Human Gene ELF1 (uc001uxs.3) Description and Page Index
  Description: Homo sapiens E74-like factor 1 (ets domain transcription factor) (ELF1), transcript variant 1, mRNA.
RefSeq Summary (NM_172373): This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2009].
Transcript (Including UTRs)
   Position: hg19 chr13:41,506,055-41,593,508 Size: 87,454 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg19 chr13:41,507,561-41,556,190 Size: 48,630 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr13:41,506,055-41,593,508)mRNA (may differ from genome)Protein (619 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: ELF1_HUMAN
DESCRIPTION: RecName: Full=ETS-related transcription factor Elf-1; AltName: Full=E74-like factor 1;
FUNCTION: Transcription factor that activates the LYN and BLK promoters. Appears to be required for the T-cell-receptor-mediated trans activation of HIV-2 gene expression. Binds specifically to two purine-rich motifs in the HIV-2 enhancer.
SUBUNIT: Binds to the underphosphorylated form of RB. May interact with other transcription factors in order to regulate specific genes. Interacts with RUNX1.
INTERACTION: P31276:HOXC13; NbExp=3; IntAct=EBI-765526, EBI-2293590; P08047:SP1; NbExp=2; IntAct=EBI-765526, EBI-298336;
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: In fetal tissues, it is highly expressed in heart, lung liver and kidney, and weakly expressed in brain. In adult, it is highly expressed in pancreas, spleen, thymus and peripheral blood leukocytes, expressed at moderate levels in heart, placenta, lung, liver, skeletal muscle, kidney, prostate, ovary, small intestine and colon, and weakly expressed in brain and testis.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the ETS family.
SIMILARITY: Contains 1 ETS DNA-binding domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): ELF1
CDC HuGE Published Literature: ELF1
Positive Disease Associations: Lupus Erythematosus, Systemic
Related Studies:
  1. Lupus Erythematosus, Systemic
    Jing Yang et al. Human molecular genetics 2011, ELF1 is associated with systemic lupus erythematosus in Asian populations., Human molecular genetics. [PubMed 21044949]

-  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: 44.05 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 735.78 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 -83.30373-0.223 Picture PostScript Text
3' UTR -351.391506-0.233 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
IPR000418 - Ets
IPR022084 - TF_Elf_N
IPR011991 - WHTH_trsnscrt_rep_DNA-bd

Pfam Domains:
PF00178 - Ets-domain
PF12310 - Transcription factor protein N terminal

SCOP Domains:
46785 - "Winged helix" DNA-binding domain

ModBase Predicted Comparative 3D Structure on P32519
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 orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
 Gene Details    
 Gene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  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:0043565 sequence-specific DNA binding

Biological Process:
GO:0001817 regulation of cytokine production
GO:0001959 regulation of cytokine-mediated signaling pathway
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0030154 cell differentiation
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0050855 regulation of B cell receptor signaling pathway
GO:0050860 negative regulation of T cell receptor signaling pathway

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm


-  Descriptions from all associated GenBank mRNAs
  LF385015 - JP 2014500723-A/192518: Polycomb-Associated Non-Coding RNAs.
BX640798 - Homo sapiens mRNA; cDNA DKFZp686H0575 (from clone DKFZp686H0575); complete cds.
BC030507 - Homo sapiens E74-like factor 1 (ets domain transcription factor), mRNA (cDNA clone MGC:40398 IMAGE:4385989), complete cds.
BC010575 - Homo sapiens E74-like factor 1 (ets domain transcription factor), mRNA (cDNA clone IMAGE:4338775), with apparent retained intron.
M82882 - Human cis-acting sequence.
AK304289 - Homo sapiens cDNA FLJ53387 complete cds, highly similar to ETS-related transcription factor Elf-1.
DQ891709 - Synthetic construct clone IMAGE:100004339; FLH179308.01X; RZPDo839F01130D E74-like factor 1 (ets domain transcription factor) (ELF1) gene, encodes complete protein.
KJ896761 - Synthetic construct Homo sapiens clone ccsbBroadEn_06155 ELF1 gene, encodes complete protein.
DQ894886 - Synthetic construct Homo sapiens clone IMAGE:100009346; FLH179304.01L; RZPDo839F01129D E74-like factor 1 (ets domain transcription factor) (ELF1) gene, encodes complete protein.
AB385566 - Synthetic construct DNA, clone: pF1KB9418, Homo sapiens ELF1 gene for ETS-related transcription factor Elf-1, complete cds, without stop codon, in Flexi system.
CU688886 - Synthetic construct Homo sapiens gateway clone IMAGE:100019952 5' read ELF1 mRNA.
MA620592 - JP 2018138019-A/192518: Polycomb-Associated Non-Coding RNAs.
AK095466 - Homo sapiens cDNA FLJ38147 fis, clone D9OST2003762, highly similar to ETS-RELATED TRANSCRIPTION FACTOR ELF-1.
JD564558 - Sequence 545582 from Patent EP1572962.
JD284251 - Sequence 265275 from Patent EP1572962.
JD439973 - Sequence 420997 from Patent EP1572962.
JD289494 - Sequence 270518 from Patent EP1572962.
JD308696 - Sequence 289720 from Patent EP1572962.
JD025777 - Sequence 6801 from Patent EP1572962.
JD029914 - Sequence 10938 from Patent EP1572962.
JD553456 - Sequence 534480 from Patent EP1572962.
JD496832 - Sequence 477856 from Patent EP1572962.
JD020464 - Sequence 1488 from Patent EP1572962.
JD433854 - Sequence 414878 from Patent EP1572962.
JD023773 - Sequence 4797 from Patent EP1572962.
JD030843 - Sequence 11867 from Patent EP1572962.

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

Protein P32519 (Reactome details) participates in the following event(s):

R-HSA-8938913 RUNX1 binds ELF1
R-HSA-8938938 RUNX1 and ELF1 bind the IL3 gene promoter
R-HSA-8938965 RUNX1 and ELF1, ELF2 or PAX5 bind the BLK gene promoter
R-HSA-8939247 RUNX1 regulates transcription of genes involved in interleukin signaling
R-HSA-8878171 Transcriptional regulation by RUNX1
R-HSA-8939245 RUNX1 regulates transcription of genes involved in BCR signaling
R-HSA-212436 Generic Transcription Pathway
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: ELF1_HUMAN, NM_172373, NP_758961, P32519, Q8N6F6, Q9UDE1
UCSC ID: uc001uxs.3
RefSeq Accession: NM_172373
Protein: P32519 (aka ELF1_HUMAN)
CCDS: CCDS9374.1, CCDS45043.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_172373.3
exon count: 9CDS single in 3' UTR: no RNA size: 3760
ORF size: 1860CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3864.50frame shift in genome: no % Coverage: 99.44
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.