Human Gene EBF3 (uc001lki.2) Description and Page Index
  Description: Homo sapiens early B-cell factor 3 (EBF3), mRNA.
RefSeq Summary (NM_001005463): This gene encodes a member of the early B-cell factor (EBF) family of DNA binding transcription factors. EBF proteins are involved in B-cell differentiation, bone development and neurogenesis, and may also function as tumor suppressors. The encoded protein inhibits cell survival through the regulation of genes involved in cell cycle arrest and apoptosis, and aberrant methylation or deletion of this gene may play a role in multiple malignancies including glioblastoma multiforme and gastric carcinoma. [provided by RefSeq, Sep 2011]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: AL832828.1, BC130479.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA1965299, SAMEA1966682 [ECO:0000350] ##Evidence-Data-END## ##RefSeq-Attributes-START## RefSeq Select criteria :: based on conservation, expression ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr10:131,633,496-131,762,091 Size: 128,596 Total Exon Count: 16 Strand: -
Coding Region
   Position: hg19 chr10:131,636,193-131,762,032 Size: 125,840 Coding Exon Count: 16 

Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr10:131,633,496-131,762,091)mRNA (may differ from genome)Protein (551 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
OMIMPubMedStanford SOURCETreefamUniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): EBF3
CDC HuGE Published Literature: EBF3
Positive Disease Associations: Body Fat Distribution
Related Studies:
  1. Body Fat Distribution
    , , . [PubMed 0]

-  MalaCards Disease Associations
  MalaCards Gene Search: EBF3
Diseases sorted by gene-association score: hypotonia, ataxia, and delayed development syndrome* (1231), neurogenic bladder* (400), ataxia* (302), harel-yoon syndrome* (283), renal dysplasia* (283), ataxia and polyneuropathy, adult-onset* (200), intellectual disability* (170), alacrima, achalasia, and mental retardation syndrome* (68), hypotonia (8)
* = Manually curated disease association

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

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 14.62 RPKM in Adipose - Subcutaneous
Total median expression: 100.68 RPKM

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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -23.0059-0.390 Picture PostScript Text
3' UTR -665.022697-0.247 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
  Pfam Domains:
PF01833 - IPT/TIG domain
PF16422 - Transcription factor COE1 DNA-binding domain
PF16423 - Transcription factor COE1 helix-loop-helix domain

SCOP Domains:
81296 - E set domains

ModBase Predicted Comparative 3D Structure on Q9H4W6-2
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 orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Protein Sequence   

-  Descriptions from all associated GenBank mRNAs
  AL832828 - Homo sapiens mRNA; cDNA DKFZp667I0324 (from clone DKFZp667I0324).
BC130479 - Homo sapiens early B-cell factor 3, mRNA (cDNA clone MGC:163351 IMAGE:40146510), complete cds.
BC126130 - Homo sapiens early B-cell factor 3, mRNA (cDNA clone MGC:161408 IMAGE:8991846), complete cds.
HQ258299 - Synthetic construct Homo sapiens clone IMAGE:100072608 early B-cell factor 3 (EBF3) (EBF3) gene, encodes complete protein.
KJ895897 - Synthetic construct Homo sapiens clone ccsbBroadEn_05291 EBF3 gene, encodes complete protein.
AB527459 - Synthetic construct DNA, clone: pF1KB7814, Homo sapiens EBF3 gene for early B-cell factor 3, without stop codon, in Flexi system.
AK055710 - Homo sapiens cDNA FLJ31148 fis, clone IMR322001452.
AK098025 - Homo sapiens cDNA FLJ40706 fis, clone THYMU2026531.
JD022460 - Sequence 3484 from Patent EP1572962.
JD033098 - Sequence 14122 from Patent EP1572962.
JD024610 - Sequence 5634 from Patent EP1572962.
JD027784 - Sequence 8808 from Patent EP1572962.
AL713797 - Homo sapiens mRNA; cDNA DKFZp667B0210 (from clone DKFZp667B0210).
JD302720 - Sequence 283744 from Patent EP1572962.
JD498917 - Sequence 479941 from Patent EP1572962.
JD554543 - Sequence 535567 from Patent EP1572962.
JD296404 - Sequence 277428 from Patent EP1572962.
JD297610 - Sequence 278634 from Patent EP1572962.
JD171196 - Sequence 152220 from Patent EP1572962.
JD367843 - Sequence 348867 from Patent EP1572962.
JD440095 - Sequence 421119 from Patent EP1572962.
JD549255 - Sequence 530279 from Patent EP1572962.
JD494580 - Sequence 475604 from Patent EP1572962.
JD460634 - Sequence 441658 from Patent EP1572962.
JD370791 - Sequence 351815 from Patent EP1572962.
AK097335 - Homo sapiens cDNA FLJ40016 fis, clone STOMA2006325, moderately similar to TRANSCRIPTION FACTOR COE3.

-  Other Names for This Gene
  Alternate Gene Symbols: COE3, NM_001005463, NP_001005463, Q9H4W6-2
UCSC ID: uc001lki.2
RefSeq Accession: NM_001005463
Protein: Q9H4W6-2, splice isoform of Q9H4W6 CCDS: CCDS31314.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_001005463.2
exon count: 16CDS single in 3' UTR: no RNA size: 4412
ORF size: 1656CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3412.00frame 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.