FB2026_01 , released March 12, 2026
FB2026_01 , released March 12, 2026
Gene: Dmel\sala
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General Information
Symbol
Dmel\sala
Species
D. melanogaster
Name
spalt-adjacent
Annotation Symbol
CG4922
Feature Type
protein_coding_gene
FlyBase ID
FBgn0003313
Gene Model Status
Current
Stock Availability
11 publicly available
Gene Summary
Likely to be involved in the establishment of the head. (UniProt, P21750)
Contribute a Gene Snapshot for this gene.
All Summaries
Also Known As

sal, spalt

Key Links
Genomic Location
Cytogenetic map
32F2-32F2
Sequence location
Recombination map
2-44
RefSeq locus
NT_033779 REGION:11484707..11486949
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 (1 term)
Molecular Function (0 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
involved_in gastrulation
inferred from expression pattern
(Gonzalez-Aguero et al., 2005)
Terms Based on Predictions or Assertions (0 terms)
Cellular Component (0 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
    -
    Summaries
    Protein Function (UniProtKB)
    Likely to be involved in the establishment of the head.
    (UniProt, P21750)
    Gene Model and Products
    Number of Transcripts
    2
    Number of Unique Polypeptides
    1

    Please see the JBrowse view of Dmel\sala 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 P21750)

    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

    Gene model reviewed during 5.52

    Dicistronic transcript isoform(s) appear to be relatively rare based on RNA-Seq and/or EST data; may be stage- or tissue-specific.

    Gene model reviewed during 6.01

    Transcript Data
    Annotated Transcripts
    Name
    FlyBase ID
    RefSeq ID
    Length (nt)
    Assoc. CDS (aa)
    sala-RA
    FBtr0080237
    NM_078825
    698
    142
    sala-RC
    FBtr0308136
    NM_001259056
    1697
    142
    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
    sala-PA
    FBpp0079824
    14.6
    142
    7.00
    P21750
    NP_523549
    AAF53098
    sala-PC
    FBpp0300458
    14.6
    142
    7.00
    P21750
    NP_001245985
    AFH03659
    Polypeptides with Identical Sequences

    The group(s) of polypeptides indicated below share identical sequence to each other.

    142 aa isoforms: sala-PA, sala-PC
    Additional Polypeptide Data and Comments
    Reported size (kDa)

    142 (aa); 14.5 (kD predicted)

    (Frei et al., 1988)
    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\sala 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).

    -0.17

    Transcript Expression
    in situ
    Stage
    Tissue/Position (including subcellular localization)
    Reference
    embryonic stage 4 -- 6
    anlage in statu nascendi
    (Fisher et al., 2012)
    anterior endoderm anlage

    Comment: anlage in statu nascendi

    (Fisher et al., 2012)
    central brain anlage in statu nascendi
    (Fisher et al., 2012)
    clypeo-labral anlage in statu nascendi
    (Fisher et al., 2012)
    foregut anlage in statu nascendi
    (Fisher et al., 2012)
    hindgut anlage in statu nascendi
    (Fisher et al., 2012)
    mesoderm anlage

    Comment: anlage in statu nascendi

    (Fisher et al., 2012)
    posterior ectoderm anlage

    Comment: anlage in statu nascendi

    (Fisher et al., 2012)
    ventral ectoderm anlage

    Comment: 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)
    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)
    embryonic stage 7 -- 8
    antennal anlage

    Comment: reported as procephalic ectoderm anlage

    (Fisher et al., 2012)
    central brain anlage

    Comment: reported as procephalic ectoderm anlage

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

    Comment: reported as procephalic ectoderm anlage

    (Fisher et al., 2012)
    visual anlage

    Comment: reported as procephalic ectoderm anlage

    (Fisher et al., 2012)
    anterior endoderm anlage
    (Fisher et al., 2012)
    clypeo-labral anlage
    (Fisher et al., 2012)
    foregut anlage
    (Fisher et al., 2012)
    head mesoderm
    (Fisher et al., 2012)
    hindgut anlage
    (Fisher et al., 2012)
    posterior endoderm
    (Fisher et al., 2012)
    trunk mesoderm
    (Fisher et al., 2012)
    ventral ectoderm
    (Fisher et al., 2012)
    embryonic stage 9 -- 10
    antennal primordium

    Comment: reported as procephalic ectoderm primordium

    (Fisher et al., 2012)
    central brain primordium

    Comment: reported as procephalic ectoderm primordium

    (Fisher et al., 2012)
    visual primordium

    Comment: reported as procephalic ectoderm primordium

    (Fisher et al., 2012)
    dorsal head epidermis primordium

    Comment: reported as procephalic ectoderm primordium

    (Fisher et al., 2012)
    lateral head epidermis primordium

    Comment: reported as procephalic ectoderm primordium

    (Fisher et al., 2012)
    ventral head epidermis primordium

    Comment: reported as procephalic ectoderm primordium

    (Fisher et al., 2012)
    anterior endoderm
    (Fisher et al., 2012)
    clypeo-labral primordium
    (Fisher et al., 2012)
    dorsal ectoderm
    (Fisher et al., 2012)
    foregut primordium
    (Fisher et al., 2012)
    head mesoderm
    (Fisher et al., 2012)
    inclusive hindgut primordium
    (Fisher et al., 2012)
    posterior endoderm
    (Fisher et al., 2012)
    tracheal primordium

    Comment: reported as tracheal system anlage

    (Fisher et al., 2012)
    trunk mesoderm
    (Fisher et al., 2012)
    ventral ectoderm
    (Fisher et al., 2012)
    embryonic stage 10 -- 11
    embryonic/larval tracheal section
    (Chung et al., 2011)
    embryonic stage 11 -- 12
    clypeo-labral primordium
    (Fisher et al., 2012)
    dorsal epidermis primordium
    (Fisher et al., 2012)
    dorsal head epidermis primordium

    Comment: reported as head epidermis primordium

    (Fisher et al., 2012)
    lateral head epidermis primordium

    Comment: reported as head epidermis primordium

    (Fisher et al., 2012)
    ventral head epidermis primordium

    Comment: reported as head epidermis primordium

    (Fisher et al., 2012)
    tracheal primordium
    (Fisher et al., 2012)
    ventral epidermis primordium
    (Fisher et al., 2012)
    embryonic stage 13 -- 16
    embryonic primordium of adult eye
    (Fisher et al., 2012)
    larval foregut atrium
    (Fisher et al., 2012)
    dorsal head epidermis
    (Fisher et al., 2012)
    embryonic dorsal epidermis
    (Fisher et al., 2012)
    embryonic head epidermis
    (Fisher et al., 2012)
    embryonic ventral epidermis
    (Fisher et al., 2012)
    labral segment
    (Fisher et al., 2012)
    Additional Descriptive Data
    Marker for
     
    Subcellular Localization
    CV Term
    Polypeptide Expression
    Additional Descriptive Data
    Marker for
     
    Subcellular Localization
    CV Term
    Evidence
    References
    Expression Deduced from Reporters
    High-Throughput Expression Data
    Associated Tools

    JBrowse - Visual display of RNA-Seq signals

    View Dmel\sala 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) 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 ( 1 )
    For All Classical and Insertion Alleles Show
     
    Other relevant insertions
    Transgenic Constructs ( 11 )
    For All Alleles Carried on Transgenic Constructs Show
    Transgenic constructs containing/affecting coding region of sala
    Transgenic constructs containing regulatory region of sala
    Aberrations (Deficiencies and Duplications) ( 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) (0)
    Danio rerio (Zebrafish) (0)
    Caenorhabditis elegans (Nematode, roundworm) (0)
    Anopheles gambiae (African malaria mosquito) (0)
    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:sala. 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
      sala - CG10209
      two hybrid, anti tag coimmunoprecipitation, anti tag western blot
      (Tang et al., 2023, Hu et al., 2017.6.13)
      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
      salm
      suppressible
      sala
      (Frei et al., 1988)
      External Data
      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
      2-44
      Cytogenetic map
      32F2-32F2
      Sequence location
      FlyBase Computed Cytological Location
      Cytogenetic map
      Evidence for location
      32F2-32F2
      Limits computationally determined from genome sequence between P{PZ}salm03602 and P{PZ}crol04418&P{EP}crolEP1183
      Experimentally Determined Cytological Location
      Cytogenetic map
      Notes
      References
      33A-33A
      (determined by in situ hybridisation)
      (Wagner-Bernholz et al., 1991)
      32F-33E
      (determined by in situ hybridisation)
      (Frei et al., 1988)
      Experimentally Determined Recombination Data
      Location

      2-44

      (FlyBase, 2016)

      2-38.2

      (Comeron et al., 2012)
      Left of (cM)
      Right of (cM)
      Notes
      Stocks and Reagents
      Stocks (11)
      Genomic Clones (21)
      cDNA Clones (63)
       

      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

            Duplicate transcripts identified and eliminated during the migration of annotations from the release 5 genome assembly to the release 6 assembly.

            (FlyBase Genome Annotators, 2014)

            sala encodes a secreted protein from which a functional signal sequence is cleaved off. sala is zygotically expressed in temporally and spatially restricted patterns during embryogenesis and its initial expression domain at the blastoderm stage is under the control of activities of the maternal organiser system, which are required for the development of the anterior, ventral and terminal pattern elements in the embryo.

            (Reuter et al., 1996)

            The previously reported "sal" transcription unit was misidentified, and is actually sala rather than salm.

            (Kuhnlein et al., 1994)

            sala sequences are restricted to the melanogaster group of the subgenus Sophophora. This suggests that the formation of normal head and tail structures is independent of sala function in the Drosophila genus. Therefore, sala is likely to serve an accessory or modulating function that acts in combination with other genes.

            (Reuter et al., 1989)

            sala was first cloned and sequenced on the assumption that it was the spalt locus. It turned out (Wagner-Bernholz, Wilson, Gibson, Schuh and Gehring, 1991) that it is the immediately proximal gene to spalt. To avoid confusion it was renamed spalt accessory (sala) and the 'real' spalt was renamed spalt major (salm).

            sala is 19kb proximal to salm.

            The role of sala in spalt function (if any) is not yet clear.

            Relationship to Other Genes
            Source for database merge of

            Source for merge of: sala BcDNA:RE40068

            (FlyBase, 1996-)
            Additional comments

            One or more of the processed transcripts for these genes contain two non-overlapping open reading frames (ORFs). The non-overlapping ORFs are represented by CG43355 (FBgn0263087) and sala (CG4922, FBgn0003313).

            (FlyBase Genome Annotators, 2011)

            Source for merge of sala BcDNA:RE40068 was TrEMBL update ( date:020807 ).

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

            Source for identity of: sala CG4922

            (Zhong, 1999.11)
            Nomenclature comments
            Etymology
            Synonyms and Secondary IDs (13)
            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
            KEGG Genes - Molecular building blocks of life in the genomic space.
            MARRVEL_MODEL - MARRVEL (model organism gene)
            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 (66)