Human Gene BCL9 (ENST00000234739.8_8) from GENCODE V47lift37
  Description: BCL9 transcription coactivator (from RefSeq NM_004326.4)
Gencode Transcript: ENST00000234739.8_8
Gencode Gene: ENSG00000116128.12_12
Transcript (Including UTRs)
   Position: hg19 chr1:147,013,271-147,098,017 Size: 84,747 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg19 chr1:147,083,636-147,096,760 Size: 13,125 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:147,013,271-147,098,017)mRNA (may differ from genome)Protein (1426 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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-  Comments and Description Text from UniProtKB
  ID: BCL9_HUMAN
DESCRIPTION: RecName: Full=B-cell CLL/lymphoma 9 protein; Short=B-cell lymphoma 9 protein; Short=Bcl-9; AltName: Full=Protein legless homolog;
FUNCTION: Involved in signal transduction through the Wnt pathway. Promotes beta-catenin's transcriptional activity (By similarity).
SUBUNIT: Binds to beta-catenin (CTNNB1), PYGO1 and PYGO2.
INTERACTION: P18824:arm (xeno); NbExp=3; IntAct=EBI-533127, EBI-216128; Q6P1J9:CDC73; NbExp=2; IntAct=EBI-533127, EBI-930143; P35222:CTNNB1; NbExp=2; IntAct=EBI-533127, EBI-491549; Q9V9W8:pygo (xeno); NbExp=3; IntAct=EBI-533127, EBI-152653; Q9Y3Y4:PYGO1; NbExp=7; IntAct=EBI-533127, EBI-3397474;
SUBCELLULAR LOCATION: Nucleus (By similarity).
TISSUE SPECIFICITY: Detected at low levels in thymus, prostate, testis, ovary and small intestine, and at lower levels in spleen, colon and blood.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
DISEASE: Note=A chromosomal aberration involving BCL9 is found in a patient with precusor B-cell acute lymphoblastic leukemia (ALL). Translocation t(1;14)(q21;q32). This translocation leaves the coding region intact, but may have pathogenic effects due to alterations in the expression level of BCL9. Several cases of translocations within the 3'-UTR of BCL9 have been found in B-cell malignancies.
SIMILARITY: Belongs to the BCL9 family.
CAUTION: It is uncertain whether Met-1 or Met-27 is the initiator.
SEQUENCE CAUTION: Sequence=CAA73942.1; Type=Frameshift; Positions=1391;
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/BCL9ID466.html";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: BCL9
Diseases sorted by gene-association score: lymphoblastic leukemia (15), lymphoma (8), retinitis pigmentosa (0)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 13.08 RPKM in Fallopian Tube
Total median expression: 261.28 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 -212.80651-0.327 Picture PostScript Text
3' UTR -344.701256-0.274 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
IPR015668 - Bcl-9
IPR024670 - BCL9_beta-catenin-bd_dom

Pfam Domains:
PF11502 - B-cell lymphoma 9 protein

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2GL7 - X-ray MuPIT 2VP7 - X-ray MuPIT 2VPB - X-ray MuPIT 2VPD - X-ray MuPIT 2VPE - X-ray MuPIT 2VPG - X-ray MuPIT 3SL9 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O00512
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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 DetailsGene Details Gene Details  
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003713 transcription coactivator activity
GO:0005515 protein binding
GO:0008013 beta-catenin binding

Biological Process:
GO:0014908 myotube differentiation involved in skeletal muscle regeneration
GO:0016055 Wnt signaling pathway
GO:0035019 somatic stem cell population maintenance
GO:0035914 skeletal muscle cell differentiation
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0060070 canonical Wnt signaling pathway
GO:1904837 beta-catenin-TCF complex assembly
GO:0017015 regulation of transforming growth factor beta receptor signaling pathway

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005794 Golgi apparatus
GO:0005801 cis-Golgi network
GO:1990907 beta-catenin-TCF complex


-  Descriptions from all associated GenBank mRNAs
  Y13620 - Homo sapiens mRNA for B-cell CLL/lymphoma 9 (BCL9 gene).
AK298105 - Homo sapiens cDNA FLJ60744 complete cds, moderately similar to B-cell lymphoma 9 protein.
JD135545 - Sequence 116569 from Patent EP1572962.
JD555834 - Sequence 536858 from Patent EP1572962.
JD321807 - Sequence 302831 from Patent EP1572962.
JD373502 - Sequence 354526 from Patent EP1572962.
JD275089 - Sequence 256113 from Patent EP1572962.
JD186876 - Sequence 167900 from Patent EP1572962.
JD373239 - Sequence 354263 from Patent EP1572962.
JD470959 - Sequence 451983 from Patent EP1572962.
JD036642 - Sequence 17666 from Patent EP1572962.
JD475490 - Sequence 456514 from Patent EP1572962.
BC116451 - Homo sapiens B-cell CLL/lymphoma 9, mRNA (cDNA clone MGC:131591 IMAGE:7961941), complete cds.
AB385170 - Synthetic construct DNA, clone: pF1KB7004, Homo sapiens BCL9 gene for B-cell lymphoma 9 protein, complete cds, without stop codon, in Flexi system.
JD111814 - Sequence 92838 from Patent EP1572962.
JD111815 - Sequence 92839 from Patent EP1572962.
JD483575 - Sequence 464599 from Patent EP1572962.
JD274365 - Sequence 255389 from Patent EP1572962.
JD372384 - Sequence 353408 from Patent EP1572962.
JD088150 - Sequence 69174 from Patent EP1572962.
JD147329 - Sequence 128353 from Patent EP1572962.
JD301482 - Sequence 282506 from Patent EP1572962.
JD145470 - Sequence 126494 from Patent EP1572962.
JD469508 - Sequence 450532 from Patent EP1572962.
JD171728 - Sequence 152752 from Patent EP1572962.
JD286051 - Sequence 267075 from Patent EP1572962.
JD128311 - Sequence 109335 from Patent EP1572962.
JD147916 - Sequence 128940 from Patent EP1572962.
JD230394 - Sequence 211418 from Patent EP1572962.
JD125103 - Sequence 106127 from Patent EP1572962.
JD520147 - Sequence 501171 from Patent EP1572962.
JD232035 - Sequence 213059 from Patent EP1572962.
JD301729 - Sequence 282753 from Patent EP1572962.
JD151767 - Sequence 132791 from Patent EP1572962.

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

Protein O00512 (Reactome details) participates in the following event(s):

R-HSA-201712 Beta-catenin:TCF associates with BCL9 and PYGO
R-HSA-3364014 Recruitment of SET1 methyltransferase complex
R-HSA-3364026 SET1 complex trimethylates H3K4 at the MYC gene
R-HSA-201722 Formation of the beta-catenin:TCF transactivating complex
R-HSA-3769402 Deactivation of the beta-catenin transactivating complex
R-HSA-201681 TCF dependent signaling in response to WNT
R-HSA-195721 Signaling by WNT
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: BCL9_HUMAN, ENST00000234739.1, ENST00000234739.2, ENST00000234739.3, ENST00000234739.4, ENST00000234739.5, ENST00000234739.6, ENST00000234739.7, NM_004326, O00512, Q5T489, uc317dzp.1, uc317dzp.2
UCSC ID: ENST00000234739.8_8
RefSeq Accession: NM_004326.4
Protein: O00512 (aka BCL9_HUMAN)

-  Gene Model Information
  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.