FB2025_05 , released December 11, 2025
Gene: Dmel\Spn
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General Information
Symbol
Dmel\Spn
Species
D. melanogaster
Name
Spinophilin
Annotation Symbol
CG16757
Feature Type
protein_coding_gene
FlyBase ID
FBgn0010905
Gene Model Status
Current
Stock Availability
13 publicly available
Gene Summary
Spinophilin (Spn) encodes a scaffold protein protein that regulates the neurexin/neuroligin signalling at the presynaptic active zone. [Date last reviewed: 2019-09-19] (FlyBase Gene Snapshot)
All Summaries
Also Known As

l(3)06911, d-spinophilin

Key Links
Genomic Location
Cytogenetic map
62E4-62E5
Sequence location
Recombination map
3-3
RefSeq locus
NT_037436 REGION:2505245..2554292
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 (12 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
enables neurexin family protein binding
inferred from physical interaction with FLYBASE:Nrx-1; FB:FBgn0038975
(Muhammad et al., 2015)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
enables actin filament binding
inferred from biological aspect of ancestor with PANTHER:PTN000414425
(GO Reference Genome Project, 2011-)
Biological Process (4 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
involved_in negative regulation of presynaptic active zone assembly
inferred from mutant phenotype
(Muhammad et al., 2015)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
involved_in actin filament organization
inferred from biological aspect of ancestor with PANTHER:PTN000414425
(GO Reference Genome Project, 2011-)
involved_in calcium-mediated signaling
inferred from biological aspect of ancestor with PANTHER:PTN000414425
(GO Reference Genome Project, 2011-)
involved_in neuron projection development
inferred from biological aspect of ancestor with PANTHER:PTN000414425
(GO Reference Genome Project, 2011-)
Cellular Component (6 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
located_in apical cortex
inferred from high throughput direct assay
(Lye et al., 2014)
colocalizes_with contractile ring
inferred from high throughput direct assay
(Lye et al., 2014)
Terms Based on Predictions or Assertions (4 terms)
CV Term
Evidence
References
is_active_in actin cytoskeleton
inferred from biological aspect of ancestor with PANTHER:PTN000414425
(GO Reference Genome Project, 2011-)
is_active_in cytoplasm
inferred from biological aspect of ancestor with PANTHER:PTN000414425
(GO Reference Genome Project, 2011-)
is_active_in dendrite
inferred from biological aspect of ancestor with PANTHER:PTN000414425
(GO Reference Genome Project, 2011-)
is_active_in postsynaptic density
inferred from biological aspect of ancestor with PANTHER:PTN000414425
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Snapshot
Spinophilin (Spn) encodes a scaffold protein protein that regulates the neurexin/neuroligin signalling at the presynaptic active zone. [Date last reviewed: 2019-09-19]
Summary (Interactive Fly)

Scaffolding protein - Neurexin/Neuroligin signalling - control of synaptic active zone number and functionality, a Protein-phosphatase 1 (PP1) targeting protein

Gene Model and Products
Number of Transcripts
11
Number of Unique Polypeptides
9

Please see the JBrowse view of Dmel\Spn 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 M9NFI9)

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

Tissue-specific extension of 3' UTRs observed during later stages (FBrf0218523, FBrf0219848); all variants may not be annotated

Gene model reviewed during 5.46

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

Annotated transcripts do not represent all possible combinations of alternative exons and/or alternative promoters.

Gene model reviewed during 5.55

Multiphase exon postulated: exon reading frame differs in alternative transcripts; overlap >20aa.

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Spn-RB
FBtr0304613
NM_001259641
7334
2134
Spn-RC
FBtr0304614
NM_001259642
10136
2134
Spn-RD
FBtr0304615
NM_001259643
7343
2137
Spn-RE
FBtr0304616
NM_001259644
6383
1817
Spn-RF
FBtr0304617
NM_001259645
6520
1684
Spn-RG
FBtr0304618
NM_001259646
7295
2121
Spn-RH
FBtr0304619
NM_001259647
9544
2134
Spn-RI
FBtr0304620
NM_001259648
8756
2116
Spn-RJ
FBtr0304621
NM_001259649
7376
2148
Spn-RS
FBtr0345046
NM_080516
7289
2119
Spn-RT
FBtr0345047
NM_001299992
6425
1831
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
Spn-PB
FBpp0293155
232.0
2134
5.00
M9NEY3
NP_001246570
AFH04241
Spn-PC
FBpp0293156
232.0
2134
5.00
M9NEY3
NP_001246571
AFH04242
Spn-PD
FBpp0293157
232.4
2137
5.00
H5V864
NP_001246572
AFH04243
Spn-PE
FBpp0293158
198.4
1817
4.89
M9NFI2
NP_001246573
AFH04244
Spn-PF
FBpp0293159
183.3
1684
4.71
M9ND28
NP_001246574
AFH04245
Spn-PG
FBpp0293160
230.7
2121
4.99
M9NEY5
NP_001246575
AFH04246
Spn-PH
FBpp0293161
232.0
2134
5.00
M9NEY3
NP_001246576
AFH04247
Spn-PI
FBpp0293162
229.9
2116
4.98
M9NDX8
NP_001246577
AFH04248
Spn-PJ
FBpp0293163
233.4
2148
5.02
M9NFI9
NP_001246578
AFH04249
Spn-PS
FBpp0311289
230.3
2119
5.01
Q9W003
NP_536777
AAF47657
Spn-PT
FBpp0311290
199.8
1831
4.90
X2JC06
NP_001286921
AHN57946
Polypeptides with Identical Sequences

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

2134 aa isoforms: Spn-PB, Spn-PC, Spn-PH
Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
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\Spn 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).

-0.89

Transcript Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult head
(Aradska et al., 2015)
day 5 of adulthood | male -- day 7 of adulthood | male
spermatozoon
(Wasbrough et al., 2010)
day 7 of adulthood -- day 49 of adulthood
adult heart
(Cammarato et al., 2011)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in apical cortex
inferred from high throughput direct assay
(Lye et al., 2014)
colocalizes_with contractile ring
inferred from high throughput direct assay
(Lye et al., 2014)
Expression Deduced from Reporters
Reporter: PBac{681.P.FSVS-1}SpnCPTI001457
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
bulb
(Knowles-Barley, 2011.8.24)
calyx of adult mushroom body
(Knowles-Barley, 2011.8.24)
adult brain | faint | ubiquitous

Comment: expression throughout the adult brain, higher in some regions

(Knowles-Barley, 2011.8.24)
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Spn 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
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
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 20 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 9 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Spn
Transgenic constructs containing regulatory region of Spn
Aberrations (Deficiencies and Duplications) ( 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) (4)
Hsap\PPP1R9A
11 of 14
Yes
Yes
1  
Hsap\PPP1R9B
11 of 14
Yes
Yes
Hsap\SAMD14
4 of 14
No
Yes
Hsap\SAMD3
1 of 14
No
Yes
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) (4)
Rnor\Ppp1r9a
11 of 14
Yes
Yes
Rnor\Ppp1r9b
10 of 14
No
Yes
Rnor\Samd14
2 of 14
No
Yes
Rnor\Samd3
1 of 14
No
Yes
Mus musculus (laboratory mouse) (4)
Mmus\Ppp1r9b
11 of 14
Yes
Yes
Mmus\Ppp1r9a
10 of 14
No
Yes
Mmus\Samd14
4 of 14
No
Yes
Mmus\Samd3
1 of 14
No
Yes
Xenopus tropicalis (Western clawed frog) (5)
Xtro\ppp1r9al
6 of 13
Yes
Yes
Xtro\ppp1r9a
5 of 13
No
Yes
Xtro\ppp1r9b
5 of 13
No
Yes
Xtro\dmtf1
1 of 13
No
Yes
Xtro\lgmn
1 of 13
No
No
Danio rerio (Zebrafish) (7)
Drer\ppp1r9a
10 of 14
Yes
Yes
Drer\ppp1r9ba
9 of 14
No
Yes
Drer\ppp1r9ala
8 of 14
No
Yes
Drer\ppp1r9alb
8 of 14
No
Yes
Drer\ppp1r9bb
8 of 14
No
Yes
Drer\samd14
2 of 14
No
Yes
Drer\si:ch211-193k19.2
1 of 14
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\nab-1
8 of 14
Yes
Yes
Anopheles gambiae (African malaria mosquito) (1)
Agam\AgaP_AGAP005943
10 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:Spn. 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) (1)
Ir68b
1 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?
    PPP1R9A; protein phosphatase 1 regulatory subunit 9A
    11 of 14
    602468
         
        PPP1R9B; protein phosphatase 1 regulatory subunit 9B
        11 of 14
        603325
            SAMD14; sterile alpha motif domain containing 14
            4 of 14
            619233
                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
                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
                SignaLink - A signaling pathway resource with multi-layered regulatory networks.
                Class of Gene
                Genomic Location and Detailed Mapping Data
                Chromosome (arm)
                3L
                Recombination map
                3-3
                Cytogenetic map
                62E4-62E5
                Sequence location
                FlyBase Computed Cytological Location
                Cytogenetic map
                Evidence for location
                62E4-62E5
                Limits computationally determined from genome sequence between P{PZ}slsrL182 and P{PZ}Spn06911
                Experimentally Determined Cytological Location
                Cytogenetic map
                Notes
                References
                62E-62E
                (Keegan et al., 2000, Keegan and Garza, 1998)
                62E4-62E5
                (BDGP Project Members, 1994-1999)
                Experimentally Determined Recombination Data
                Location

                3-3

                (FlyBase, 2016)

                3-5.0

                (Comeron et al., 2012)
                Left of (cM)
                Right of (cM)
                Notes
                Stocks and Reagents
                Stocks (13)
                Genomic Clones (46)
                cDNA Clones (44)
                 

                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

                (Muhammad et al., 2015)
                Commercially Available Antibodies
                 
                Cell Line Information
                Publicly Available Cell Lines
                 
                  Other Stable Cell Lines
                   
                    Other Comments

                    dsRNA made from templates generated with primers directed against this gene tested in RNAi screen for effects on Kc167 and S2R+ cell morphology.

                    (Kiger et al., 2003)

                    Transcription unit spans the central region of the early-late puff at 62E.

                    (Keegan et al., 2000)

                    Cloning and molecular analysis has identified the Spn transcription unit spanning at least 20 kb of genomic DNA from the central region of the 62E puff that is induced following the metamorphic pulse of ecdysone at the end of the third larval instar.

                    (Keegan and Garza, 1998)
                    Relationship to Other Genes
                    Source for database merge of

                    Source for merge of: E62 l(3)06911

                    (Keegan et al., 2001)

                    Source for merge of: E62 CG16757

                    (FlyBase, 1996-)

                    Source for merge of: Spn BcDNA:GM16129

                    (FlyBase, 1996-)
                    Additional comments

                    Release 2 annotation CG16757 split into CG32295 and CG16757 (which corresponds to Spn) in release 3 of the genome annotation.

                    (FlyBase Genome Annotators, 2002-2003)

                    Source for merge of E62 CG16757 was sequence comparison ( date:001223 ).

                    (FlyBase, 1996-)

                    Source for merge of Spn BcDNA:GM16129 was a shared cDNA ( date:030728 ).

                    (FlyBase, 1996-)
                    Nomenclature History
                    Source for database identify of
                    Nomenclature comments
                    Etymology
                    Synonyms and Secondary IDs (11)
                    Datasets (0)
                    Study focus (0)
                    Experimental Role
                    Project
                    Project Type
                    Title
                    Study result (0)
                    Result
                    Result Type
                    Title
                    External Crossreferences and Linkouts ( 93 )
                    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.
                    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)
                    Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
                    MIST (protein-protein) - An integrated Molecular Interaction Database
                    SignaLink - A signaling pathway resource with multi-layered regulatory networks.
                    References (97)