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Protein

Transcription factor COE3

Gene

EBF3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Transcriptional activator (PubMed:28017373, PubMed:28017372, PubMed:28017370). Recognizes variations of the palindromic sequence 5'-ATTCCCNNGGGAATT-3' (By similarity).By similarity3 Publications

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri151 – 170C5-typeSequence analysisAdd BLAST20

GO - Molecular functioni

GO - Biological processi

  • multicellular organism development Source: UniProtKB-KW
  • positive regulation of transcription, DNA-templated Source: UniProtKB

Keywordsi

Molecular functionActivator, Developmental protein, DNA-binding
Biological processTranscription, Transcription regulation
LigandMetal-binding, Zinc

Enzyme and pathway databases

SIGNORiQ9H4W6.

Names & Taxonomyi

Protein namesi
Recommended name:
Transcription factor COE3
Alternative name(s):
Early B-cell factor 3
Short name:
EBF-3
Olf-1/EBF-like 2
Short name:
O/E-2
Short name:
OE-2
Gene namesi
Name:EBF3
Synonyms:COE3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 10

Organism-specific databases

EuPathDBiHostDB:ENSG00000108001.13.
HGNCiHGNC:19087. EBF3.

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Involvement in diseasei

Hypotonia, ataxia, and delayed development syndrome (HADDS)3 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionAn autosomal dominant neurodevelopmental syndrome characterized by global developmental delay, moderate to severe intellectual disability, cerebellar ataxia, hypotonia, speech delay, variable dysmorphic features, and genitourinary abnormalities including vesicoureteric reflux.
See also OMIM:617330
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_07803366N → D in HADDS; significant loss of transcriptional activator activity; localizes both in the cytoplasm and the nucleus; decreased chromatin binding. 1 Publication1
Natural variantiVAR_078034141Y → C in HADDS; significant loss of transcriptional activator activity; localizes both in the cytoplasm and the nucleus; decreased chromatin-binding. 1 Publication1
Natural variantiVAR_078035159I → IHEI in HADDS; significant loss of transcriptional activator activity; localizes both in the cytoplasm and the nucleus; decreased chromatin-binding. 1 Publication1
Natural variantiVAR_078036163R → L in HADDS; partial loss of transcriptional activator activity. 1 Publication1
Natural variantiVAR_078037163R → P in HADDS; loss of transcriptional activator activity. 1 Publication1
Natural variantiVAR_078038163R → Q in HADDS; loss of transcriptional activator activity. 1 Publication1
Natural variantiVAR_078039171G → D in HADDS; significant loss of transcriptional activator activity; localizes both in the cytoplasm and the nucleus; decreased chromatin-binding. 1 Publication1
Natural variantiVAR_078040177P → L in HADDS; according to PubMed:28017373 shows significant loss of transcriptional activator activity while according to PubMed:28017370 shows partial loss of transcriptional activator activity; localizes both in the cytoplasm and the nucleus; decreased chromatin-binding. 2 PublicationsCorresponds to variant dbSNP:rs869312668Ensembl.1
Natural variantiVAR_078041193K → N in HADDS; significant loss of transcriptional activator activity. 1 Publication1
Natural variantiVAR_078042209R → W in HADDS; significant loss of transcriptional activator activity; localizes both in the cytoplasm and the nucleus; decreased chromatin-binding. 1 Publication1

Keywords - Diseasei

Disease mutation, Mental retardation

Organism-specific databases

DisGeNETi253738.
MIMi617330. phenotype.
OpenTargetsiENSG00000108001.
PharmGKBiPA134972607.

Polymorphism and mutation databases

BioMutaiEBF3.
DMDMi13959320.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001078321 – 596Transcription factor COE3Add BLAST596

Proteomic databases

MaxQBiQ9H4W6.
PeptideAtlasiQ9H4W6.
PRIDEiQ9H4W6.

PTM databases

iPTMnetiQ9H4W6.
PhosphoSitePlusiQ9H4W6.

Expressioni

Tissue specificityi

Expressed in brain.1 Publication

Gene expression databases

BgeeiENSG00000108001.
CleanExiHS_EBF3.
ExpressionAtlasiQ9H4W6. baseline and differential.
GenevisibleiQ9H4W6. HS.

Organism-specific databases

HPAiHPA061169.

Interactioni

Subunit structurei

Forms either a homodimer or a heterodimer with a related family member.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei163Interaction with DNABy similarity1
Sitei172Interaction with DNABy similarity1

Protein-protein interaction databases

BioGridi128985. 7 interactors.
IntActiQ9H4W6. 7 interactors.

Structurei

Secondary structure

1596
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi264 – 274Combined sources11
Beta strandi280 – 287Combined sources8
Beta strandi293 – 296Combined sources4
Beta strandi299 – 301Combined sources3
Beta strandi303 – 307Combined sources5
Beta strandi310 – 314Combined sources5
Beta strandi322 – 330Combined sources9
Beta strandi333 – 335Combined sources3
Beta strandi337 – 339Combined sources3
Beta strandi341 – 346Combined sources6
Helixi353 – 363Combined sources11
Helixi376 – 391Combined sources16
Helixi396 – 412Combined sources17

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3MUJX-ray1.92A/B261-395[»]
3N50X-ray3.10A/B/C/D/E/F261-415[»]
ProteinModelPortaliQ9H4W6.
SMRiQ9H4W6.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9H4W6.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini263 – 346IPT/TIGAdd BLAST84

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni63 – 66Interaction with DNABy similarity4
Regioni197 – 204Interaction with DNABy similarity8
Regioni236 – 239Interaction with DNABy similarity4

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi464 – 555Pro/Ser/Thr-richAdd BLAST92

Sequence similaritiesi

Belongs to the COE family.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri151 – 170C5-typeSequence analysisAdd BLAST20

Keywords - Domaini

Zinc-finger

Phylogenomic databases

GeneTreeiENSGT00390000014051.
HOGENOMiHOG000092311.
HOVERGENiHBG005108.
InParanoidiQ9H4W6.
KOiK09103.
OMAiIRLIDSM.
OrthoDBiEOG091G0A9D.
PhylomeDBiQ9H4W6.
TreeFamiTF313391.

Family and domain databases

Gene3Di2.60.40.10. 1 hit.
InterProiView protein in InterPro
IPR032200. COE_DBD.
IPR032201. COE_HLH.
IPR013783. Ig-like_fold.
IPR014756. Ig_E-set.
IPR002909. IPT.
IPR003523. Transcription_factor_COE.
IPR018350. Transcription_factor_COE_CS.
PANTHERiPTHR10747. PTHR10747. 1 hit.
PfamiView protein in Pfam
PF16422. COE1_DBD. 1 hit.
PF16423. COE1_HLH. 1 hit.
PF01833. TIG. 1 hit.
SMARTiView protein in SMART
SM00429. IPT. 1 hit.
SUPFAMiSSF81296. SSF81296. 1 hit.
PROSITEiView protein in PROSITE
PS01345. COE. 1 hit.

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform Long (identifier: Q9H4W6-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MFGIQENIPR GGTTMKEEPL GSGMNPVRSW MHTAGVVDAN TAAQSGVGLA
60 70 80 90 100
RAHFEKQPPS NLRKSNFFHF VLALYDRQGQ PVEIERTAFV DFVEKEKEPN
110 120 130 140 150
NEKTNNGIHY KLQLLYSNGV RTEQDLYVRL IDSMTKQAIV YEGQDKNPEM
160 170 180 190 200
CRVLLTHEIM CSRCCDKKSC GNRNETPSDP VIIDRFFLKF FLKCNQNCLK
210 220 230 240 250
NAGNPRDMRR FQVVVSTTVN VDGHVLAVSD NMFVHNNSKH GRRARRLDPS
260 270 280 290 300
EGTAPSYLEN ATPCIKAISP SEGWTTGGAT VIIIGDNFFD GLQVVFGTML
310 320 330 340 350
VWSELITPHA IRVQTPPRHI PGVVEVTLSY KSKQFCKGAP GRFVYTALNE
360 370 380 390 400
PTIDYGFQRL QKVIPRHPGD PERLPKEVLL KRAADLVEAL YGMPHNNQEI
410 420 430 440 450
ILKRAADIAE ALYSVPRNHN QIPTLGNNPA HTGMMGVNSF SSQLAVNVSE
460 470 480 490 500
TSQANDQVGY SRNTSSVSPR GYVPSSTPQQ SNYNTVSTSM NGYGSGAMAS
510 520 530 540 550
LGVPGSPGFL NGSSANSPYG IVPSSPTMAA SSVTLPSNCS STHGIFSFSP
560 570 580 590
ANVISAVKQK SAFAPVVRPQ ASPPPSCTSA NGNGLQAMSG LVVPPM
Length:596
Mass (Da):64,864
Last modified:May 4, 2001 - v2
Checksum:iEE5C9D10CD3DED02
GO
Isoform Short (identifier: Q9H4W6-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     252-260: Missing.
     521-558: IVPSSPTMAASSVTLPSNCSSTHGIFSFSPANVISAVK → MK

Show »
Length:551
Mass (Da):60,415
Checksum:i0813B855111FAB12
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_07803366N → D in HADDS; significant loss of transcriptional activator activity; localizes both in the cytoplasm and the nucleus; decreased chromatin binding. 1 Publication1
Natural variantiVAR_078034141Y → C in HADDS; significant loss of transcriptional activator activity; localizes both in the cytoplasm and the nucleus; decreased chromatin-binding. 1 Publication1
Natural variantiVAR_078035159I → IHEI in HADDS; significant loss of transcriptional activator activity; localizes both in the cytoplasm and the nucleus; decreased chromatin-binding. 1 Publication1
Natural variantiVAR_078036163R → L in HADDS; partial loss of transcriptional activator activity. 1 Publication1
Natural variantiVAR_078037163R → P in HADDS; loss of transcriptional activator activity. 1 Publication1
Natural variantiVAR_078038163R → Q in HADDS; loss of transcriptional activator activity. 1 Publication1
Natural variantiVAR_078039171G → D in HADDS; significant loss of transcriptional activator activity; localizes both in the cytoplasm and the nucleus; decreased chromatin-binding. 1 Publication1
Natural variantiVAR_078040177P → L in HADDS; according to PubMed:28017373 shows significant loss of transcriptional activator activity while according to PubMed:28017370 shows partial loss of transcriptional activator activity; localizes both in the cytoplasm and the nucleus; decreased chromatin-binding. 2 PublicationsCorresponds to variant dbSNP:rs869312668Ensembl.1
Natural variantiVAR_078041193K → N in HADDS; significant loss of transcriptional activator activity. 1 Publication1
Natural variantiVAR_078042209R → W in HADDS; significant loss of transcriptional activator activity; localizes both in the cytoplasm and the nucleus; decreased chromatin-binding. 1 Publication1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_001113252 – 260Missing in isoform Short. 1 Publication9
Alternative sequenceiVSP_001114521 – 558IVPSS…ISAVK → MK in isoform Short. 1 PublicationAdd BLAST38

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL354950 Genomic DNA. Translation: CAI12792.1.
AL354950 Genomic DNA. Translation: CAI12793.1.
CH471066 Genomic DNA. Translation: EAW49160.1.
BC126130 mRNA. Translation: AAI26131.1.
BC130479 mRNA. Translation: AAI30480.1.
CCDSiCCDS31314.1. [Q9H4W6-2]
RefSeqiNP_001005463.1. NM_001005463.2. [Q9H4W6-2]
XP_005252725.1. XM_005252668.3. [Q9H4W6-1]
UniGeneiHs.591374.

Genome annotation databases

EnsembliENST00000355311; ENSP00000347463; ENSG00000108001. [Q9H4W6-1]
ENST00000368648; ENSP00000357637; ENSG00000108001. [Q9H4W6-2]
GeneIDi253738.
KEGGihsa:253738.
UCSCiuc001lki.3. human. [Q9H4W6-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiCOE3_HUMAN
AccessioniPrimary (citable) accession number: Q9H4W6
Secondary accession number(s): A0AUY1, Q5T6H9, Q9H4W5
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 4, 2001
Last sequence update: May 4, 2001
Last modified: September 27, 2017
This is version 141 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 10
    Human chromosome 10: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families