Human Gene ELF3 (uc001gxi.4) Description and Page Index
  Description: Homo sapiens E74-like factor 3 (ets domain transcription factor, epithelial-specific ) (ELF3), transcript variant 2, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr1:201,979,690-201,986,315 Size: 6,626 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr1:201,980,265-201,984,451 Size: 4,187 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: 2013-06-15

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr1:201,979,690-201,986,315)mRNA (may differ from genome)Protein (371 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
neXtProtOMIMPubMedReactomeStanford SOURCETreefam

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=ETS-related transcription factor Elf-3; AltName: Full=E74-like factor 3; AltName: Full=Epithelial-restricted with serine box; AltName: Full=Epithelium-restricted Ets protein ESX; AltName: Full=Epithelium-specific Ets transcription factor 1; Short=ESE-1;
FUNCTION: Transcriptional activator that binds and transactivates ETS sequences containing the consensus nucleotide core sequence GGA[AT]. Acts synergistically with POU2F3 to transactivate the SPRR2A promoter and with RUNX1 to transactivate the ANGPT1 promoter. Also transactivates collagenase, CCL20, CLND7, FLG, KRT8, NOS2, PTGS2, SPRR2B, TGFBR2 and TGM3 promoters. Represses KRT4 promoter activity. Involved in mediating vascular inflammation. May play an important role in epithelial cell differentiation and tumorigenesis. May be a critical downstream effector of the ERBB2 signaling pathway. May be associated with mammary gland development and involution. Plays an important role in the regulation of transcription with TATA-less promoters in preimplantation embryos, which is essential in preimplantation development (By similarity).
SUBUNIT: Interacts with TBP. Interacts with CREBBP and EP300; these act as transcriptional coactivators of ELF3 and positively modulate its function. Interacts with XRCC5/KU86 and XRCC6/KU70; these inhibit the ability of ELF3 to bind DNA and negatively modulate its transcriptional activity. Associated with CLND7 and POU2F3.
SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Note=Localizes to the cytoplasm where it has been shown to transform MCF-12A mammary epithelial cells via a novel cytoplasmic mechanism. Also transiently expressed and localized to the nucleus where it induces apoptosis in non-transformed breast epithelial cells MCF- 10A and MCF-12A via a transcription-dependent mechanism.
TISSUE SPECIFICITY: Expressed exclusively in tissues containing a high content of terminally differentiated epithelial cells including mammary gland, colon, trachea, kidney, prostate, uterus, stomach and skin.
INDUCTION: Transcriptionally regulated by ERBB2 receptor signaling in breast cancer epithelial cells. Up-regulated by phorbol 12- myristate 13-acetate (PMA) in bronchial epithelial cells. By retinoic acid in MCF-7 mammary epithelial cells (at protein level).
DOMAIN: the 9aaTAD motif is a transactivation domain present in a large number of yeast and animal transcription factors.
SIMILARITY: Belongs to the ETS family.
SIMILARITY: Contains 1 ETS DNA-binding domain.
SIMILARITY: Contains 1 PNT (pointed) domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): ELF3
CDC HuGE Published Literature: ELF3
Positive Disease Associations: Asthma , Waist Circumference
Related Studies:
  1. Asthma
    C Ober et al. American journal of human genetics 2000, A second-generation genomewide screen for asthma-susceptibility alleles in a founder population., American journal of human genetics. [PubMed 11022011]
  2. Asthma
    C Ober et al. American journal of human genetics 2000, A second-generation genomewide screen for asthma-susceptibility alleles in a founder population., American journal of human genetics. [PubMed 11022011]
  3. Waist Circumference
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: ELF3
Diseases sorted by gene-association score: sarcoma, synovial (3), n syndrome (2), growth hormone deficiency, isolated, type ii (1)

-  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: 103.11 RPKM in Bladder
Total median expression: 577.20 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 -106.40267-0.399 Picture PostScript Text
3' UTR -646.761864-0.347 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
IPR017956 - AT_hook_DNA-bd_motif
IPR000418 - Ets
IPR003118 - Pointed_dom
IPR013761 - SAM/pointed
IPR011991 - WHTH_trsnscrt_rep_DNA-bd

Pfam Domains:
PF00178 - Ets-domain
PF02178 - AT hook motif
PF02198 - Sterile alpha motif (SAM)/Pointed domain

SCOP Domains:
46785 - "Winged helix" DNA-binding domain
47769 - SAM/Pointed domain

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


ModBase Predicted Comparative 3D Structure on P78545
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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 Protein Sequence    

-  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:0003713 transcription coactivator activity
GO:0005515 protein binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0001824 blastocyst development
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006366 transcription from RNA polymerase II promoter
GO:0006954 inflammatory response
GO:0007275 multicellular organism development
GO:0008544 epidermis development
GO:0009653 anatomical structure morphogenesis
GO:0030154 cell differentiation
GO:0030198 extracellular matrix organization
GO:0030855 epithelial cell differentiation
GO:0045747 positive regulation of Notch signaling pathway
GO:0045892 negative regulation of transcription, DNA-templated
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0060056 mammary gland involution

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005794 Golgi apparatus
GO:0005829 cytosol

-  Descriptions from all associated GenBank mRNAs
  LF205364 - JP 2014500723-A/12867: Polycomb-Associated Non-Coding RNAs.
BX537368 - Homo sapiens mRNA; cDNA DKFZp686F2495 (from clone DKFZp686F2495); complete cds.
AK310814 - Homo sapiens cDNA, FLJ17856.
AK309265 - Homo sapiens cDNA, FLJ99306.
AK312273 - Homo sapiens cDNA, FLJ92570, Homo sapiens E74-like factor 3 (ets domain transcription factor,epithelial-specific) (ELF3), mRNA.
AF017307 - Homo sapiens Ets-related transcription factor (ERT) mRNA, complete cds.
U97156 - Homo sapiens epithelial-specific ets protein (jen) mRNA, complete cds.
BC003569 - Homo sapiens E74-like factor 3 (ets domain transcription factor, epithelial-specific), mRNA (cDNA clone MGC:2088 IMAGE:3537846), complete cds.
U73843 - Homo sapiens epithelial-specific transcription factor ESE-1b (ESE-1) mRNA, complete cds.
U73844 - Homo sapiens epithelial-specific transcription factor ESE-1a (ESE-1) mRNA, complete cds.
AF016295 - Homo sapiens Ets transcription factor (ELF3) mRNA, complete cds.
U66894 - Human epithelium-restricted Ets protein ESX mRNA, complete cds.
AK225446 - Homo sapiens mRNA for E74-like factor 3 variant, clone: HSI00755.
AF517841 - Homo sapiens E74-like factor 3 (ELF3) mRNA, complete cds.
KJ904458 - Synthetic construct Homo sapiens clone ccsbBroadEn_13852 ELF3 gene, encodes complete protein.
AB527744 - Synthetic construct DNA, clone: pF1KB7935, Homo sapiens ELF3 gene for E74-like factor 3, without stop codon, in Flexi system.
DQ890691 - Synthetic construct clone IMAGE:100003321; FLH165169.01X; RZPDo839G10158D E74-like factor 3 (ets domain transcription factor, epithelial-specific) (ELF3) gene, encodes complete protein.
DQ893874 - Synthetic construct Homo sapiens clone IMAGE:100008334; FLH165165.01L; RZPDo839G10157D E74-like factor 3 (ets domain transcription factor, epithelial-specific) (ELF3) gene, encodes complete protein.
CR457106 - Homo sapiens full open reading frame cDNA clone RZPDo834G1111D for gene ELF3, E74-like factor 3 (ets domain transcription factor, epithelial-specific); complete cds, incl. stopcodon.
MA440941 - JP 2018138019-A/12867: Polycomb-Associated Non-Coding RNAs.
JD268690 - Sequence 249714 from Patent EP1572962.
JD164185 - Sequence 145209 from Patent EP1572962.
LF319677 - JP 2014500723-A/127180: Polycomb-Associated Non-Coding RNAs.
JD368053 - Sequence 349077 from Patent EP1572962.
JD055577 - Sequence 36601 from Patent EP1572962.
JD504420 - Sequence 485444 from Patent EP1572962.
LF319676 - JP 2014500723-A/127179: Polycomb-Associated Non-Coding RNAs.
JD086618 - Sequence 67642 from Patent EP1572962.
JD527295 - Sequence 508319 from Patent EP1572962.
JD048858 - Sequence 29882 from Patent EP1572962.
JD210739 - Sequence 191763 from Patent EP1572962.
JD451991 - Sequence 433015 from Patent EP1572962.
JD056470 - Sequence 37494 from Patent EP1572962.
JD267995 - Sequence 249019 from Patent EP1572962.
JD099539 - Sequence 80563 from Patent EP1572962.
JD231007 - Sequence 212031 from Patent EP1572962.
JD415791 - Sequence 396815 from Patent EP1572962.
JD118916 - Sequence 99940 from Patent EP1572962.
JD170695 - Sequence 151719 from Patent EP1572962.
JD207104 - Sequence 188128 from Patent EP1572962.
JD160456 - Sequence 141480 from Patent EP1572962.
JD508096 - Sequence 489120 from Patent EP1572962.
JD355118 - Sequence 336142 from Patent EP1572962.
JD174683 - Sequence 155707 from Patent EP1572962.
JD436692 - Sequence 417716 from Patent EP1572962.
JD078537 - Sequence 59561 from Patent EP1572962.
JD155414 - Sequence 136438 from Patent EP1572962.
JD113336 - Sequence 94360 from Patent EP1572962.
JD160238 - Sequence 141262 from Patent EP1572962.
JD202435 - Sequence 183459 from Patent EP1572962.
JD564722 - Sequence 545746 from Patent EP1572962.
MA555254 - JP 2018138019-A/127180: Polycomb-Associated Non-Coding RNAs.
MA555253 - JP 2018138019-A/127179: Polycomb-Associated Non-Coding RNAs.

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

Protein P78545 (Reactome details) participates in the following event(s):

R-HSA-9021364 ELF3 binds NOTCH3 gene promoter
R-HSA-9021357 PRKCI phosphorylates ELF3
R-HSA-1912408 Pre-NOTCH Transcription and Translation
R-HSA-1912422 Pre-NOTCH Expression and Processing
R-HSA-157118 Signaling by NOTCH
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: B2R5Q6, ELF3_HUMAN, ERT, ESX, JEN, NM_001114309, NP_004424, P78545, Q6IAP8, Q7RU03, Q7Z3X2, Q8NFG2, Q99718
UCSC ID: uc001gxi.4
RefSeq Accession: NM_001114309
Protein: P78545 (aka ELF3_HUMAN)
CCDS: CCDS1419.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_001114309.1
exon count: 9CDS single in 3' UTR: no RNA size: 3263
ORF size: 1116CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2355.00frame shift in genome: no % Coverage: 99.51
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.