Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
10  structures 322  species 0  interactions 1594  sequences 17  architectures

Family: COE1_DBD (PF16422)

Summary: Transcription factor COE1 DNA-binding domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "EBF1". More...

EBF1 Edit Wikipedia article

Protein EBF1 PDB 3LYR.png
Available structures
PDBOrtholog search: PDBe RCSB
AliasesEBF1, COE1, EBF, O/E-1, OLF1, early B-cell factor 1, early B cell factor 1, EBF transcription factor 1
External IDsOMIM: 164343 MGI: 95275 HomoloGene: 7297 GeneCards: EBF1
Gene location (Human)
Chromosome 5 (human)
Chr.Chromosome 5 (human)[1]
Chromosome 5 (human)
Genomic location for EBF1
Genomic location for EBF1
Band5q33.3Start158,695,916 bp[1]
End159,099,916 bp[1]
RefSeq (mRNA)


RefSeq (protein)
Location (UCSC)Chr 5: 158.7 – 159.1 MbChr 11: 44.62 – 45.01 Mb
PubMed search[3][4]
View/Edit HumanView/Edit Mouse

Transcription factor COE1 is a protein that in humans is encoded by the EBF1 gene. EBF1 stands for Early B-Cell Factor 1.[5][6][7]

EBF1 controls the expression of key proteins required for B cell differentiation, signal transduction and function.[8][9] The crucial role of this factor is shown in the regulation of expression of SLAM family co-receptors in B-cells.[10]


EBF1 has been shown to interact with ZNF423[11] and CREB binding protein.[12]


  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000164330 - Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000057098 - Ensembl, May 2017
  3. ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. ^ "Symbol Report: EBF1". HUGO Gene Nomenclature Committee.
  6. ^ Milatovich A, Qiu RG, Grosschedl R, Francke U (Jul 1994). "Gene for a tissue-specific transcriptional activator (EBF or Olf-1), expressed in early B lymphocytes, adipocytes, and olfactory neurons, is located on human chromosome 5, band q34, and proximal mouse chromosome 11". Mamm. Genome. 5 (4): 211–5. doi:10.1007/BF00360547. PMID 8012110.
  7. ^ "Entrez Gene: EBF1 early B-cell factor 1".
  8. ^ Treiber, Thomas; Mandel, Elizabeth M.; Pott, Sebastian; Györy, Ildiko; Firner, Sonja; Liu, Edison T.; Grosschedl, Rudolf (2010). "Early B Cell Factor 1 Regulates B Cell Gene Networks by Activation, Repression, and Transcription- Independent Poising of Chromatin". Immunity. 32 (5): 714–725. doi:10.1016/j.immuni.2010.04.013. PMID 20451411.
  9. ^ Hagman, James; Ramírez, Julita; Lukin, Kara (2012-01-01). "B lymphocyte lineage specification, commitment and epigenetic control of transcription by early B cell factor 1". Current Topics in Microbiology and Immunology. 356: 17–38. doi:10.1007/82_2011_139. ISBN 978-3-642-24102-4. ISSN 0070-217X. PMC 3925327. PMID 21735360.
  10. ^ Schwartz, Anton M.; Putlyaeva, Lidia V.; Covich, Milica; Klepikova, Anna V.; Akulich, Kseniya A.; Vorontsov, Ilya E.; Korneev, Kirill V.; Dmitriev, Sergey E.; Polanovsky, Oleg L. (2016-10-01). "Early B-cell factor 1 (EBF1) is critical for transcriptional control of SLAMF1 gene in human B cells". Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. 1859 (10): 1259–1268. doi:10.1016/j.bbagrm.2016.07.004. PMID 27424222.
  11. ^ Tsai RY, Reed RR (Jun 1997). "Cloning and functional characterization of Roaz, a zinc finger protein that interacts with O/E-1 to regulate gene expression: implications for olfactory neuronal development". J. Neurosci. 17 (11): 4159–69. doi:10.1523/JNEUROSCI.17-11-04159.1997. PMID 9151733.
  12. ^ Zhao F, McCarrick-Walmsley R, Akerblad P, Sigvardsson M, Kadesch T (Jun 2003). "Inhibition of p300/CBP by early B-cell factor" (PDF). Mol. Cell. Biol. 23 (11): 3837–46. doi:10.1128/MCB.23.11.3837-3846.2003. PMC 155219. PMID 12748286.

Further reading

External links

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Transcription factor COE1 DNA-binding domain Provide feedback

No Pfam abstract.

Literature references

  1. Treiber N, Treiber T, Zocher G, Grosschedl R;, Genes Dev. 2010;24:2270-2275.: Structure of an Ebf1:DNA complex reveals unusual DNA recognition and structural homology with Rel proteins. PUBMED:20876732 EPMC:20876732

This tab holds annotation information from the InterPro database.

InterPro entry IPR032200

This entry represents the DNA-binding domain of COE1, COE2, COE3 and COE4 (also known as Ebf1, Ebf2, Ebf3 and Ebf4), they belong to the early B cell factor family. COE1 is a key transcriptional determinant of B-lymphocyte differentiation [PUBMED:20876732]. COE3 is a transcription factor involved in neuronal differentiation and maturation [PUBMED:28017373].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...


We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

Representative proteomes UniProt
Jalview View  View  View  View  View  View  View  View   
HTML View  View               
PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

Representative proteomes UniProt

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

Representative proteomes UniProt
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download    
Gzipped Download   Download   Download   Download   Download   Download   Download   Download    

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...


This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: PDB:3mln
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Eberhardt R
Number in seed: 6
Number in full: 1594
Average length of the domain: 183.40 aa
Average identity of full alignment: 77 %
Average coverage of the sequence by the domain: 38.44 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.7 27.3
Noise cut-off 26.6 26.4
Model length: 231
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

Sunburst controls


Weight segments by...

Change the size of the sunburst


Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls


The tree shows the occurrence of this domain across different species. More...


Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.


For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the COE1_DBD domain has been found. There are 10 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

Loading structure mapping...