Human Gene PBX1 (uc010pkv.2) Description and Page Index
  Description: Homo sapiens pre-B-cell leukemia homeobox 1 (PBX1), transcript variant 1, mRNA.
RefSeq Summary (NM_002585): This gene encodes a nuclear protein that belongs to the PBX homeobox family of transcriptional factors. Studies in mice suggest that this gene may be involved in the regulation of osteogenesis and required for skeletal patterning and programming. A chromosomal translocation, t(1;19) involving this gene and TCF3/E2A gene, is associated with pre-B-cell acute lymphoblastic leukemia. The resulting fusion protein, in which the DNA binding domain of E2A is replaced by the DNA binding domain of this protein, transforms cells by constitutively activating transcription of genes regulated by the PBX protein family. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2017].
Transcript (Including UTRs)
   Position: hg19 chr1:164,528,597-164,821,060 Size: 292,464 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg19 chr1:164,529,235-164,815,913 Size: 286,679 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr1:164,528,597-164,821,060)mRNA (may differ from genome)Protein (347 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
ReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Pre-B-cell leukemia transcription factor 1; AltName: Full=Homeobox protein PBX1; AltName: Full=Homeobox protein PRL;
FUNCTION: Binds the sequence 5'-ATCAATCAA-3'. Acts as a transcriptional activator of PF4 in complex with MEIS1. Converted into a potent transcriptional activator by the (1;19) translocation. May have a role in steroidogenesis and, subsequently, sexual development and differentiation.
SUBUNIT: Forms a heterodimer with MEIS1 which binds DNA including a cAMP-responsive sequence in CYP17. Also forms heterotrimers with MEIS1 and a number of HOX proteins including HOXA9, HOXD4, HOXD9 and HOXD10. Interacts with PBXIP1.
TISSUE SPECIFICITY: Expressed in all tissues except in cells of the B and T lineage.
DISEASE: Note=A chromosomal aberration involving PBX1 is a cause of pre-B-cell acute lymphoblastic leukemia (B-ALL). Translocation t(1;19)(q23;p13.3) with TCF3. TCF3-PBX1 transforms cells by constitutively activating transcription of genes regulated by PBX1 or by other members of the PBX protein family.
SIMILARITY: Belongs to the TALE/PBX homeobox family.
SIMILARITY: Contains 1 homeobox DNA-binding domain.
SEQUENCE CAUTION: Sequence=AAA36764.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PBX1
CDC HuGE Published Literature: PBX1
Positive Disease Associations: Body Height , monocyte chemoattractant protein 1 (66-77) , Varicose Veins
Related Studies:
  1. Body Height
    Damien C Croteau-Chonka et al. Obesity (Silver Spring, Md.) 2011, Genome-wide association study of anthropometric traits and evidence of interactions with age and study year in Filipino women., Obesity (Silver Spring, Md.). [PubMed 20966902]
  2. monocyte chemoattractant protein 1 (66-77)
    , , . [PubMed 0]
  3. monocyte chemoattractant protein 1 (66-77)
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: PBX1
Diseases sorted by gene-association score: congenital anomalies of kidney and urinary tract syndrome with or without hearing loss, abnormal ears, or developmental delay* (900), leukemia, acute lymphoblastic 3* (184), acute pre-b-cell lymphoblastic leukemia* (100), leukemia (35), lymphoblastic leukemia (21), childhood leukemia (11), hypothyroidism, congenital, nongoitrous 4 (7), b-cell adult acute lymphocytic leukemia (7)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 50.99 RPKM in Uterus
Total median expression: 526.08 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -232.92638-0.365 Picture PostScript Text
3' UTR -1459.725147-0.284 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR017970 - Homeobox_CS
IPR001356 - Homeodomain
IPR009057 - Homeodomain-like
IPR005542 - PBX

Pfam Domains:
PF00046 - Homeobox domain
PF03792 - PBC domain
PF05920 - Homeobox KN domain

SCOP Domains:
46689 - Homeodomain-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help

- X-ray MuPIT

- X-ray MuPIT

ModBase Predicted Comparative 3D Structure on P40424
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding
GO:0008134 transcription factor binding
GO:0043565 sequence-specific DNA binding
GO:0046982 protein heterodimerization activity
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding

Biological Process:
GO:0001655 urogenital system development
GO:0001658 branching involved in ureteric bud morphogenesis
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0006694 steroid biosynthetic process
GO:0007221 positive regulation of transcription of Notch receptor target
GO:0007275 multicellular organism development
GO:0007548 sex differentiation
GO:0008284 positive regulation of cell proliferation
GO:0009887 animal organ morphogenesis
GO:0009952 anterior/posterior pattern specification
GO:0009954 proximal/distal pattern formation
GO:0010971 positive regulation of G2/M transition of mitotic cell cycle
GO:0030154 cell differentiation
GO:0030278 regulation of ossification
GO:0030325 adrenal gland development
GO:0030326 embryonic limb morphogenesis
GO:0035019 somatic stem cell population maintenance
GO:0035162 embryonic hemopoiesis
GO:0042127 regulation of cell proliferation
GO:0043433 negative regulation of sequence-specific DNA binding transcription factor activity
GO:0045665 negative regulation of neuron differentiation
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048536 spleen development
GO:0048538 thymus development
GO:0048568 embryonic organ development
GO:0048706 embryonic skeletal system development

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005667 transcription factor complex
GO:0005737 cytoplasm
GO:0090575 RNA polymerase II transcription factor complex

-  Descriptions from all associated GenBank mRNAs
  AK291415 - Homo sapiens cDNA FLJ76851 complete cds, highly similar to Homo sapiens pre-B-cell leukemia transcription factor 1 (PBX1), mRNA.
M86546 - H.sapiens PBX1a and PBX1b mRNA, complete cds.
AK299673 - Homo sapiens cDNA FLJ61369 complete cds, highly similar to Pre-B-cell leukemia transcription factor 1.
BC101578 - Homo sapiens pre-B-cell leukemia homeobox 1, mRNA (cDNA clone MGC:126627 IMAGE:8069084), complete cds.
BC143435 - Homo sapiens cDNA clone IMAGE:9051943.
BC143451 - Homo sapiens cDNA clone IMAGE:9051959.
BT006705 - Homo sapiens pre-B-cell leukemia transcription factor 1 mRNA, complete cds.
AB384885 - Synthetic construct DNA, clone: pF1KB4019, Homo sapiens PBX1 gene for pre-B-cell leukemia transcription factor 1, complete cds, without stop codon, in Flexi system.
AK301540 - Homo sapiens cDNA FLJ52874 complete cds, highly similar to Pre-B-cell leukemia transcription factor 1.
JD049672 - Sequence 30696 from Patent EP1572962.
JD181677 - Sequence 162701 from Patent EP1572962.
MH401086 - Homo sapiens TCF3-PBX1 fusion protein mRNA, partial cds.
M31522 - Human translocation (t1;19) fusion protein (E2A/PRL) mRNA, 3' end.
M31170 - Human homeo box containing (prl) protein mRNA, 3' end.
CR749446 - Homo sapiens mRNA; cDNA DKFZp686B09108 (from clone DKFZp686B09108).
BX647313 - Homo sapiens mRNA; cDNA DKFZp686N1593 (from clone DKFZp686N1593).
JD125476 - Sequence 106500 from Patent EP1572962.
JD188982 - Sequence 170006 from Patent EP1572962.
JD486425 - Sequence 467449 from Patent EP1572962.
JD055968 - Sequence 36992 from Patent EP1572962.
JD086872 - Sequence 67896 from Patent EP1572962.
AK022962 - Homo sapiens cDNA FLJ12900 fis, clone NT2RP2004321.
AK022520 - Homo sapiens cDNA FLJ12458 fis, clone NT2RM1000672.
AL049381 - Homo sapiens mRNA; cDNA DKFZp586J2118 (from clone DKFZp586J2118).
BC044624 - Homo sapiens cDNA clone IMAGE:5288080.
JD263058 - Sequence 244082 from Patent EP1572962.
JD209624 - Sequence 190648 from Patent EP1572962.
JD385097 - Sequence 366121 from Patent EP1572962.
JD305928 - Sequence 286952 from Patent EP1572962.
JD314770 - Sequence 295794 from Patent EP1572962.
JD247945 - Sequence 228969 from Patent EP1572962.
JD056921 - Sequence 37945 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P40424 (Reactome details) participates in the following event(s):

R-HSA-480204 POU5F1 (OCT4), SOX2, NANOG, KLF4, PBX1, SMAD2 bind the NANOG promoter
R-HSA-452723 Transcriptional regulation of pluripotent stem cells
R-HSA-9013508 NOTCH3 Intracellular Domain Regulates Transcription
R-HSA-5617472 Activation of anterior HOX genes in hindbrain development during early embryogenesis
R-HSA-1266738 Developmental Biology
R-HSA-9012852 Signaling by NOTCH3
R-HSA-5619507 Activation of HOX genes during differentiation
R-HSA-157118 Signaling by NOTCH
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: B4DSC1, BC143435, F5H4U9, P40424, PBX1_HUMAN, PRL, Q5T488
UCSC ID: uc010pkv.2
RefSeq Accession: NM_002585
Protein: P40424 (aka PBX1_HUMAN)

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: BC143435.1
exon count: 8CDS single in 3' UTR: no RNA size: 1314
ORF size: 1044CDS single in intron: no Alignment % ID: 99.85
txCdsPredict score: 1995.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.