Human Gene PBX3 (uc004bqb.3) Description and Page Index
  Description: Homo sapiens pre-B-cell leukemia homeobox 3 (PBX3), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr9:128,509,617-128,729,655 Size: 220,039 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr9:128,509,733-128,728,202 Size: 218,470 Coding Exon Count: 9 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:128,509,617-128,729,655)mRNA (may differ from genome)Protein (434 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: PBX3_HUMAN
DESCRIPTION: RecName: Full=Pre-B-cell leukemia transcription factor 3; AltName: Full=Homeobox protein PBX3;
FUNCTION: Transcriptional activator that binds the sequence 5'- ATCAATCAA-3'.
SUBUNIT: Interacts with PBXIP1.
SUBCELLULAR LOCATION: Nucleus (Probable).
TISSUE SPECIFICITY: Ubiquitously expressed.
SIMILARITY: Belongs to the TALE/PBX homeobox family.
SIMILARITY: Contains 1 homeobox DNA-binding domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PBX3
CDC HuGE Published Literature: PBX3
Positive Disease Associations: Glucose , Myocardial Infarction , Potassium , Risperidone , Tunica Media
Related Studies:
  1. Glucose
    , , . [PubMed 0]
  2. Myocardial Infarction
    , , . [PubMed 0]
  3. Myocardial Infarction
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: PBX3
Diseases sorted by gene-association score: childhood pilocytic astrocytoma (6), pilocytic astrocytoma (5), leukemia, acute myeloid (0)

-  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: 34.57 RPKM in Ovary
Total median expression: 459.44 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 -32.39116-0.279 Picture PostScript Text
3' UTR -346.221453-0.238 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

ModBase Predicted Comparative 3D Structure on P40426
FrontTopSide
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:0000980 RNA polymerase II distal enhancer sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001205 transcriptional activator activity, RNA polymerase II distal enhancer sequence-specific binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0002087 regulation of respiratory gaseous exchange by neurological system process
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0007387 anterior compartment pattern formation
GO:0007388 posterior compartment specification
GO:0007585 respiratory gaseous exchange
GO:0008344 adult locomotory behavior
GO:0021516 dorsal spinal cord development
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048666 neuron development

Cellular Component:
GO:0005634 nucleus
GO:0005667 transcription factor complex


-  Descriptions from all associated GenBank mRNAs
  AJ420602 - Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 783180.
X59841 - Human PBX3 mRNA.
BC094883 - Homo sapiens pre-B-cell leukemia homeobox 3, mRNA (cDNA clone MGC:105042 IMAGE:5212090), complete cds.
AK312717 - Homo sapiens cDNA, FLJ93121.
AB464062 - Synthetic construct DNA, clone: pF1KB7779, Homo sapiens PBX3 gene for pre-B-cell leukemia homeobox 3, without stop codon, in Flexi system.
AF355141 - Homo sapiens pre-B-cell leukemia transcription factor 3C (PBX3) mRNA, complete cds, alternatively spliced.
AF355142 - Homo sapiens pre-B-cell leukemia transcription factor 3D (PBX3) mRNA, complete cds, alternatively spliced.
AK297093 - Homo sapiens cDNA FLJ60125 complete cds, highly similar to Pre-B-cell leukemia transcription factor 3.
AK289376 - Homo sapiens cDNA FLJ76694 complete cds, highly similar to Homo sapiens pre-B-cell leukemia transcription factor 3C (PBX3) mRNA.
AK309713 - Homo sapiens cDNA, FLJ99754.
AK092148 - Homo sapiens cDNA FLJ34829 fis, clone NT2NE2009426, highly similar to PRE-B-CELL LEUKEMIA TRANSCRIPTION FACTOR-3.
AK299267 - Homo sapiens cDNA FLJ55160 complete cds, highly similar to Pre-B-cell leukemia transcription factor 3.
BC016977 - Homo sapiens pre-B-cell leukemia homeobox 3, mRNA (cDNA clone IMAGE:4447228), partial cds.
KJ901623 - Synthetic construct Homo sapiens clone ccsbBroadEn_11017 PBX3 gene, encodes complete protein.
CU677785 - Synthetic construct Homo sapiens gateway clone IMAGE:100018701 5' read PBX3 mRNA.
JD397619 - Sequence 378643 from Patent EP1572962.
JD390529 - Sequence 371553 from Patent EP1572962.
JD397620 - Sequence 378644 from Patent EP1572962.
JD167185 - Sequence 148209 from Patent EP1572962.
JD458524 - Sequence 439548 from Patent EP1572962.
JD052777 - Sequence 33801 from Patent EP1572962.
JD560813 - Sequence 541837 from Patent EP1572962.
JD420695 - Sequence 401719 from Patent EP1572962.
JD559455 - Sequence 540479 from Patent EP1572962.
JD396682 - Sequence 377706 from Patent EP1572962.
JD454796 - Sequence 435820 from Patent EP1572962.
JD307971 - Sequence 288995 from Patent EP1572962.
JD295297 - Sequence 276321 from Patent EP1572962.
JD041897 - Sequence 22921 from Patent EP1572962.
JD234844 - Sequence 215868 from Patent EP1572962.
JD090880 - Sequence 71904 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_006195, NP_001128250, P40426, PBX3_HUMAN, Q5JSA0, Q5JSA1, Q5VXL3, Q96PF9, Q96PG0
UCSC ID: uc004bqb.3
RefSeq Accession: NM_006195
Protein: P40426 (aka PBX3_HUMAN)
CCDS: CCDS6865.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_006195.5
exon count: 9CDS single in 3' UTR: no RNA size: 2911
ORF size: 1305CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2747.00frame shift in genome: no % Coverage: 98.73
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.