FlyBase Gene Report: Dmel\smash

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\smash 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 (0 terms)

Molecular Function (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Cellular Component (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

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

expression microarray

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

adult fat body

Comment: cyclical, peak ZT17-20

(Xu et al., 2011)

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 3

organism | ubiquitous

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 4 -- 6

dorsal ectoderm anlage

Comment: anlage in statu nascendi

(Fisher et al., 2012)

organism | faint | ubiquitous

(Fisher et al., 2012)

ventral ectoderm anlage

Comment: anlage in statu nascendi

(Fisher et al., 2012)

embryonic stage 7 -- 8

organism | faint | ubiquitous

(Fisher et al., 2012)

embryonic stage 9 -- 10

organism | faint | ubiquitous

(Fisher et al., 2012)

dorsal ectoderm

(Fisher et al., 2012)

embryonic stage 11 -- 12

hindgut proper primordium

(Fisher et al., 2012)

organism | faint | ubiquitous

(Fisher et al., 2012)

posterior spiracle primordium

Comment: reported as posterior spiracle specific anlage

(Fisher et al., 2012)

dorsal epidermis primordium

(Fisher et al., 2012)

tracheal primordium

(Fisher et al., 2012)

Additional Descriptive Data

Expressed cyclically in the adult fat body.

(Xu et al., 2011)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 13 -- 14

embryonic/larval epidermis

(Beati et al., 2018)

embryonic stage 13

embryonic/larval foregut

(Beati et al., 2018)

embryonic/larval Malpighian tubule

(Beati et al., 2018)

amnioserosa

(Beati et al., 2018)

embryonic/larval trachea

(Beati et al., 2018)

embryonic stage 15

embryonic/larval hindgut

(Beati et al., 2018)

embryonic/larval salivary gland

(Beati et al., 2018)

embryonic/larval visceral muscle

(Beati et al., 2018)

embryonic/larval posterior spiracle

(Beati et al., 2018)

embryonic stage 17

embryonic/larval somatic muscle

(Beati et al., 2018)

pharyngeal muscle

(Beati et al., 2018)

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

day 5 of adulthood & male -- day 7 of adulthood & male

spermatozoon

(Wasbrough et al., 2010)

adult stage

adult head

• membrane

(Aradska et al., 2015)

Additional Descriptive Data

smash protein is detectable from embryonic stage 5 on in all ectodermally-derived epithelia, including epidermis, foregut, hindgut, Malpighian tubules, salivary glands, amnioserosa, and the tracheal tree. It is also observed in somatic, pharyngeal, and visceral muscles. No expression is observed in neuroblasts and their descendents.

(Beati et al., 2018)

Marker for

Subcellular Localization

CV Term

Evidence

References

Expression Deduced from Reporters

Reporter: PBac{768.FSVS-0}smash^CPTI003445

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

adult protocerebrum | faint

(Knowles-Barley, 2011.8.24)

fan-shaped body | faint | restricted

(Knowles-Barley, 2011.8.24)

adult gnathal ganglion | restricted

(Knowles-Barley, 2011.8.24)

bulb

(Knowles-Barley, 2011.8.24)

High-Throughput Expression Data

Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\smash in GBrowse 2

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\smash

View exonic expression by tissue for Dmel\smash

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

FBgn0263346

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 ( 27 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 18 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of smash

Transgenic constructs containing regulatory region of smash

Deletions and Duplications ( 2 )

Not disrupted in

Df(3R)rpk-Karyβ3

(Tsubouchi et al., 2012)

Partially disrupted in

Df(3R)smash³⁵

(Beati et al., 2018)

Phenotypes

For more details about a specific phenotype click on the relevant allele symbol.

Lethality

Allele

lethal - all die before end of larval stage, with Scer\GAL4^αTub84B.PL

smash^PM.UAS.GFP

lethal - all die before end of P-stage, with Scer\GAL4^αTub84B.PL

smash^PI.UAS.GFP

viable, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

viable, with Scer\GAL4^Mef2.PR

viable, with Scer\GAL4^pnr-MD237

viable, with Scer\GAL4^tin.CΔ4

Other Phenotypes

Allele

cell shape defective | adult stage | cell autonomous | somatic clone, with Scer\GAL4^Act5C.PP

smash^PM.UAS.GFP

majority die during larval stage, with Scer\GAL4^αTub84B.PL

size defective | embryonic stage, with Scer\GAL4^btl.PS

smash^PM.UAS.GFP

small body | adult stage, with Scer\GAL4^αTub84B.PL

smash^PI.UAS.GFP

some die during embryonic stage, with Scer\GAL4^αTub84B.PL

smash^PM.UAS.GFP

some die during pupal stage, with Scer\GAL4^αTub84B.PL

smash^PI.UAS.GFP

Phenotype manifest in

Allele

cuticle | embryonic stage, with Scer\GAL4^αTub84B.PL

smash^PM.UAS.GFP

oocyte associated follicular epithelium | adult stage | cell autonomous | somatic clone, with Scer\GAL4^Act5C.PP

smash^PM.UAS.GFP

tracheal lumen | embryonic stage, with Scer\GAL4^btl.PS

smash^PM.UAS.GFP

Orthologs

Downloads

Download All DIOPT Orthologs

Download All OrthoDB Orthologs

Human Orthologs (via DIOPT v7.1)

Homo sapiens (Human) (3)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Hsap\LIMCH1

3 of 15

Yes

Hsap\LMO7

3 of 15

Yes

Hsap\SCEL

1 of 15

Yes

Model Organism Orthologs (via DIOPT v7.1)

Mus musculus (laboratory mouse) (4)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Mmus\Limch1

4 of 15

Yes

Mmus\Lmo7

2 of 15

Yes

Mmus\Peak1

1 of 15

Mmus\Scel

1 of 15

Yes

Rattus norvegicus (Norway rat) (2)

Rnor\Limch1

2 of 13

Yes

Rnor\Lmo7

1 of 13

Yes

Xenopus tropicalis (Western clawed frog) (3)

Xtro\lmo7

2 of 12

Yes

Xtro\limch1

1 of 12

Yes

Xtro\scel

1 of 12

Yes

Danio rerio (Zebrafish) (5)

Drer\limch1a

3 of 15

Yes

Drer\lmo7a

3 of 15

Yes

Drer\limch1b

1 of 15

Yes

Drer\lmo7b

1 of 15

Yes

Drer\scel

1 of 15

Yes

Caenorhabditis elegans (Nematode, roundworm) (1)

Cele\lim-8

5 of 15

Yes

Arabidopsis thaliana (thale-cress) (0)

No records found.

Saccharomyces cerevisiae (Brewer's yeast) (0)

No records found.

Schizosaccharomyces pombe (Fission yeast) (0)

No records found.

Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG091902K9 )

Organism

Common Name

Gene

AAA Syntenic Ortholog

Multiple Dmel Genes in this Orthologous Group

Drosophila melanogaster

fruit fly

Dmel\smash

Drosophila suzukii

Spotted wing Drosophila

Drosophila simulans

Drosophila sechellia

Drosophila sechellia

Drosophila erecta

Drosophila yakuba

Drosophila ananassae

Drosophila pseudoobscura pseudoobscura

Dpse\GA30203

Drosophila persimilis

Dper\GL22331

Drosophila persimilis

Dper\GL22332

Drosophila willistoni

Dwil\GK12820

Drosophila virilis

Dvir\GJ23955

Drosophila mojavensis

Dmoj\GI23771

Drosophila grimshawi

Dgri\GH19501

Drosophila grimshawi

Dgri\GH19500

Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091500DD )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Musca domestica

House fly

Mdoa\17014781

Glossina morsitans

Tsetse fly

Gmor\GMOY001569

Lucilia cuprina

Australian sheep blowfly

Lcup\FF38_13120

Mayetiola destructor

Hessian fly

Mdes\Mdes009895

Aedes aegypti

Yellow fever mosquito

Aaeg\AAEL007290

Culex quinquefasciatus

Southern house mosquito

Cqui\CPIJ015493

Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( None identified )

No non-Dipteran orthologies identified

Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( None identified )

No non-Insect Arthropod orthologies identified

Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G00G0 )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strongylocentrotus purpuratus

Purple sea urchin

Spur\Sp-Slc5a3_2

Strongylocentrotus purpuratus

Purple sea urchin

Spur\SPU_023916gn

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 ( 1 )

Allele

Disease

Interaction

References

smash^GD10286

ameliorates tauopathy

modeled by Hsap\MAPT^R406W.UAS

(Butzlaff et al., 2015)

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?

LIMCH1; LIM and calponin homology domains 1

3 of 15

617750

LMO7; LIM domain 7

3 of 15

604362

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

Interactions Browser

View in Interactions Browser

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

smash - Src42A

anti tag coimmunoprecipitation, anti tag western blot

(Beati et al., 2018)

smash - baz

two hybrid, nuclear magnetic resonance, predetermined participant, anti tag coimmunoprecipitation, western blot

(Beati et al., 2018)

smash - cno

nuclear magnetic resonance, predetermined participant

(Beati et al., 2018)

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.

FBgn0263346

MIST (protein-protein) - An integrated Molecular Interaction Database

CG43427

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-47.1

Cytogenetic map

82D2-82D2

Sequence location

3R:4,659,579..4,712,193 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

82D2-82D2

Limits computationally determined from genome sequence between P{PZ}l(3)02733⁰²⁷³³ and P{EP}EP974

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-47.1

(FlyBase, 2016)

3-44.1

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (18)

Bloomington

85073

w¹¹¹⁸; PBac{PB}smash^c06749

62701

w¹¹¹⁸; PBac{IT.GAL4}smash^0071-G4

52982

y¹ v¹; P{TRiP.HMJ21669}attP40/CyO

32684

y¹ w^*; Mi{MIC}smash^MI00418

42345

y¹ w^*; Mi{MIC}smash^MI05757

56566

y¹ w^*; Mi{MIC}smash^MI05470

Kyoto

124050

w¹¹¹⁸; P{RS3}smash^CB-6326-3

115407

w¹¹¹⁸; PBac{768.FSVS-0}smash^CPTI003445

VDRC

v100636

P{KK104543}VIE-260B

v21366

w¹¹¹⁸; P{GD10286}v21366

v318490

PBac{fTRG00176.sfGFP-TVPTBF}VK00033

v40276

w¹¹¹⁸; P{GD10283}v40276/CyO

More stocks available...

Genomic Clones (36)

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

cDNA Clones (100)

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.

FBgn0263346

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

RNAi and Array Information

Linkouts

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

40583

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Tanaka et al., 2019, Beati et al., 2018)

Commercially Available Antibodies

Other Information

Relationship to Other Genes

Source for database identify of

Source for identity of: smash CG43427

(Beati et al., 2018)

Source for database merge of

Source for merge of: CG1054 CG14653

(FlyBase Genome Annotators, 2002-2003)

Source for merge of: CG31534 anon-WO0140519.95

(FlyBase, 1996-)

Source for merge of: CG18253 CG1055

(FlyBase, 1996-)

Source for merge of: CG31531 CG31534

(FlyBase Genome Annotators, 2011)

Additional comments

shk may correspond to CG43427: the P{PZ}shk¹ insertion maps within the transcription unit.

(Gene Disruption Project members, 2015.10.8)

Annotations CG31531 and CG31534 merged as CG43427 in release 5.40 of the genome annotation.

(FlyBase Genome Annotators, 2011)

Merge supported by RNA-seq junction and RNA-seq expression data.

(FlyBase Genome Annotators, 2011)

Annotations CG1054 and CG14653 merged as CG31531 in release 3 of the genome annotation.

(FlyBase Genome Annotators, 2002-2003)

Annotations CG1055, CG18253 merged as CG31534 in release 3 of the genome annotation.

(FlyBase Genome Annotators, 2002-2003)

Source for merge of CG31534 anon-WO0140519.95 was sequence comparison ( date:051113 ).

(FlyBase, 1996-)

Source for merge of CG18253 CG1055 was a shared cDNA ( date:010720 ).

(FlyBase, 1996-)

Other Comments

dsRNA made from templates generated with primers directed against this gene tested in RNAi screen for effects on Kc167 and S2R⁺ cell morphology.

(Kiger et al., 2003)

Origin and Etymology

Discoverer

Etymology

Named 'smallish' because overexpression results in almost complete lethality with very rare escaper flies that are strongly reduced in size.

(Beati et al., 2018)

Identification

External Crossreferences and Linkouts ( 79 )

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.

40583

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

Q0KIC3

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

FBgn0263346

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones

FBgn0263346

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

40583

InterPro - A database of protein families, domains and functional sites

KEGG Genes - Molecular building blocks of life in the genomic space.

Dmel_CG43427

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0263346

MIST (protein-protein) - An integrated Molecular Interaction Database

CG43427

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

Synonyms and Secondary IDs (11)

Reported As

Symbol Synonym

CG1054

CG1055

(Stanyon et al., 2004)

CG14653

CG18253

(Asha et al., 2003)

CG31531

(Ashwal-Fluss et al., 2014, Takahashi et al., 2012, Tsubouchi et al., 2012, Carreira et al., 2011, Friedman et al., 2011, Magwire et al., 2010, Keleman et al., 2009.8.5, Lee et al., 2008, Stapleton et al., 2006)

CG31534

(Sarov et al., 2016, Butzlaff et al., 2015, Japanese National Institute of Genetics, 2012.5.21, Xu et al., 2011, Wasbrough et al., 2010)

CG43427

(Beati et al., 2018, Clandinin and Owens, 2016-, Gene Disruption Project members, 2016-, Rodriguez et al., 2012, FlyBase Genome Annotators, 2011, Ni et al., 2010.12.1)

Smash

(Tanaka et al., 2019)

anon-WO0140519.95

smash

(Tanaka et al., 2019, Beati et al., 2018)

Name Synonyms

smallish

(Tanaka et al., 2019, Beati et al., 2018)

Secondary FlyBase IDs

FBgn0051531
FBgn0037266
FBgn0037267
FBgn0051534
FBgn0037268
FBgn0037269
FBgn0044530

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

References (60)

Report Sections

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