FB2026_01 , released March 12, 2026
FB2026_01 , released March 12, 2026
Gene: Dmel\Sym
Open Close
General Information
Symbol
Dmel\Sym
Species
D. melanogaster
Name
Symplekin
Annotation Symbol
CG2097
Feature Type
protein_coding_gene
FlyBase ID
FBgn0037371
Gene Model Status
Current
Stock Availability
11 publicly available
Gene Summary
Symplekin (Sym) encodes a large protein that contains many protein interaction sites, and acts as a scaffold for protein complexes in the nucleus. It functions in RNA 3' end formation for both polyadenyated mRNAs and non-polyadenylated histone mRNAs. In some cells it also localizes to the cell cortex, especially the tricellular junctions of some epithelia. [Date last reviewed: 2018-10-25] (FlyBase Gene Snapshot)
All Summaries
Also Known As

Symp

Key Links
Genomic Location
Cytogenetic map
83C1-83C2
Sequence location
Recombination map
3-47.5
RefSeq locus
NT_033777 REGION:5738178..5742476
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 (7 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
enables protein binding
inferred from physical interaction with UniProtKB:A1Z802
(Sullivan et al., 2009)
inferred from physical interaction with UniProtKB:Q9V3D6
(Sullivan et al., 2009)
inferred from physical interaction with UniProtKB:Q9VAN6
(Sullivan et al., 2009)
inferred from physical interaction with UniProtKB:Q9VE51
(Sullivan et al., 2009)
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 co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway
inferred from mutant phenotype
(Sullivan et al., 2009)
involved_in mRNA 3'-end processing by stem-loop binding and cleavage
inferred from mutant phenotype
(Tatomer et al., 2014, Sullivan et al., 2009, Wagner et al., 2007)
Terms Based on Predictions or Assertions (0 terms)
Cellular Component (4 terms)
Terms Based on Experimental Evidence (4 terms)
CV Term
Evidence
References
is_active_in histone locus body
inferred from direct assay
(Tatomer et al., 2014)
located_in histone locus body
inferred from direct assay
(Wagner et al., 2007)
part_of mRNA cleavage and polyadenylation specificity factor complex
inferred from direct assay
(Sullivan et al., 2009)
located_in nucleus
inferred from direct assay
(Wagner et al., 2007)
located_in tricellular tight junction
inferred from direct assay
(Tatomer et al., 2014)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
part_of mRNA cleavage and polyadenylation specificity factor complex
inferred from biological aspect of ancestor with PANTHER:PTN000391745
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the Symplekin family. (Q8MSU4)
Protein Signatures (InterPro)
Summaries
Gene Snapshot
Symplekin (Sym) encodes a large protein that contains many protein interaction sites, and acts as a scaffold for protein complexes in the nucleus. It functions in RNA 3' end formation for both polyadenyated mRNAs and non-polyadenylated histone mRNAs. In some cells it also localizes to the cell cortex, especially the tricellular junctions of some epithelia. [Date last reviewed: 2018-10-25]
Gene Group (FlyBase)
HISTONE PRE-MRNA CLEAVAGE COMPLEX -
Histone cleavage complex includes endonucleases and polyadenylation factors involved in processing of histone pre-mRNA. (Adapted from FBrf0223323 and PMID:23071092).
CORE CLEAVAGE COMPLEX -
The core cleavage complex is a component of two distinct complexes, the cleavage/polyadenylation complex and the histone pre-mRNA cleavage complex that processes nonpolyadenylated histone pre-mRNAs. (Adapted from FBrf0229062 and FBrf0208078).
Protein Function (UniProtKB)
Component of a protein complex required for cotranscriptional processing of 3'-ends of polyadenylated and histone pre-mRNA (PubMed:18042462, PubMed:19450530). Involved in germline stem cell transit amplification, differentiation and mitosis-to-meiosis transition (PubMed:28190776).
(UniProt, Q8MSU4)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Sym 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 Q8MSU4)

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

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)
Sym-RA
FBtr0078723
NM_141323
3986
1165
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
Sym-PA
FBpp0078372
132.1
1165
6.45
Q8MSU4
NP_649580
AAF51962
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)
Comments
External Data
Subunit Structure (UniProtKB)

Interacts with Cpsf73 and Cpsf100 forming a core cleavage factor required for both polyadenylated and histone mRNA processing. Interacts with Slbp and Lsm11.

(UniProt, Q8MSU4)
Domain

The HEAT repeats have been determined based on 3D-structure analysis and are not detected by sequence-based prediction programs.

(UniProt, Q8MSU4)
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\Sym 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).

-0.29

Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage 1 -- 3
organism

Comment: maternally deposited

(Fisher et al., 2012)
embryonic stage 4 -- 6
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 7 -- 8
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 9 -- 10
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 11 -- 12
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 13 -- 16
organism | faint | ubiquitous
(Fisher et al., 2012)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
day 5 of adulthood | male -- day 7 of adulthood | male
spermatozoon
(Wasbrough et al., 2010)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
is_active_in histone locus body
inferred from direct assay
(Tatomer et al., 2014)
located_in histone locus body
inferred from direct assay
(Wagner et al., 2007)
part_of mRNA cleavage and polyadenylation specificity factor complex
inferred from direct assay
(Sullivan et al., 2009)
located_in nucleus
inferred from direct assay
(Wagner et al., 2007)
located_in tricellular tight junction
inferred from direct assay
(Tatomer et al., 2014)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Sym 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
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 9 )
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 Sym
Transgenic constructs containing regulatory region of Sym
Aberrations (Deficiencies and Duplications) ( 5 )
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) (1)
Hsap\SYMPK
14 of 14
Yes
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) (1)
Rnor\Sympk
14 of 14
Yes
Yes
Mus musculus (laboratory mouse) (1)
Mmus\Sympk
13 of 14
Yes
Yes
Xenopus tropicalis (Western clawed frog) (1)
Xtro\sympk
8 of 13
Yes
Yes
Danio rerio (Zebrafish) (1)
Drer\sympk
14 of 14
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\symk-1
14 of 14
Yes
Yes
Anopheles gambiae (African malaria mosquito) (1)
Agam\AgaP_AGAP002618
12 of 12
Yes
Yes
Arabidopsis thaliana (thale-cress) (3)
Atha\ESP4
10 of 13
Yes
Yes
Atha\AT1G27595
9 of 13
No
Yes
Atha\AT1G27570
2 of 13
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\PTA1
6 of 13
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\pta1
6 of 12
Yes
Yes
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Sym. 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?
SYMPK; symplekin scaffold protein
14 of 14
602388
      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
      RNA-protein
      Physical Interaction
      Assay
      References
      Sym - His3
      affinity technology, Identification by mass spectrometry, pull down, anti tag western blot, western blot
      (Skrajna et al., 2018, Skrajna et al., 2017)
      Sym - snRNA:U7
      pull down, western blot, peptide massfingerprinting
      (Sabath et al., 2013)
      Sym - tut
      rna three hybrid
      (Shan et al., 2017)
      protein-protein
      Physical Interaction
      Assay
      References
      Sym - Cpsf100
      anti tag coimmunoprecipitation, western blot, anti bait coimmunoprecipitation
      (Harrington et al., 2017, Michalski and Steiniger, 2015, Sullivan et al., 2009)
      Sym - Cpsf73
      anti tag coimmunoprecipitation, western blot, anti bait coimmunoprecipitation
      (Harrington et al., 2017, Michalski and Steiniger, 2015, Sullivan et al., 2009)
      Sym - CstF64
      anti bait coimmunoprecipitation, western blot, peptide massfingerprinting
      (Sabath et al., 2013)
      Sym - Dcr-2
      anti bait coimmunoprecipitation, anti tag western blot, western blot, anti tag coimmunoprecipitation
      (Harrington et al., 2017)
      Sym - FLASH
      pull down, western blot, anti bait coimmunoprecipitation, peptide massfingerprinting
      (Sabath et al., 2013)
      Sym - Lsm11
      anti bait coimmunoprecipitation, western blot
      (Sullivan et al., 2009)
      Sym - Slbp
      anti bait coimmunoprecipitation, western blot
      (Sullivan et al., 2009)
      Sym - Ssu72
      molecular sieving, x-ray crystallography
      (Luo et al., 2013)
      Sym - hrg
      anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based
      (Rhee et al., 2014)
      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
      tut
      enhanceable
      Sym
      (Shan et al., 2017)
      External Data
      Subunit Structure (UniProtKB)
      Interacts with Cpsf73 and Cpsf100 forming a core cleavage factor required for both polyadenylated and histone mRNA processing. Interacts with Slbp and Lsm11.
      (UniProt, Q8MSU4 )
      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
      KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
      Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
      Class of Gene
      Genomic Location and Detailed Mapping Data
      Chromosome (arm)
      3R
      Recombination map
      3-47.5
      Cytogenetic map
      83C1-83C2
      Sequence location
      FlyBase Computed Cytological Location
      Cytogenetic map
      Evidence for location
      83C1-83C2
      Limits computationally determined from genome sequence between P{lacW}casj1C2 and P{PZ}lab01241
      Experimentally Determined Cytological Location
      Cytogenetic map
      Notes
      References
      Experimentally Determined Recombination Data
      Location

      3-47.5

      (FlyBase, 2016)

      3-44.1

      (Comeron et al., 2012)
      Left of (cM)
      Right of (cM)
      Notes
      Stocks and Reagents
      Stocks (11)
      Genomic Clones (13)
       

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

      cDNA Clones (29)
       

      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

        (Skrajna et al., 2018, Sullivan et al., 2009)
        Commercially Available Antibodies
         
        Cell Line Information
        Publicly Available Cell Lines
         
          Other Stable Cell Lines
           
          Other Comments

          Identified as a potential component of the hh signalling pathway in a genome-wide RNAi screen. dsRNA made from templates generated with primers directed affects the extent of expression of a hh signaling reporter construct in Clone 8 cells.

          (Nybakken et al., 2005)
          Relationship to Other Genes
          Source for database merge of
          Additional comments

          FlyBase curator comment: Correspondence with author Tatomer revealed that 'Symplekin' = 'CG2097'.

          (Tatomer et al., 2008)
          Nomenclature History
          Source for database identify of

          Source for identity of: Sym CG2097

          (Wagner et al., 2007)
          Nomenclature comments
          Etymology
          Synonyms and Secondary IDs (6)
          Datasets (0)
          Study focus (0)
          Experimental Role
          Project
          Project Type
          Title
          Study result (0)
          Result
          Result Type
          Title
          External Crossreferences and Linkouts ( 47 )
          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
          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
          FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
          iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
          KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
          MIST (protein-protein) - An integrated Molecular Interaction Database
          Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
          References (66)