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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
4 publicly available
Gene Snapshot
In progress.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
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI Genome Data Viewer
UCSC Genome Browser
Ensembl Genome Browser
PopFly Genome Browser
GO Summary Ribbons
Families, Domains and Molecular Function
Gene Group Membership (FlyBase)
Protein Family (UniProt, Sequence Similarities)
-
Protein Domains/Motifs
InterPro
Matrin/U1-C, C2H2-type zinc finger; Matrin/U1-C-like, C2H2-type zinc finger; SF3A2 domain; Zinc finger C2H2 superfamily
Molecular Function (see GO section for details)
Experimental Evidence
-
Predictions / Assertions
RNA binding; zinc ion binding
Summaries
Gene Group Membership
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 GBrowse view of Dmel\Sf3a2 or 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
Gene Ontology (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
RNA binding
inferred from sequence or structural similarity with HGNC:10766
(FlyBase Curators, 2008--)
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
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
mRNA splicing, via spliceosome
inferred by curator from GO:0071011,GO:0071013
(Herold et al., 2009)
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
catalytic step 2 spliceosome
inferred from high throughput direct assay
(Herold et al., 2009)
precatalytic spliceosome
inferred from high throughput direct assay
(Herold et al., 2009)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
catalytic step 2 spliceosome
inferred from biological aspect of ancestor with PANTHER:PTN000574843
(assigned by GO_Central )
(Gaudet et al., 2011)
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)
U2-type prespliceosome
inferred from biological aspect of ancestor with PANTHER:PTN000574843
(assigned by GO_Central )
(Gaudet et al., 2011)
Expression Data
Transcript Expression
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
catalytic step 2 spliceosome
inferred from high throughput direct assay
(Herold et al., 2009)
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, Transgenic Constructs and Phenotypes
Classical and Insertion Alleles ( 1 )
For All Classical and Insertion Alleles Show
 
Allele of Sf3a2
Class
Mutagen
Associated Insertion
Stocks
Known lesion
Sf3a2f03161
1
Yes
Other relevant insertions
Transgenic Constructs ( 3 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Sf3a2
Allele of Sf3a2
Mutagen
Associated Transgenic Construct
Stocks
Sf3a2GD7087
2
Sf3a2HMC03799
1
Sf3a2NIG.10754R
0
Transgenic constructs containing regulatory region of Sf3a2
Deletions and Duplications ( 0 )
Summary of Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v7.1)
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 v7.1)
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
10 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
13 of 15
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\sap62
11 of 12
Yes
Yes
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG09190F58 )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Dmel\Sf3a2
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
Human Disease Model Data
FlyBase Human Disease Model Reports
    Alleles Reported to Model Human Disease (Disease Ontology)
    Download
    Models ( 0 )
    Allele
    Disease
    Evidence
    References
    Interactions ( 0 )
    Allele
    Disease
    Interaction
    References
    Comments ( 0 )
     
    Human Orthologs (via DIOPT v7.1)
    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
    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
      esyN Network Diagram
      Show neighbor-neighbor interactions:
      Select Layout:
      Legend:
      Protein
      RNA
      Selected Interactor(s)
      Interactions Browser
      View in Interactions Browser
      Please look at the Interaction Group reports for full details of the physical interactions
      protein-protein
      Interacting group
      Assay
      References
      Sf3a2 - Sf3a1
      experimental knowledge based
      (Guruharsha et al., 2011)
      Sf3a2 - Sf3b5
      anti tag coimmunoprecipitation, peptide massfingerprinting
      (Stegeman et al., 2016)
      Sf3a2 - noi
      experimental knowledge based
      (Guruharsha et al., 2011)
      Sf3a2 - snf
      anti tag coimmunoprecipitation, peptide massfingerprinting
      (Stegeman et al., 2016)
      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.
      Pathways
      Gene Group - Pathway Membership (FlyBase)
      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 (4)
      Genomic Clones (17)
      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 sequences
      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
       
      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 ( 31 )
      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
      InterPro - A database of protein families, domains and functional sites
      KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
      Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
      Linkouts
      BioGRID - A database of protein and genetic interactions.
      Drosophila Genomics Resource Center - Drosophila Genomics Resource Center cDNA clones
      DPiM - Drosophila Protein interaction map
      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.
      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
      FlyMine - An integrated database for Drosophila genomics
      GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
      InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
      KEGG Genes - Molecular building blocks of life in the genomic space.
      modMine - A data warehouse for the modENCODE project
      Synonyms and Secondary IDs (4)
      Datasets (0)
      Study focus (0)
      Experimental Role
      Project
      Project Type
      Title
      References (35)