FB2019_06, released Dec 19, 2019

Gene: Dmel\swm

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General Information
Symbol
Dmel\swm
Species
D. melanogaster
Name
second mitotic wave missing
Annotation Symbol
CG10084
Feature Type
protein_coding_gene
FlyBase ID
FBgn0002044
Gene Model Status
Current
Stock Availability
11 publicly available
Gene Snapshot
In progress.Contributions welcome.
Other Summaries
Also Known As
l(2)E1, S(rux)2B, l(2)37Dh
Key Links
Genomic Location
Cytogenetic map
37E4-37E4
Sequence location
2L:19,493,251..19,497,978 [+]
Recombination map
2-54
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
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Molecular Function (GO)
[Detailed GO annotations]
Experimental Evidence
mRNA binding; protein binding
Predictions / Assertions
metal ion binding; mRNA binding
Summaries
Protein Function (UniProtKB)
Negatively regulates Hedgehog (hh) protein signal in wing development (PubMed:18245841). Regulates neural-specific glycosylation by binding to FucTA mRNA and facilitating its nuclear export in neural cells (PubMed:21203496).
(UniProt, Q9VIV2)
Phenotypic Description (Red Book; Lindsley and Zimm 1992)
l(2)37Dh
Interferes with M and M-like mutants.
Gene Model and Products
Number of Transcripts
4
Number of Unique Polypeptides
2

Please see the GBrowse view of Dmel\swm or the JBrowse view of Dmel\swm 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
Low-frequency RNA-Seq exon junction(s) not annotated.
Gene model reviewed during 5.44
Tissue-specific extension of 3' UTRs observed during later stages (FBrf0218523, FBrf0219848); all variants may not be annotated
Annotated transcripts do not represent all supported alternative splices within 5' UTR.
Sequence Ontology: Class of Gene
gene_with_edited_transcript
(Graveley et al., 2011)
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
swm-RA
FBtr0081244
NM_136132
4005
1062
swm-RB
FBtr0081245
NM_165304
4114
1062
swm-RC
FBtr0331325
NM_001273657
4151
1063
swm-RD
FBtr0331326
NM_001273658
3974
1063
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
swm-PA
FBpp0080785
115.7
1062
9.82
NP_609976
AAF53812
swm-PB
FBpp0080786
115.7
1062
9.82
NP_724201
AAN11045
swm-PC
FBpp0303743
115.8
1063
9.82
NP_001260586
AGB93121
swm-PD
FBpp0303744
115.8
1063
9.82
NP_001260587
AGB93122
Polypeptides with Identical Sequences

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

1062 aa isoforms: swm-PA, swm-PB
1063 aa isoforms: swm-PC, swm-PD
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\swm 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 (7 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
mRNA binding
inferred from direct assay
(Yamamoto-Hino et al., 2010)
protein binding
inferred from physical interaction with UniProtKB:Q9VSK8
(assigned by UniProt )
(Hurt et al., 2009)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
metal ion binding
inferred from electronic annotation with InterPro:IPR000571
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
mRNA binding
inferred from biological aspect of ancestor with PANTHER:PTN000373411
(assigned by GO_Central )
(Gaudet et al., 2011)
Biological Process (3 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
negative regulation of mRNA polyadenylation
inferred from mutant phenotype
(Yamamoto-Hino et al., 2010)
positive regulation of gene expression
inferred from mutant phenotype
(Yamamoto-Hino et al., 2010)
positive regulation of RNA export from nucleus
inferred from mutant phenotype
(Yamamoto-Hino et al., 2010)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
positive regulation of RNA export from nucleus
inferred from biological aspect of ancestor with PANTHER:PTN000373411
(assigned by GO_Central )
(Gaudet et al., 2011)
Cellular Component (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
nucleus
inferred from direct assay
(Casso et al., 2008)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
nucleus
inferred from biological aspect of ancestor with PANTHER:PTN000373411
(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
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage
organism | ubiquitous
(Casso et al., 2008)
ventral midline
(Casso et al., 2008)
third instar larval stage
imaginal disc
(Casso et al., 2008)
embryonic/larval salivary gland
(Casso et al., 2008)
embryonic/larval optic lobe
(Casso et al., 2008)
embryonic/larval fat body
(Casso et al., 2008)
embryonic/larval garland cell
(Casso et al., 2008)
gastric caecum
(Casso et al., 2008)
Additional Descriptive Data
swm is detected at all stages of embryogenesis tested. It is present in precellularized embryos, is later enriched in the ventral midline and in segmental stripes and is ubiquitous in later embryos. It is observed in third instar larvae in imaginal discs, salivary gland, optic lobe, fat body, and in the wreath cells and gastric caecae of the gut.
(Casso et al., 2008)
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult head
• membrane
(Aradska et al., 2015)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
nucleus
inferred from direct assay
(Casso et al., 2008)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\swm 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
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
FlyBase Wiki
Image Based Resources
Alleles, Insertions, and Transgenic Constructs
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
FlyBase_internaltransgene_features:cell lethal:cell lethal | somatic clone
lethal
lethal, with Scer\GAL4nub-AC-62
lethal (with Df(2L)ED1272)
lethal | female limited, with Scer\GAL4dome-PG14
lethal | recessive
lethal - all die before end of larval stage (with swm37Dh-1)
lethal - all die before end of larval stage (with swmF15)
partially lethal - majority die, with Scer\GAL4pnr-MD237
Sterility
Allele
female semi-sterile, with Scer\GAL4VP16.otu
Other Phenotypes
Allele
decreased occurrence of cell division | third instar larval stage
increased cell size (with swm37Dh-1)
increased cell size (with swmF14)
increased cell size (with swmF15)
size defective | adult stage
some die during larval stage (with swm37Dh-1)
some die during larval stage (with swmF15)
some die during pupal stage, with Scer\GAL4pnr-MD237
visible, with Scer\GAL4pnr-MD237
visible, with Scer\GAL4ptc-559.1
Phenotype manifest in
Allele
adult brain
eye
mesothoracic tergum, with Scer\GAL4pnr-MD237
wing (with Df(2L)Exel8041)
wing (with swm37Dh-1)
wing (with swmF15)
wing hair (with Df(2L)Exel8041)
wing hair (with swm37Dh-1)
wing hair (with swmF14)
wing hair (with swmF15)
wing vein, with Scer\GAL4ptc-559.1
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (2)
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\RBM26
14 of 15
Yes
Yes
Hsap\RBM27
13 of 15
No
Yes
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (2)
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\Rbm26
12 of 15
Yes
Yes
Mmus\Rbm27
12 of 15
Yes
Yes
Rattus norvegicus (Norway rat) (2)
Rnor\Rbm26
12 of 13
Yes
Yes
Rnor\Rbm27
8 of 13
No
Yes
Xenopus tropicalis (Western clawed frog) (2)
Xtro\rbm26
7 of 12
Yes
Yes
Xtro\rbm27
7 of 12
Yes
Yes
Danio rerio (Zebrafish) (2)
Drer\rbm27
13 of 15
Yes
Yes
Drer\rbm26
8 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\B0336.3
12 of 15
Yes
Yes
Arabidopsis thaliana (thale-cress) (1)
Atha\AT3G27700
4 of 9
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (0)
No records found.
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\SPBC902.04
6 of 12
Yes
Yes
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG091902YQ )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Dmel\swm
Drosophila simulans
Dsim\GD24214
Drosophila sechellia
Dsec\GM17355
Drosophila erecta
Dere\GG21189
Drosophila yakuba
Dyak\GE13261
Drosophila ananassae
Dana\GF14241
Drosophila pseudoobscura pseudoobscura
Dpse\GA10061
Drosophila persimilis
Dper\GL21218
Drosophila willistoni
Dwil\GK18188
Drosophila virilis
Dvir\GJ18137
Drosophila mojavensis
Dmoj\GI18229
Drosophila grimshawi
Dgri\GH11107
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG0915033W )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17021624
Glossina morsitans
Tsetse fly
Gmor\GMOY001962
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_08380
Mayetiola destructor
Hessian fly
Mdes\Mdes006770
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL009061
Anopheles darlingi
American malaria mosquito
Adar\ADAC000076
Anopheles gambiae
Malaria mosquito
Agam\AGAP009601
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ000485
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W04AB )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Bmor\BGIBMGA011381
Bombyx mori
Silkmoth
Bmor\BGIBMGA011380
Danaus plexippus
Monarch butterfly
Dple\DPOGS211737-PA
Danaus plexippus
Monarch butterfly
Dple\DPOGS214406-PA
Heliconius melpomene
Postman butterfly
Hmel\HMEL014188
Apis florea
Little honeybee
Aflo\2548167444
Apis mellifera
Western honey bee
Amel\GB53614
Bombus impatiens
Common eastern bumble bee
Bimp\BIMP17358
Bombus terrestris
Buff-tailed bumblebee
Bter\15213180
Linepithema humile
Argentine ant
Lhum\LH17122
Megachile rotundata
Alfalfa leafcutting bee
Mrot\MROTU:00172e
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG012923
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_02163
Tribolium castaneum
Red flour beetle
Tcas\TC033397
Pediculus humanus
Human body louse
Phum\PHUM423560
Rhodnius prolixus
Kissing bug
Rpro\RPRC013700
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI002555
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_18248
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0470 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Smar\SMAR011454
Ixodes scapularis
Black-legged tick
Isca\ISCW015614
Stegodyphus mimosarum
African social velvet spider
Smim\KFM60967.1
Tetranychus urticae
Two-spotted spider mite
Turt\tetur18g00890
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_9256
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_8266
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_8235
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_229100
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G08U0 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Rbm26L
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Rbm27L
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Rbm26
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000003516
Gallus gallus
Domestic chicken
Ggal\RBM27
Gallus gallus
Domestic chicken
Ggal\RBM26
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v7.1)
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 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?
    RBM26; RNA binding motif protein 26
    14 of 15
        RBM27; RNA binding motif protein 27
        13 of 15
            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
            RNA-protein
            Physical Interaction
            Assay
            References
            swm - FucTA
            anti tag coimmunoprecipitation, quantitative reverse transcription pcr
            (Yamamoto-Hino et al., 2010)
            protein-protein
            Physical Interaction
            Assay
            References
            swm - ZC3H3
            anti tag coimmunoprecipitation, anti tag western blot, tandem affinity purification, Identification by mass spectrometry
            (Hurt et al., 2009)
            Summary of Genetic Interactions
            esyN Network Diagram
            esyN Network Key:
            Suppression
            Enhancement
            View in Interactions Browser
            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
            cnk
            enhanceable
            swm
            (Baril et al., 2014)
            hh
            enhanceable
            swm
            (Casso et al., 2008)
            rux
            suppressible
            swm
            (Casso et al., 2008, Dong et al., 1997)
            smo
            suppressible
            swm
            (Casso et al., 2008)
            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 (genetic) - An integrated Molecular Interaction Database
            MIST (protein-protein) - An integrated Molecular Interaction Database
            Pathways
            Signaling Pathways (FlyBase)
            Metabolic Pathways
            External Data
            Linkouts
            Genomic Location and Detailed Mapping Data
            Chromosome (arm)
            2L
            Recombination map
            2-54
            Cytogenetic map
            37E4-37E4
            Sequence location
            2L:19,493,251..19,497,978 [+]
            FlyBase Computed Cytological Location
            Cytogenetic map
            Evidence for location
            37E4-37E4
            Limits computationally determined from genome sequence between P{EP}dntEP2158 and P{EP}EP623&P{PZ}spi01068
            Experimentally Determined Cytological Location
            Cytogenetic map
            Notes
            References
            Experimentally Determined Recombination Data
            Location
            2-54
            (FlyBase, 2016, Dong et al., 1997)
            2-53.7
            (Comeron et al., 2012)
            2-[54]
            Left of (cM)
            Right of (cM)
            Notes
            Stocks and Reagents
            Stocks (11)
            Genomic Clones (22)
            cDNA Clones (118)
             

            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 database merge of
              Source for merge of: l(2)37Dh S(rux)2B CG10084
              (Thomas, 2005.8)
              Additional comments
              Other Comments
              Isolated in a screen to identify dominant suppressors of the adult rough eye phenotype of a weak rux allele.
              (Dong et al., 1997)
              The wild type function of S(rux)2C is required for entry to S phase.
              (Dong et al., 1997)
              Interferes with M and M-like mutants.
              Origin and Etymology
              Discoverer
              Etymology
              Identification
              External Crossreferences and Linkouts ( 44 )
              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/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
              UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
              Other crossreferences
              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
              ApoDroso - Functional genomic database for photoreceptor development, survival and function
              BioGRID - A database of protein and genetic interactions.
              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.
              MIST (genetic) - An integrated Molecular Interaction Database
              MIST (protein-protein) - An integrated Molecular Interaction Database
              Synonyms and Secondary IDs (11)
              Datasets (0)
              Study focus (0)
              Experimental Role
              Project
              Project Type
              Title
              References (48)