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13  structures 223  species 0  interactions 533  sequences 8  architectures

Family: COE1_HLH (PF16423)

Summary: Transcription factor COE1 helix-loop-helix 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

EBF1
Protein EBF1 PDB 3LYR.png
Available structures
PDB Ortholog search: PDBe RCSB
Identifiers
Aliases EBF1, COE1, EBF, O/E-1, OLF1, early B-cell factor 1
External IDs MGI: 95275 HomoloGene: 7297 GeneCards: EBF1
Genetically Related Diseases
breast cancer, obesity[1]
Orthologs
Species Human Mouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_001290709
NM_001290710
NM_001290711
NM_007897

RefSeq (protein)

NP_031923.1
NP_001277638
NP_001277639
NP_001277640
NP_031923

Location (UCSC) Chr 5: 158.7 – 159.1 Mb Chr 11: 44.62 – 45.01 Mb
PubMed search [2] [3]
Wikidata
View/Edit Human View/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.[4][5][6]

EBF1 controls the expression of key proteins required for B cell differentiation, signal transduction and function.[7][8] The crucial role of this factor is shown in the regulation of expression of SLAM family co-receptors in B-cells.[9]

Interactions

EBF1 has been shown to interact with ZNF423[10] and CREB binding protein.[11]

References

  1. ^ "Diseases that are genetically associated with EBF1 view/edit references on wikidata". 
  2. ^ "Human PubMed Reference:". 
  3. ^ "Mouse PubMed Reference:". 
  4. ^ http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=3126.  Missing or empty |title= (help)
  5. ^ 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. 
  6. ^ "Entrez Gene: EBF1 early B-cell factor 1". 
  7. ^ Treiber, Thomas; Mandel, Elizabeth M.; Pott, Sebastian; Györy, Ildiko; Firner, Sonja; Liu, Edison T.; Grosschedl, Rudolf. "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. 
  8. ^ 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. ISSN 0070-217X. PMC 3925327Freely accessible. PMID 21735360. 
  9. ^ 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. 
  10. ^ 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. PMID 9151733. 
  11. ^ Zhao F, McCarrick-Walmsley R, Akerblad P, Sigvardsson M, Kadesch T (Jun 2003). "Inhibition of p300/CBP by early B-cell factor". Mol. Cell. Biol. 23 (11): 3837–46. doi:10.1128/MCB.23.11.3837-3846.2003. PMC 155219Freely accessible. 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 helix-loop-helix domain Provide feedback

This is the helix-loop-helix domain of transcription factor COE1. It is responsible for dimerisation [1].

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


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR032201

This is the helix-loop-helix domain of transcription factor COE. It is responsible for dimerisation [PUBMED:20876732].

Domain organisation

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

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Alignments

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...

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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.

  Seed
(7)
Full
(533)
Representative proteomes UniProt
(778)
NCBI
(2392)
Meta
(0)
RP15
(93)
RP35
(175)
RP55
(349)
RP75
(455)
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Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(7)
Full
(533)
Representative proteomes UniProt
(778)
NCBI
(2392)
Meta
(0)
RP15
(93)
RP35
(175)
RP55
(349)
RP75
(455)
Alignment:
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Sequence:
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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.

  Seed
(7)
Full
(533)
Representative proteomes UniProt
(778)
NCBI
(2392)
Meta
(0)
RP15
(93)
RP35
(175)
RP55
(349)
RP75
(455)
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...

Trees

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.

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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: Jackhmmer:Q07802
Previous IDs: none
Type: Domain
Author: Eberhardt RY
Number in seed: 7
Number in full: 533
Average length of the domain: 43.50 aa
Average identity of full alignment: 88 %
Average coverage of the sequence by the domain: 8.75 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 28.1 34.5
Noise cut-off 26.7 26.6
Model length: 44
Family (HMM) version: 4
Download: download the raw HMM for this family

Species distribution

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Structures

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_HLH domain has been found. There are 13 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 seqence.

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