 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20283 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20282 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20281 Neighboring gene VISTA enhancer hs1030 Neighboring gene VISTA enhancer hs818 Neighboring gene VISTA enhancer hs1102 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:128540192-128540692 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:128541469-128542156 Neighboring gene PBX3 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29015 Neighboring gene uncharacterized LOC124902271 Neighboring gene Sharpr-MPRA regulatory region 15662 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:128640594-128641187 Neighboring gene VISTA enhancer hs1017 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20284 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:128713417-128713932 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:128750389-128751195 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:128751196-128752001 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:128761012-128761512 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:128761513-128762013 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:128786371-128786870 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:128792624-128793228 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:128793229-128793833 Neighboring gene uncharacterized LOC105376273 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:128821617-128822118 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:128822119-128822618 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:128830736-128831236 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:128836813-128837313 Neighboring gene VISTA enhancer hs987 Neighboring gene uncharacterized LOC105376274 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:128908419-128909393

    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 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. PBX3 as a biomarker for the early diagnosis and prediction of prognosis of glioma. Pan C, et al. PLoS One, 2024. PMID 38324550, Free PMC Article
    2. Regulation of PBX3 expression by androgen and Let-7d in prostate cancer. Ramberg H, et al. Mol Cancer, 2011 May 6. PMID 21548940, Free PMC Article
    3. PBX3 is overexpressed in gastric cancer and regulates cell proliferation. Li Y, et al. Tumour Biol, 2014 May. PMID 24375258
    4. PBX3 is a putative biomarker of aggressive prostate cancer. Ramberg H, et al. Int J Cancer, 2016 Oct 15. PMID 27273830
    5. PBX3 is essential for leukemia stem cell maintenance in MLL-rearranged leukemia. Guo H, et al. Int J Cancer, 2017 Jul 15. PMID 28411381

    See all (86) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Exosomal circKIAA1797 Regulates Cell Progression and Glycolysis by Targeting miR-4429/PBX3 Pathway in Gastric Cancer.
      Title: Exosomal circKIAA1797 Regulates Cell Progression and Glycolysis by Targeting miR-4429/PBX3 Pathway in Gastric Cancer.
    2. Low expression of miR-182 caused by DNA hypermethylation accelerates acute lymphocyte leukemia development by targeting PBX3 and BCL2: miR-182 promoter methylation is a predictive marker for hypomethylation agents + BCL2 inhibitor venetoclax.
      Title: Low expression of miR-182 caused by DNA hypermethylation accelerates acute lymphocyte leukemia development by targeting PBX3 and BCL2: miR-182 promoter methylation is a predictive marker for hypomethylation agents + BCL2 inhibitor venetoclax.
    3. PBX3 as a biomarker for the early diagnosis and prediction of prognosis of glioma.
      Title: PBX3 as a biomarker for the early diagnosis and prediction of prognosis of glioma.
    4. LncRNA LINC00885 promotes bladder cancer progression by targeting the miR-98-5p/PBX3 axis.
      Title: LncRNA LINC00885 promotes bladder cancer progression by targeting the miR-98-5p/PBX3 axis.
    5. USF1-ATRAP-PBX3 Axis Promote Breast Cancer Glycolysis and Malignant Phenotype by Activating AKT/mTOR Signaling.
      Title: USF1-ATRAP-PBX3 Axis Promote Breast Cancer Glycolysis and Malignant Phenotype by Activating AKT/mTOR Signaling.
    6. Long non-coding RNA DSCAM-AS1 promotes pancreatic cancer progression via regulating the miR-136-5p/PBX3 axis.
      Title: Long non-coding RNA DSCAM-AS1 promotes pancreatic cancer progression via regulating the miR-136-5p/PBX3 axis.
    7. Circular RNA circ_0032962 promotes trophoblast cell progression as ceRNA to target PBX3 via sponging miR-326 in preeclampsia.
      Title: Circular RNA circ_0032962 promotes trophoblast cell progression as ceRNA to target PBX3 via sponging miR-326 in preeclampsia.
    8. The transcription factor PBX3 promotes tumor cell growth through transcriptional suppression of the tumor suppressor p53.
      Title: The transcription factor PBX3 promotes tumor cell growth through transcriptional suppression of the tumor suppressor p53.
    9. SNHG10/DDX54/PBX3 Feedback Loop Contributes to Gastric Cancer Cell Growth.
      Title: SNHG10/DDX54/PBX3 Feedback Loop Contributes to Gastric Cancer Cell Growth.
    10. MiR-320a inhibits malignant phenotype of melanoma cells via targeting PBX3.
      Title: MiR-320a inhibits malignant phenotype of melanoma cells via targeting PBX3.
    Submit: New GeneRIF Correction See all GeneRIFs (47)

    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
    Genome-wide association study for biomarker identification of Rapamycin and Everolimus using a lymphoblastoid cell line system.
    EBI GWAS Catalog

    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

    Pathways from PubChem

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    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 DNA-binding transcription activator activity, RNA polymerase II-specific IEA
    Inferred from Electronic Annotation
    more info
    		  
    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
    		  
    Process Evidence Code Pubs
    involved_in adult locomotory behavior IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in animal organ morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in anterior compartment pattern formation TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in brain development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in dorsal spinal cord development IEA
    Inferred from Electronic Annotation
    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 transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in posterior compartment specification TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of respiratory gaseous exchange by nervous system process 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
    		  
    involved_in respiratory gaseous exchange by respiratory system IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of transcription regulator complex IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    pre-B-cell leukemia transcription factor 3
    Names
    homeobox protein PBX3
    pre-B-cell leukemia homeobox 3

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001134778.2 → NP_001128250.1  pre-B-cell leukemia transcription factor 3 isoform 2

      See identical proteins and their annotated locations for NP_001128250.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) utilizes an alternate first exon and 5'UTR; thus, the first likely translation initiation site corresponds to an internal methionine in variant 1. The predicted protein (isoform 2) is N-terminally truncated compared to isoform 1 and is not predicted to have a signal peptide.
      Source sequence(s)
      AK309713, AL358074, BC094883, CD675622, CN372830, CN372832
      Consensus CDS
      CCDS48021.1
      UniProtKB/TrEMBL
      Q96AL5
      Related
      ENSP00000387456.2, ENST00000447726.6
      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. NM_001330782.2 → NP_001317711.1  pre-B-cell leukemia transcription factor 3 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL358074, AL445186, BC094883, BP340711, DA692140
      Consensus CDS
      CCDS83416.1
      UniProtKB/Swiss-Prot
      P40426
      Related
      ENSP00000341990.5, ENST00000342287.9
      Conserved Domains (2) summary
      cd00086
      Location:236 → 296
      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:43 → 234
      PBC; PBC domain

    3. NM_001411009.1 → NP_001397938.1  pre-B-cell leukemia transcription factor 3 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL358074, AL445186
      Consensus CDS
      CCDS94482.1
      UniProtKB/TrEMBL
      Q5JS98
      Related
      ENSP00000362586.4, ENST00000373487.8

    4. NM_006195.6 → NP_006186.1  pre-B-cell leukemia transcription factor 3 isoform 1

      See identical proteins and their annotated locations for NP_006186.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) utilizes an alternate first exon containing a predicted translation initiation site with a strong Kozak signal; the resulting protein isoform (1) is predicted to have a signal peptide.
      Source sequence(s)
      BC016977, BC094883, X59841
      Consensus CDS
      CCDS6865.1
      UniProtKB/Swiss-Prot
      E9PB27, P40426, Q5JSA0, Q5JSA1, Q5VXL3, Q96PF9, Q96PG0
      UniProtKB/TrEMBL
      B7Z4A9
      Related
      ENSP00000362588.5, ENST00000373489.10
      Conserved Domains (2) summary
      cd00086
      Location:236 → 296
      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:43 → 234
      PBC; PBC domain

    RNA

    1. NR_024122.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) omits a coding exon resulting in a frameshift and truncated open reading frame. The transcript is predicted to be a candidate for nonsense-mediated decay and likely does not encode a protein.
      Source sequence(s)
      AF355141, AI479638, BC094883, CD675622, CN372830, CN372832, X59841

    2. NR_024123.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) omits two coding exons resulting in a frameshift and truncated open reading frame. The transcript is predicted to be a candidate for nonsense-mediated decay and likely does not encode a protein.
      Source sequence(s)
      AF355142, AI479638, BC094883, CD675622, CN372830, CN372832, X59841

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      125747373..125967377
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047423441.1 → XP_047279397.1  pre-B-cell leukemia transcription factor 3 isoform X2

    2. XM_047423443.1 → XP_047279399.1  pre-B-cell leukemia transcription factor 3 isoform X4

    3. XM_011518755.3 → XP_011517057.1  pre-B-cell leukemia transcription factor 3 isoform X1

      UniProtKB/TrEMBL
      Q96AL5
      Conserved Domains (2) summary
      cd00086
      Location:161 → 242
      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

    4. XM_047423445.1 → XP_047279401.1  pre-B-cell leukemia transcription factor 3 isoform X6

    5. XM_047423442.1 → XP_047279398.1  pre-B-cell leukemia transcription factor 3 isoform X3

    6. XM_047423444.1 → XP_047279400.1  pre-B-cell leukemia transcription factor 3 isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      137947324..138172756
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054363048.1 → XP_054219023.1  pre-B-cell leukemia transcription factor 3 isoform X2

    2. XM_054363047.1 → XP_054219022.1  pre-B-cell leukemia transcription factor 3 isoform X1

    3. XM_054363050.1 → XP_054219025.1  pre-B-cell leukemia transcription factor 3 isoform X6

    4. XM_054363049.1 → XP_054219024.1  pre-B-cell leukemia transcription factor 3 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P40426.1 GenPept UniProtKB/Swiss-Prot:P40426

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