FB2026_01 , released March 12, 2026
FB2026_01 , released March 12, 2026
Gene: Dmel\Elba1
Open Close
General Information
Symbol
Dmel\Elba1
Species
D. melanogaster
Name
Early boundary activity 1
Annotation Symbol
CG12205
Feature Type
protein_coding_gene
FlyBase ID
FBgn0000227
Gene Model Status
Current
Stock Availability
9 publicly available
Gene Summary
The heterotrimeric Elba complex is required for chromatin domain boundary function during early embryogenesis. It binds to a 8-bp sequence 5'-CCAATAAG-3' in the Fab-7 insulator or boundary element in the bithorax complex and contributes to its insulator or boundary activity (PubMed:23240086). Elba1 may act as a transcriptional repressor and binds the palindromic sequence 5'-CCAATTGG-3' to mediate transcriptional repression (PubMed:25561495). (UniProt, Q9VR17)
Contribute a Gene Snapshot for this gene.
All Summaries
Also Known As

Bsg25A, Elba, Blastoderm-specific gene 25A

Key Links
Genomic Location
Cytogenetic map
25A3-25A3
Sequence location
Recombination map
2-13
RefSeq locus
NT_033779 REGION:4683052..4684461
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
Gene Ontology (GO) Annotations (10 terms)
Molecular Function (4 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
contributes_to chromatin insulator sequence binding
inferred from direct assay
(Aoki et al., 2012)
enables chromatin insulator sequence binding
inferred from direct assay
(Aoki et al., 2014)
contributes_to sequence-specific DNA binding
inferred from direct assay
(Aoki et al., 2012)
enables sequence-specific DNA binding
inferred from direct assay
(Dai et al., 2015)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
enables DNA binding
inferred from electronic annotation with InterPro:IPR018379
(InterPro Project Members, 2004-)
enables transcription corepressor activity
inferred from electronic annotation with InterPro:IPR037496
(InterPro Project Members, 2004-)
Biological Process (4 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
involved_in embryonic development via the syncytial blastoderm
inferred from expression pattern
(Singer and Lengyel, 1997)
involved_in heterochromatin boundary formation
inferred from mutant phenotype
(Aoki et al., 2012)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
involved_in negative regulation of Notch signaling pathway
inferred from electronic annotation with InterPro:IPR037496
(InterPro Project Members, 2004-)
involved_in positive regulation of neuron differentiation
inferred from electronic annotation with InterPro:IPR037496
(InterPro Project Members, 2004-)
Cellular Component (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
part_of chromatin silencing complex
inferred from direct assay
(Aoki et al., 2012)
located_in nucleus
inferred from direct assay
(Dai et al., 2015)
inferred from direct assay
(Aoki et al., 2012)
Terms Based on Predictions or Assertions (0 terms)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Group (FlyBase)
ELBA BOUNDARY FACTOR COMPLEX -
The heterotrimeric insulator complex ELBA is a chromatin boundary factor, which binds to specific DNA and confers insulator activity during early embryogenesis. (Adapted from FBrf0227658 and FBrf0221291).
Protein Function (UniProtKB)
The heterotrimeric Elba complex is required for chromatin domain boundary function during early embryogenesis. It binds to a 8-bp sequence 5'-CCAATAAG-3' in the Fab-7 insulator or boundary element in the bithorax complex and contributes to its insulator or boundary activity (PubMed:23240086). Elba1 may act as a transcriptional repressor and binds the palindromic sequence 5'-CCAATTGG-3' to mediate transcriptional repression (PubMed:25561495).
(UniProt, Q9VR17)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Elba1 for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)
Isoform displayed:
Pfam protein domains
InterPro name
classification
start
end
Protein Domains (via SMART)
Isoform displayed:
SMART protein domains
InterPro name
classification
start
end
Structure
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry Q9VR17)

If you don't see a structure in the viewer, refresh your browser.
Model Confidence:
  • Very high (pLDDT > 90)
  • Confident (90 > pLDDT > 70)
  • Low (70 > pLDDT > 50)
  • Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures
Crossreferences
PDB - An information portal to biological macromolecular structures
Comments on Gene Model

Gene model reviewed during 5.52

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Elba1-RA
FBtr0077423
NM_078748
1352
363
Additional Transcript Data and Comments
Reported size (kB)

1.7 (northern blot)

(Singer and Lengyel, 1997)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
Elba1-PA
FBpp0077114
41.6
363
4.77
Q9VR17
NP_523472
AAF50991
Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments
Reported size (kDa)

209 (aa); 23 (kD predicted)

(Singer and Lengyel, 1997)
Comments
External Data
Subunit Structure (UniProtKB)

The heterotrimeric Elba complex consists of Elba1, Elba2 and Elba3.

(UniProt, Q9VR17)
Domain

The BEN domain mediates DNA-binding.

(UniProt, Q9VR17)
Crossreferences
InterPro - A database of protein families, domains and functional sites
PDB - An information portal to biological macromolecular structures
Linkouts
Sequences Consistent with the Gene Model
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Elba1 using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Expression Data
Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

-0.19

Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage 1 -- 3
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 4 -- 6
antennal anlage in statu nascendi

Comment: reported as procephalic ectoderm anlage in statu nascendi

(Fisher et al., 2012)
dorsal head epidermis anlage in statu nascendi

Comment: reported as procephalic ectoderm anlage in statu nascendi

(Fisher et al., 2012)
visual anlage in statu nascendi

Comment: reported as procephalic ectoderm anlage in statu nascendi

(Fisher et al., 2012)
anlage in statu nascendi
(Fisher et al., 2012)
central brain anlage in statu nascendi
(Fisher et al., 2012)
ectoderm anlage

Comment: anlage in statu nascendi

(Fisher et al., 2012)
northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage 4
(Singer and Lengyel, 1997)
organism
(Singer and Lengyel, 1997)
embryonic stage 5 -- 8
(Aoki et al., 2012)
Additional Descriptive Data

Elba1 transcript expression peaks at the blastoderm stage (2-4 hours) of embryogenesis and then disappears. It is expressed in oogenesis and is not observed in 0-2 hour embryos.

(Aoki et al., 2012)

Elba1 transcripts are first detected at nuclear cycle 10 and peak during nuclear cycle 13 (late syncytial blastoderm). They rapidly disappear during the cellular blastoderm stage. They are not detected at any other point in the life cycle.

(Singer and Lengyel, 1997)
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
part_of chromatin silencing complex
inferred from direct assay
(Aoki et al., 2012)
located_in nucleus
inferred from direct assay
(Dai et al., 2015)
inferred from direct assay
(Aoki et al., 2012)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Elba1 in JBrowse
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Bulk Downloads
RNA-Seq RPKM values for all genes
Reference
See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
Developmental Proteome: Life Cycle
Developmental Proteome: Embryogenesis
External Data and Images
Linkouts
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyExpress - Embryonic expression images (BDGP data)
  • Stages(s) 1-3
  • Stages(s) 4-6
  • Stages(s) 13-16
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 4 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 6 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Elba1
Transgenic constructs containing regulatory region of Elba1
Aberrations (Deficiencies and Duplications) ( 0 )
Inferred from experimentation ( 0 )
Inferred from location ( 4 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
viable, with Dcr-2UAS.cDa, Scer\GAL4elav.PLu
viable, with Scer\GAL4Mef2.PR
viable, with Scer\GAL4pnr-MD237
Phenotype manifest in
Allele
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (0)
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (0)
Mus musculus (laboratory mouse) (0)
Xenopus tropicalis (Western clawed frog) (1)
Xtro\XB5788060
1 of 13
Yes
Yes
Danio rerio (Zebrafish) (0)
Caenorhabditis elegans (Nematode, roundworm) (0)
Anopheles gambiae (African malaria mosquito) (1)
Agam\AgaP_AGAP009151
4 of 12
Yes
Yes
Arabidopsis thaliana (thale-cress) (0)
Saccharomyces cerevisiae (Brewer's yeast) (0)
Schizosaccharomyces pombe (Fission yeast) (0)
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Elba1. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Gene Symbol
Score
Source
Compara
Domainoid
eggNOG
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Drosophila melanogaster (Fruit fly) (2)
insv
5 of 13
Elba2
3 of 13
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Ontology (DO) Annotations
    Models Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Evidence
    References
    Potential Models Based on Orthology ( 0 )
    Human Ortholog
    Disease
    Evidence
    References
    Modifiers Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Interaction
    References
    Disease Associations of Human Orthologs (via DIOPT v9.1 and OMIM)
    Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
    Homo sapiens (Human)
    Gene name
    Score
    OMIM
    OMIM Phenotype
    DO term
    Complementation?
    Transgene?
    Functional Complementation Data
    Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
    Interactions
    Summary of Physical Interactions
    Summary of Genetic Interactions
    Interaction Browsers
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    External Data
    Subunit Structure (UniProtKB)
    The heterotrimeric Elba complex consists of Elba1, Elba2 and Elba3.
    (UniProt, Q9VR17 )
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DroID - A comprehensive database of gene and protein interactions.
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Pathways
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    FlyBase
    External Links
    External Data
    Linkouts
    Class of Gene
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    2L
    Recombination map
    2-13
    Cytogenetic map
    25A3-25A3
    Sequence location
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    25A3-25A3
    Limits computationally determined from genome sequence between P{lacW}Tps1k08903&P{EP}morgueEP1184 and P{lacW}l(2)k10004k10004&P{EP}CG3036EP963
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    25A1-25A2
    (Singer, 1996.12.2)
    25A1-25A2
    (determined by in situ hybridisation)
    (Singer and Lengyel, 1997)
    Experimentally Determined Recombination Data
    Location

    2-13

    (FlyBase, 2016)

    2-13.9

    (Comeron et al., 2012)
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (9)
    Genomic Clones (18)
     

    Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

    cDNA Clones (20)
     

    Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see JBrowse for alignment of the cDNAs and ESTs to the gene model.

    cDNA clones, fully sequenced
    BDGP DGC clones
    Other clones
      Drosophila Genomics Resource Center cDNA clones

      For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

      cDNA Clones, End Sequenced (ESTs)
      BDGP DGC clones
      Other clones
      RNAi and Array Information
      Linkouts
      DRSC - Results frm RNAi screens
      Antibody Information
      Laboratory Generated Antibodies
       

      polyclonal

      (Aoki et al., 2012)
      Commercially Available Antibodies
       
      Cell Line Information
      Publicly Available Cell Lines
       
        Other Stable Cell Lines
         
          Other Comments

          Bsg25A, Elba2 and Elba3 form a hetero-tripartite protein complex that acts as a developmentally restricted chromatin boundary factor.

          (Aoki et al., 2012)

          dsRNA has been made from templates generated with primers directed against this gene.

          (Pilot et al., 2006)

          Temporal and spatial expression and the predicted gene product of Bsg25A are identified.

          (Singer and Lengyel, 1997)
          Relationship to Other Genes
          Source for database merge of
          Additional comments
          Nomenclature History
          Source for database identify of

          Source for identity of: Elba1 Bsg25A

          (Aoki et al., 2012)
          Nomenclature comments
          Etymology
          Synonyms and Secondary IDs (12)
          Datasets (0)
          Study focus (0)
          Experimental Role
          Project
          Project Type
          Title
          Study result (0)
          Result
          Result Type
          Title
          External Crossreferences and Linkouts ( 36 )
          Sequence Crossreferences
          NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
          GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.
          GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
          RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
          UniProt/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.
          UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
          UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
          Other crossreferences
          AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.
          BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
          DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
          EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
          FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
          FlyMine - An integrated database for Drosophila genomics
          InterPro - A database of protein families, domains and functional sites
          KEGG Genes - Molecular building blocks of life in the genomic space.
          MARRVEL_MODEL - MARRVEL (model organism gene)
          PDB - An information portal to biological macromolecular structures
          Linkouts
          BioGRID - A database of protein and genetic interactions.
          Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
          DroID - A comprehensive database of gene and protein interactions.
          DRSC - Results frm RNAi screens
          Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
          FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
          FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
          Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
          Flygut - An atlas of the Drosophila adult midgut
          iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
          MIST (protein-protein) - An integrated Molecular Interaction Database
          References (45)