FB2019_05, released Oct 15, 2019

Gene: Dmel\Sf3a1

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General Information
Symbol
Dmel\Sf3a1
Species
D. melanogaster
Name
Splicing factor 3a subunit 1
Annotation Symbol
CG16941
Feature Type
protein_coding_gene
FlyBase ID
FBgn0266917
Gene Model Status
Current
Stock Availability
5 publicly available
Gene Snapshot
In progress.Contributions welcome.
Other Summaries
Key Links
Genomic Location
Cytogenetic map
89E6-89E7
Sequence location
3R:16,999,384..17,002,355 [-]
Recombination map
3-59
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 Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Molecular Function (GO)
[Detailed GO annotations]
Experimental Evidence
-
Predictions / Assertions
RNA binding
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 GBrowse view of Dmel\Sf3a1 or the JBrowse view of Dmel\Sf3a1 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 5.48
Sequence Ontology: Class of Gene
gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Sf3a1-RA
FBtr0083374
NM_142326
2558
784
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
Sf3a1-PA
FBpp0082817
88.1
784
6.33
NP_650583
AAF55372
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\Sf3a1 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 (10 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
RNA binding
inferred from sequence or structural similarity with HGNC:10765
(FlyBase Curators, 2008--)
inferred from biological aspect of ancestor with PANTHER:PTN000393333
(assigned by GO_Central )
(Gaudet et al., 2011)
Biological Process (4 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
mitotic cell cycle
inferred from high throughput mutant phenotype
(Ducat et al., 2008)
regulation of alternative mRNA splicing, via spliceosome
inferred from high throughput mutant phenotype
(Park et al., 2004)
spermatogenesis
inferred from mutant phenotype
(Wu et al., 2016)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
mRNA splicing, via spliceosome
inferred by curator from GO:0071011,GO:0071013
(Herold et al., 2009)
inferred from sequence or structural similarity with SGD:S000003739
(Mount and Salz, 2000)
Cellular Component (5 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 (4 terms)
CV Term
Evidence
References
catalytic step 2 spliceosome
inferred from biological aspect of ancestor with PANTHER:PTN000393333
(assigned by GO_Central )
(Gaudet et al., 2011)
nucleus
inferred by curator from GO:0000381
(Park et al., 2004)
U2 snRNP
inferred from sequence or structural similarity with SGD:S000003739
(Mount and Salz, 2000)
inferred from biological aspect of ancestor with PANTHER:PTN000393333
(assigned by GO_Central )
(Gaudet et al., 2011)
U2-type prespliceosome
inferred from biological aspect of ancestor with PANTHER:PTN000393333
(assigned by GO_Central )
(Gaudet et al., 2011)
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
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult head
(Aradska et al., 2015)
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\Sf3a1 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
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Images
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 ( 4 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Sf3a1
Transgenic constructs containing regulatory region of Sf3a1
Deletions and Duplications ( 0 )
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\SF3A1
14 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\Sf3a1
13 of 15
Yes
Yes
Rattus norvegicus (Norway rat) (1)
Rnor\Sf3a1
13 of 13
Yes
Yes
Xenopus tropicalis (Western clawed frog) (1)
Xtro\sf3a1
8 of 12
Yes
Yes
Danio rerio (Zebrafish) (1)
Drer\sf3a1
14 of 15
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\prp-21
14 of 15
Yes
Yes
Arabidopsis thaliana (thale-cress) (10)
Atha\AT1G14650
8 of 9
Yes
Yes
Atha\AT1G14640
6 of 9
No
Yes
Atha\AT4G16200
3 of 9
No
Yes
Atha\AT5G06520
3 of 9
No
Yes
Atha\AT2G43960
2 of 9
No
Yes
Atha\AT5G12280
2 of 9
No
Yes
Atha\AT1G18050
1 of 9
No
Yes
Atha\AT3G27600
1 of 9
No
Yes
Atha\AT3G49130
1 of 9
No
Yes
Atha\AT5G06890
1 of 9
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\PRP21
9 of 15
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\sap114
11 of 12
Yes
Yes
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG091904OK )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Dmel\Sf3a1
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00009649
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00009651
Drosophila simulans
Dsim\GD15098
Drosophila sechellia
Dsec\GM15394
Drosophila erecta
Dere\GG16800
Drosophila yakuba
Dyak\GE26116
Drosophila ananassae
Dana\GF17916
Drosophila pseudoobscura pseudoobscura
Dpse\GA14228
Drosophila persimilis
Dper\GL22994
Drosophila willistoni
Dwil\GK12756
Drosophila virilis
Dvir\GJ10593
Drosophila mojavensis
Dmoj\GI23747
Drosophila grimshawi
Dgri\GH18068
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091502V9 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17015360
Glossina morsitans
Tsetse fly
Gmor\GMOY002459
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_01975
Mayetiola destructor
Hessian fly
Mdes\Mdes012007
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL013818
Anopheles darlingi
American malaria mosquito
Adar\ADAC002178
Anopheles gambiae
Malaria mosquito
Agam\AGAP011328
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ015416
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W025F )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Bmor\BGIBMGA013594
Danaus plexippus
Monarch butterfly
Dple\DPOGS204107-PA
Heliconius melpomene
Postman butterfly
Hmel\HMEL010984
Apis florea
Little honeybee
Aflo\4048563396
Apis mellifera
Western honey bee
Amel\SF3A1
Bombus impatiens
Common eastern bumble bee
Bimp\BIMP12852
Bombus terrestris
Buff-tailed bumblebee
Bter\15215960
Linepithema humile
Argentine ant
Lhum\LH10601
Megachile rotundata
Alfalfa leafcutting bee
Mrot\MROTU:0001fe
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG004600
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG004590
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_05475
Tribolium castaneum
Red flour beetle
Tcas\TC004839
Pediculus humanus
Human body louse
Phum\PHUM259560
Rhodnius prolixus
Kissing bug
Rpro\RPRC001043
Rhodnius prolixus
Kissing bug
Rpro\RPRC006987
Cimex lectularius
Bed bug
Clec\CLEC008973
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI065062
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI001764
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_15013
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X022N )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Smar\SMAR014474
Stegodyphus mimosarum
African social velvet spider
Smim\KFM81592.1
Stegodyphus mimosarum
African social velvet spider
Smim\KFM81590.1
Stegodyphus mimosarum
African social velvet spider
Smim\KFM81591.1
Tetranychus urticae
Two-spotted spider mite
Turt\tetur03g03630
Tetranychus urticae
Two-spotted spider mite
Turt\tetur03g03590
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_196815
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0539 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Sf3a1L
Strongylocentrotus purpuratus
Purple sea urchin
Spur\SPU_007585gn
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Sf3a1_1
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Sf3a1_2
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Sf3a1
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000008526
Gallus gallus
Domestic chicken
Ggal\SF3A1
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (1)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
scaf6
1 of 10
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
    Comments on Models/Modifiers Based on Experimental Evidence ( 0 )
     
    Disease Associations of Human Orthologs (via DIOPT v7.1 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?
    SF3A1; splicing factor 3a subunit 1
    14 of 15
    605595
        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 see the Physical Interaction reports below for full details
        protein-protein
        Physical Interaction
        Assay
        References
        Sf3a1 - Sf3a2
        experimental knowledge based
        (Guruharsha et al., 2011)
        Sf3a1 - Sf3b5
        anti tag coimmunoprecipitation, peptide massfingerprinting
        (Stegeman et al., 2016)
        Sf3a1 - noi
        experimental knowledge based
        (Guruharsha et al., 2011)
        Sf3a1 - snf
        anti tag coimmunoprecipitation, peptide massfingerprinting
        (Stegeman et al., 2016)
        Sf3a1 - vers
        two hybrid
        (Hu et al., 2017.6.13)
        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
        DroID - A comprehensive database of gene and protein interactions.
        MIST (protein-protein) - An integrated Molecular Interaction Database
        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)
        3R
        Recombination map
        3-59
        Cytogenetic map
        89E6-89E7
        Sequence location
        3R:16,999,384..17,002,355 [-]
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        89E6-89E7
        Limits computationally determined from genome sequence between P{EP}MESK4EP1015 and P{EP}CG5208EP562&P{EP}DadEP3196
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        89E4-89E4
        (Oh et al., 2003)
        Experimentally Determined Recombination Data
        Location
        3-59
        (FlyBase, 2016)
        3-59.0
        (Comeron et al., 2012)
        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (5)
        Genomic Clones (7)
         

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

        cDNA Clones (77)
         

        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
        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: Sf3a1 CG16941
        (Stegeman et al., 2016)
        Source for database merge of
        Source for merge of: l(3)SH146 CG16941
        (FlyBase, 1996-)
        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)
        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)
        RNAi generated by PCR using primers directed to this gene causes a cell growth and viability phenotype when assayed in Kc167 and S2R+ cells.
        (Boutros et al., 2004)
        1 allele of l(3)SH146 recovered in a P-insertion screen.
        (Oh et al., 2003)
        Origin and Etymology
        Discoverer
        Etymology
        Identification
        External Crossreferences and Linkouts ( 28 )
        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
        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.
        KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
        Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
        Linkouts
        DroID - A comprehensive database of gene and protein interactions.
        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 (11)
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        References (56)