FB2026_02 , released June 18, 2026
Gene: Dmel\Reph
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General Information
Symbol
Dmel\Reph
Species
D. melanogaster
Name
Regulator of eph expression
Annotation Symbol
CG3920
Feature Type
protein_coding_gene
FlyBase ID
FBgn0021800
Gene Model Status
Current
Stock Availability
16 publicly available
Gene Summary
Regulator of eph expression (Reph) encodes a putative nuclear protein involved in visual system development via the regulation of the product of Eph. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)
All Summaries
Also Known As

l(2)k16918

Key Links
Genomic Location
Cytogenetic map
24C5-24C5
Sequence location
Recombination map
2-11
RefSeq locus
NT_033779 REGION:3803545..3810671
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 (3 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
involved_in ephrin receptor signaling pathway
inferred from genetic interaction with FLYBASE:Eph; FB:FBgn0025936,FLYBASE:Ephrin; FB:FBgn0040324
(Dearborn et al., 2012)
involved_in peripheral nervous system development
inferred from mutant phenotype
(Dearborn et al., 2012)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
involved_in ephrin receptor signaling pathway
inferred from biological aspect of ancestor with PANTHER:PTN005124345
(GO Reference Genome Project, 2011-)
involved_in peripheral nervous system development
inferred from biological aspect of ancestor with PANTHER:PTN005124345
(GO Reference Genome Project, 2011-)
Cellular Component (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
located_in cytoplasm
inferred from high throughput direct assay
(Sarov et al., 2016)
Terms Based on Predictions or Assertions (0 terms)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
    -
    Summaries
    Gene Snapshot
    Regulator of eph expression (Reph) encodes a putative nuclear protein involved in visual system development via the regulation of the product of Eph. [Date last reviewed: 2019-03-14]
    Gene Model and Products
    Number of Transcripts
    2
    Number of Unique Polypeptides
    2

    Please see the JBrowse view of Dmel\Reph 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 Q8MRQ2)

    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
    Comments on Gene Model

    Low-frequency RNA-Seq exon junction(s) not annotated.

    Gene model reviewed during 5.47

    Transcript Data
    Annotated Transcripts
    Name
    FlyBase ID
    RefSeq ID
    Length (nt)
    Assoc. CDS (aa)
    Reph-RA
    FBtr0077497
    NM_143795
    3750
    351
    Reph-RB
    FBtr0077498
    NM_164561
    2928
    401
    Additional Transcript Data and Comments
    Reported size (kB)
    Comments
    External Data
    Crossreferences
    Polypeptide Data
    Annotated Polypeptides
    Name
    FlyBase ID
    Predicted MW (kDa)
    Length (aa)
    Theoretical pI
    UniProt
    RefSeq ID
    GenBank
    Reph-PA
    FBpp0077186
    36.7
    351
    8.12
    Q9VQV2
    NP_652052
    AAF51060
    Reph-PB
    FBpp0077187
    42.7
    401
    8.12
    Q8MRQ2
    NP_722945
    AAN10362
    Polypeptides with Identical Sequences

    None of the polypeptides share 100% sequence identity.

    Additional Polypeptide Data and Comments
    Reported size (kDa)
    Comments
    External Data
    Crossreferences
    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\Reph 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).

    -0.74

    Transcript Expression
    Polypeptide Expression
    Additional Descriptive Data
    Marker for
     
    Subcellular Localization
    CV Term
    Evidence
    References
    located_in cytoplasm
    inferred from high throughput direct assay
    (Sarov et al., 2016)
    Expression Deduced from Reporters
    High-Throughput Expression Data
    Associated Tools

    JBrowse - Visual display of RNA-Seq signals

    View Dmel\Reph 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) 7-8
    • Stages(s) 9-10
    • Stages(s) 11-12
    • Stages(s) 13-16
    FlyBase Wiki
    Image Based Resources
    Alleles, Insertions, Transgenic Constructs, and Aberrations
    Classical and Insertion Alleles ( 26 )
    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 Reph
    Transgenic constructs containing regulatory region of Reph
    Aberrations (Deficiencies and Duplications) ( 3 )
    Inferred from experimentation ( 3 )
    Gene not disrupted in
    Df(2L)ed1
    (Spradling et al., 1999, BDGP Project Members, 1994-1999)
    Gene disrupted in
    Df(2L)Exel6009
    (Ryder, 2004.4.26)
    Df(2L)sc19-8
    (Dearborn et al., 2012)
    Inferred from location ( 4 )
    Variants
    Variant Molecular Consequences
    Alleles Representing Disease-Implicated Variants
    Phenotypes
    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\MGC86483
    1 of 13
    Yes
    Yes
    Danio rerio (Zebrafish) (1)
    Drer\si:dkey-16j16.4
    2 of 14
    Yes
    Yes
    Caenorhabditis elegans (Nematode, roundworm) (0)
    Anopheles gambiae (African malaria mosquito) (1)
    Agam\AgaP_AGAP009144
    9 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:Reph. Refer to their site for version information.
    Paralogs
    Downloads
    Download All DIOPT Paralogs
    Paralogs (via DIOPT v9.1)
    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
      Interaction Browsers
      View in FlyBase Interactions Browser   View in MIST tool (external link)
      Please see the Physical Interaction reports below for full details
      protein-protein
      Physical Interaction
      Assay
      References
      Reph - mnb
      experimental knowledge based
      (Guruharsha et al., 2011)
      Reph - wap
      experimental knowledge based
      (Guruharsha et al., 2011)
      Summary of Genetic Interactions
      Interaction Browsers
      View in FlyBase Interactions Browser   View in MIST tool (external link)
      Please look at the allele data for full details of the genetic interactions
      Starting gene(s)
      Interaction type
      Interacting gene(s)
      Reference
      Starting gene(s)
      Interaction type
      Interacting gene(s)
      Reference
      Eph
      enhanceable
      Reph
      (Dearborn et al., 2012, Bettencourt da Cruz et al., 2008)
      Ephrin
      enhanceable
      Reph
      (Dearborn et al., 2012, Bettencourt da Cruz et al., 2008)
      Ephrin
      suppressible
      Reph
      (Dearborn et al., 2012)
      External Data
      Linkouts
      DroID - A comprehensive database of gene and protein interactions.
      MIST (genetic) - An integrated Molecular Interaction Database
      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
      2-11
      Cytogenetic map
      24C5-24C5
      Sequence location
      FlyBase Computed Cytological Location
      Cytogenetic map
      Evidence for location
      24C5-24C5
      Limits computationally determined from genome sequence between P{EP}EP2595EP2595 and P{lacW}edk01102
      Experimentally Determined Cytological Location
      Cytogenetic map
      Notes
      References
      24C8-24C9
      (determined by in situ hybridisation)
      (Spradling et al., 1999)
      24C8-24C9
      (BDGP Project Members, 1994-1999)
      Experimentally Determined Recombination Data
      Location

      2-11

      (FlyBase, 2016)

      2-10.1

      (Comeron et al., 2012)
      Left of (cM)
      Right of (cM)
      Notes
      Stocks and Reagents
      Stocks (16)
      Genomic Clones (12)
       

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

      cDNA Clones (138)
       

      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
       
      Commercially Available Antibodies
       
      Cell Line Information
      Publicly Available Cell Lines
       
        Other Stable Cell Lines
         
          Other Comments

          Identification: One of a collection of genes identified with defective larval growth that extend larval life. Not studied further due to problems with background/multiple lesion effects.

          (Galloni and Edgar, 1999)
          Relationship to Other Genes
          Source for database merge of

          Source for merge of: l(2)k16918 CG3920

          (FlyBase, 1996-)
          Additional comments

          Source for merge of l(2)k16918 CG3920 was a shared cDNA (GH05923) ( date:011030 ).

          (FlyBase, 1996-)
          Nomenclature History
          Source for database identify of

          Source for identity of: Reph l(2)k16918

          (Dearborn et al., 2012)
          Nomenclature comments
          Etymology
          Synonyms and Secondary IDs (7)
          Reported As
          Symbol Synonym
          CG3920
          (National Institute of Genetics Fly Stocks, 2022-, Hosono et al., 2015, Dearborn et al., 2012, Ni et al., 2010.12.1, Stanyon et al., 2004)
          Reph
          (Clandinin and Owens, 2016-, Sarov et al., 2016)
          l(2)k16918
          (Sarov et al., 2016, Levis et al., 2011.12.16, Zhang et al., 2007)
          reph
          (Dearborn et al., 2012)
          Name Synonyms
          Regulator of eph expression
          lethal (2) k16918
          regulator of eph expression
          (Dearborn et al., 2012)
          Secondary FlyBase IDs
          • FBgn0031572
          Datasets (0)
          Study focus (0)
          Experimental Role
          Project
          Project Type
          Title
          Study result (0)
          Result
          Result Type
          Title
          External Crossreferences and Linkouts ( 46 )
          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/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
          KEGG Genes - Molecular building blocks of life in the genomic space.
          MARRVEL_MODEL - MARRVEL (model organism gene)
          Linkouts
          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 (genetic) - An integrated Molecular Interaction Database
          MIST (protein-protein) - An integrated Molecular Interaction Database
          References (38)