FB2020_06, released Dec 22, 2020

Gene: Dmel\Sf3a2

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General Information
Symbol
Dmel\Sf3a2
Species
D. melanogaster
Name
Splicing factor 3a subunit 2
Annotation Symbol
CG10754
Feature Type
protein_coding_gene
FlyBase ID
FBgn0036314
Gene Model Status
Current
Stock Availability
3 publicly available
Gene Snapshot
Contributions welcome
Other Summaries
Key Links
Genomic Location
Cytogenetic map
69E4-69E4
Sequence location
3L:12,813,028..12,814,019 [-]
Recombination map

3-39

RefSeq locus
NT_037436 REGION:12813028..12814019
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
GO Summary Ribbons
Gene Ontology (GO) Annotations (9 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
enables RNA binding
inferred from sequence or structural similarity with HGNC:10766
(FlyBase Curators, 2008--)
enables zinc ion binding
inferred from electronic annotation with InterPro:IPR000690, InterPro:IPR003604
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
Biological Process (3 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
involved_in positive regulation of gene expression
inferred from mutant phenotype
(Ashton-Beaucage et al., 2014)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
involved_in mRNA splicing, via spliceosome
inferred by curator from GO:0071011,GO:0071013
(Herold et al., 2009)
involved_in spliceosomal complex assembly
inferred from biological aspect of ancestor with PANTHER:PTN000574843
(assigned by GO_Central )
(Gaudet et al., 2011)
Cellular Component (4 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
part_of catalytic step 2 spliceosome
inferred from high throughput direct assay
(Herold et al., 2009)
part_of precatalytic spliceosome
inferred from high throughput direct assay
(Herold et al., 2009)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
part_of catalytic step 2 spliceosome
inferred from biological aspect of ancestor with PANTHER:PTN000574843
(assigned by GO_Central )
(Gaudet et al., 2011)
part_of U2 snRNP
inferred from biological aspect of ancestor with PANTHER:PTN000574843
(assigned by GO_Central )
(Gaudet et al., 2011)
inferred from sequence or structural similarity with SGD:S000002201
(Mount and Salz, 2000)
part_of U2-type prespliceosome
inferred from biological aspect of ancestor with PANTHER:PTN000574843
(assigned by GO_Central )
(Gaudet et al., 2011)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Group (FlyBase)
U2 SMALL NUCLEAR RIBONUCLEOPROTEIN PARTICLE -
The U2 small nuclear ribonucleoprotein particle (U2 snRNP) contains U2 snRNA. It is recruited to the spliceosome after U1 snRNP and forms a stable interaction with the branch site and 3' splice site in pre-mRNA. (Adapted from PMID:23829528 and PMID:21441581).
SPLICEOSOME COMPLEX A -
Nuclear pre-mRNA splicing is catalyzed by the spliceosome which assembles in a step-wise manner. Complex A, the pre-spliceosome, is composed of U1 and U2 snRNPs and proteins involved in recognition of the 5' splice site and branch point. (Adapted from PMID:24452469 and PMID:23118483).
SPLICEOSOME COMPLEX B -
Nuclear pre-mRNA splicing is catalyzed by the spliceosome which assembles in a step-wise manner. After the assembly of complex A on pre-mRNA, the U4-U6 and U5 snRNPs are recruited as a preassembled tri-snRNP to form complex B. U5 snRNP binds exons at the 5' site. (Adapted from PMID:24452469 and PMID:23118483).
SPLICEOSOME COMPLEX C -
Nuclear pre-mRNA splicing is catalyzed by the spliceosome which assembles in a step-wise manner. Complex B undergoes a number of structural rearrangements and U4 and U1 snRNPs dissociate to generate complex C, the catalytic spliceosome. (Adapted from PMID:24452469 and PMID:23118483).
SPLICEOSOME COMPLEX P -
Nuclear pre-mRNA splicing is catalyzed by the spliceosome which assembles in a step-wise manner. Complex P, the post-spliceosomal complex, is formed after the catalytic removal of the intron by complex C. Complex P contains the lariat intron and spliced exons. (Adapted from PMID:24452469 and PMID:23118483).
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Sf3a2 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
Comments on Gene Model

Gene model reviewed during 5.45

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Sf3a2-RA
FBtr0075944
NM_140346
992
264
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
RefSeq ID
GenBank
Sf3a2-PA
FBpp0075676
30.3
264
10.21
NP_648603
AAF49876
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
Crossreferences
InterPro - A database of protein families, domains and functional sites
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\Sf3a2 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
Expression Summary Ribbons
Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.
Transcript Expression
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
part_of catalytic step 2 spliceosome
inferred from high throughput direct assay
(Herold et al., 2009)
part_of precatalytic spliceosome
inferred from high throughput direct assay
(Herold et al., 2009)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Sf3a2 in GBrowse 2
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
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
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, and Transgenic Constructs
Classical and Insertion Alleles ( 1 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 3 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Sf3a2
Transgenic constructs containing regulatory region of Sf3a2
Deletions and Duplications ( 0 )
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
lethal
lethal, with Scer\GAL4Act88F.PU
lethal, with Scer\GAL4Mef2.PU
lethal, with Scer\GAL4nub-AC-62
lethal | female limited, with Scer\GAL4dome-PG14
lethal - all die during P-stage, with Scer\GAL4Mef2.PR
partially lethal, with Dcr-2UAS.cDa, Scer\GAL4elav.PLu
partially lethal, with Scer\GAL4tin.CΔ4
partially lethal - majority die, with Scer\GAL4pnr-MD237
Sterility
Allele
female sterile, with Scer\GAL4VP16.otu
Other Phenotypes
Allele
flight defective, with Scer\GAL4Act88F.PU
flightless, with Scer\GAL4Mef2.PU
neuroanatomy defective | larval stage
pain response defective | adult stage, with Dcr-2UAS.cDa, Scer\GAL4elav.PLu
size defective | adult stage, with Scer\GAL4Mef2.PU
some die during pupal stage, with Scer\GAL4Act88F.PU
some die during pupal stage, with Scer\GAL4pnr-MD237
visible, with Scer\GAL4Bx-MS1096
visible, with Scer\GAL4pnr-MD237
Phenotype manifest in
Allele
ganglion mother cell | larval stage
indirect flight muscle | pharate adult stage, with Scer\GAL4Mef2.PU
larval neuroblast | larval stage
mesothoracic tergum, with Scer\GAL4pnr-MD237
myofibril | pharate adult stage, with Scer\GAL4Mef2.PU
sarcomere | pharate adult stage, with Scer\GAL4Mef2.PU
wing, with Scer\GAL4Bx-MS1096
Z disc | pharate adult stage, with Scer\GAL4Mef2.PU
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Hsap\SF3A2
13 of 15
Yes
Yes
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Mmus\Sf3a2
13 of 15
Yes
Yes
Rattus norvegicus (Norway rat) (1)
Rnor\Sf3a2
11 of 13
Yes
Yes
Xenopus tropicalis (Western clawed frog) (1)
Xtro\sf3a2
11 of 12
Yes
Yes
Danio rerio (Zebrafish) (1)
Drer\sf3a2
14 of 15
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\repo-1
15 of 15
Yes
Yes
Arabidopsis thaliana (thale-cress) (1)
Atha\AT2G32600
9 of 9
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\PRP11
11 of 15
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\sap62
10 of 12
Yes
Yes
Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG09190F58 )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00013121
Drosophila simulans
Dsim\GD12694
Drosophila sechellia
Dsec\GM24628
Drosophila erecta
Dere\GG13802
Drosophila yakuba
Dyak\GE20095
Drosophila ananassae
Dana\GF10865
Drosophila pseudoobscura pseudoobscura
Dpse\GA10545
Drosophila persimilis
Dper\GL22896
Drosophila willistoni
Dwil\GK16828
Drosophila virilis
Dvir\GJ13983
Drosophila mojavensis
Dmoj\GI13650
Drosophila grimshawi
Dgri\GH14494
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG09150APA )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17018044
Glossina morsitans
Tsetse fly
Gmor\GMOY011243
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_12279
Mayetiola destructor
Hessian fly
Mdes\Mdes012968
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL000394
Anopheles darlingi
American malaria mosquito
Adar\ADAC005615
Anopheles gambiae
Malaria mosquito
Agam\AGAP011035
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ003364
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W0C7T )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Bmor\BGIBMGA000898
Danaus plexippus
Monarch butterfly
Dple\DPOGS211949-PA
Heliconius melpomene
Postman butterfly
Hmel\HMEL017766
Heliconius melpomene
Postman butterfly
Hmel\HMEL017767
Heliconius melpomene
Postman butterfly
Hmel\HMEL003190
Apis florea
Little honeybee
Aflo\3623902548
Apis mellifera
Western honey bee
Amel\LOC552334
Bombus impatiens
Common eastern bumble bee
Bimp\BIMP20105
Bombus terrestris
Buff-tailed bumblebee
Bter\15205924
Linepithema humile
Argentine ant
Lhum\LH23425
Megachile rotundata
Alfalfa leafcutting bee
Mrot\MROTU:00068d
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG012248
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_02233
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_01096
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_00611
Tribolium castaneum
Red flour beetle
Tcas\GLEAN_07585
Pediculus humanus
Human body louse
Phum\PHUM544530
Rhodnius prolixus
Kissing bug
Rpro\RPRC012315
Cimex lectularius
Bed bug
Clec\CLEC000039
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI000572
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_07949
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0C5N )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Smar\SMAR013997
Ixodes scapularis
Black-legged tick
Isca\ISCW017352
Stegodyphus mimosarum
African social velvet spider
Smim\KFM80423.1
Stegodyphus mimosarum
African social velvet spider
Smim\KFM71209.1
Tetranychus urticae
Two-spotted spider mite
Turt\tetur01g15440
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_226064
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0IZX )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Sf3a2
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000003319
Gallus gallus
Domestic chicken
Ggal\SF3A2
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (0)
No records found.
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Model Summary Ribbon
    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 v8.0 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?
    SF3A2; splicing factor 3a subunit 2
    13 of 15
    600796
        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
        esyN Network Diagram
        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.
        InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
        MIST (protein-protein) - An integrated Molecular Interaction Database
        Pathways
        Signaling Pathways (FlyBase)
        Metabolic Pathways
        External Data
        Linkouts
        KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
        Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        3L
        Recombination map

        3-39

        Cytogenetic map
        69E4-69E4
        Sequence location
        3L:12,813,028..12,814,019 [-]
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        69E4-69E4
        Limits computationally determined from genome sequence between P{PZ}l(3)0692406924 and P{lacW}RpS12s2783
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        Experimentally Determined Recombination Data
        Location

        3-39

        (FlyBase, 2016)

        3-33.5

        (Comeron et al., 2012)
        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (3)
        Genomic Clones (17)
         

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

        cDNA Clones (23)
         

        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 GBrowse 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
        GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
        Antibody Information
        Laboratory Generated Antibodies
         

        polyclonal

        (Pellacani et al., 2018)
        Commercially Available Antibodies
         
        Other Information
        Relationship to Other Genes
        Source for database identify of

        Source for identity of: Sf3a2 CG10754

        (Stegeman et al., 2016)
        Source for database merge of
        Additional comments
        Other Comments

        RNAi screen using dsRNA made from templates generated with primers directed against this gene results in a long metaphase spindle with misaligned chromosomes when assayed in S2 cells. This phenotype can be observed when the screen is performed with or without Cdc27 dsRNA.

        (Goshima et al., 2007)
        Origin and Etymology
        Discoverer
        Etymology
        Identification
        External Crossreferences and Linkouts ( 33 )
        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/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
        Other crossreferences
        BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
        Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
        Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
        Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
        Flygut - An atlas of the Drosophila adult midgut
        GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
        InterPro - A database of protein families, domains and functional sites
        KEGG Genes - Molecular building blocks of life in the genomic space.
        modMine - A data warehouse for the modENCODE project
        Linkouts
        BioGRID - A database of protein and genetic interactions.
        DPiM - Drosophila Protein interaction map
        DroID - A comprehensive database of gene and protein interactions.
        DRSC - Results frm RNAi screens
        FLIGHT - Cell culture data for RNAi and other high-throughput technologies
        FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
        FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
        FlyMine - An integrated database for Drosophila genomics
        InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
        KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
        MIST (protein-protein) - An integrated Molecular Interaction Database
        Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
        Synonyms and Secondary IDs (5)
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        References (39)