FlyBase Gene Report: Dmel\SmydA-8

General Information

Symbol

Dmel\SmydA-8

Species

D. melanogaster

Name

SET and MYND domain containing, arthropod-specific, member 8

Annotation Symbol

CG33548

Feature Type

protein_coding_gene

FlyBase ID

FBgn0053548

Gene Model Status

Current

Stock Availability

2 publicly available

Gene Snapshot

Contributions welcome

Other Summaries

Alliance
Auto summary
Gene Group
Interactive Fly

Also Known As

msta, EG:103B4.4

Key Links

Genomic Location

Cytogenetic map

2E2-2E2

Sequence location

X:2,205,515..2,213,809 [-]

Recombination map

1-0.8

RefSeq locus

NC_004354 REGION:2205515..2213809

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse GBrowse

Help me choose

Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

GO Summary Ribbons

Gene Ontology (GO) Annotations (5 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 histone deacetylase binding

inferred from sequence or structural similarity with FLYBASE:Smyd4-2; FB:FBgn0036282

(Thompson and Travers, 2008)

enables S-adenosylmethionine-dependent methyltransferase activity

inferred from sequence or structural similarity with SGD:S000001250

(FlyBase Curators, 2008--)

Biological Process (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

involved_in histone lysine methylation

inferred from sequence or structural similarity with SGD:S000001250

(FlyBase Curators, 2008--)

involved_in negative regulation of gene expression

inferred from sequence or structural similarity with FLYBASE:Smyd4-2; FB:FBgn0036282

(Thompson and Travers, 2008)

Cellular Component (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

located_in chromatin

inferred from sequence or structural similarity with SGD:S000001250

(FlyBase Curators, 2008--)

Gene Group (FlyBase)

SET AND MYND DOMAIN FAMILY

Protein Family (UniProt)

Belongs to the class V-like SAM-binding methyltransferase superfamily. (O46040 P83501)

Protein Signatures (InterPro)

SET domain

Summaries

Gene Group (FlyBase)

SET AND MYND DOMAIN FAMILY -: The SET and MYND (SMYD) proteins are lysine methyltransferases that catalyse the addition of one or more methyl groups, using S-adenosyl-l-methionine (SAM) as a cofactor, to the amino group of a lysine residue in the substrate resulting in a mono, di, or trimethylated lysine and the cofactor by-product S-adenosyl-l-homocysteine (SAH). (Adapted from PMID:27447830).

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\SmydA-8 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 5.51

Gene model reviewed during 5.56

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)

SmydA-8-RA

FBtr0070422

NM_001014717

1749

462

SmydA-8-RB

FBtr0070421

NM_001014718

1547

448

SmydA-8-RC

FBtr0342772

NM_001297882

681

158

SmydA-8-RD

FBtr0345599

NM_001297883

2094

462

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

SmydA-8-PA

FBpp0070406

52.2

462

7.18

NP_001014717

AAN09072

SmydA-8-PB

FBpp0070405

51.1

448

6.87

NP_001014718

AAF45751

SmydA-8-PC

FBpp0309624

18.4

158

6.76

NP_001284811

AHN59282

SmydA-8-PD

FBpp0311668

52.2

462

7.18

NP_001284812

AHN59283

Polypeptides with Identical Sequences

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

462 aa isoforms: SmydA-8-PA, SmydA-8-PD

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Crossreferences

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

SET domain

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\SmydA-8 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

expression microarray

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

eye

(Xu et al., 2004)

microinjection

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

photoreceptor cell

(Xu and Wang, 2016)

Additional Descriptive Data

mRNAs are enriched in photoreceptor cells (found by comparing mRNAs isolated from wild-type (w¹¹¹⁸) heads with gl³ heads or wild-type bodies).

(Xu and Wang, 2016)

Eye-enriched transcripts determined by ratio of expression level in wild-type heads. versus expression level in so heads.

(Xu et al., 2004)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

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

spermatozoon

(Wasbrough et al., 2010)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\SmydA-8 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\SmydA-8

View exonic expression by tissue for Dmel\SmydA-8

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

FBgn0053548

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG32799-RA;CG32800-RA

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG32800

Flygut - An atlas of the Drosophila adult midgut

FBgn0053548

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 1 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 2 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of SmydA-8

Transgenic constructs containing regulatory region of SmydA-8

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation

Gene disrupted in

Df(1)Vinc²

(Klapholz et al., 2015)

Inferred from location

Phenotypes

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

Lethality

Allele

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

SmydA-8^GD9503

viable, with Scer\GAL4^pnr-MD237

SmydA-8^GD9503

Phenotype manifest in

Allele

Orthologs

Downloads

Download All DIOPT Orthologs

Download All OrthoDB Orthologs

Human Orthologs (via DIOPT v8.0)

Homo sapiens (Human) (6)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Hsap\SMYD1

5 of 15

Yes

4 of 15

4 of 15

2 of 15

2 of 15

Yes

Hsap\SMYD5

1 of 15

Model Organism Orthologs (via DIOPT v8.0)

Mus musculus (laboratory mouse) (6)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Mmus\Smyd1

5 of 15

Yes

4 of 15

3 of 15

2 of 15

2 of 15

Yes

Mmus\Smyd5

1 of 15

Rattus norvegicus (Norway rat) (6)

Rnor\Smyd1

4 of 13

Yes

Rnor\Smyd2

4 of 13

Yes

Rnor\Smyd3

2 of 13

Rnor\Smyd4

2 of 13

Rnor\Zmynd15

2 of 13

Yes

Rnor\Smyd5

1 of 13

Xenopus tropicalis (Western clawed frog) (5)

Xtro\smyd1

4 of 12

Yes

2 of 12

2 of 12

2 of 12

1 of 12

Danio rerio (Zebrafish) (7)

Drer\smyd1a

4 of 15

Yes

Drer\smyd1b

4 of 15

Yes

Drer\smyd2a

4 of 15

Yes

Drer\smyd2b

4 of 15

Yes

Drer\smyd3

4 of 15

Yes

Drer\smyd4

2 of 15

Drer\smyd5

1 of 15

Caenorhabditis elegans (Nematode, roundworm) (5)

Cele\set-10

3 of 15

Yes

Cele\set-14

3 of 15

Yes

Cele\set-18

3 of 15

Yes

Cele\set-30

3 of 15

Yes

Cele\set-3

1 of 15

Arabidopsis thaliana (thale-cress) (2)

Atha\ASHR2

1 of 9

Yes

Atha\SDG37

1 of 9

Yes

Saccharomyces cerevisiae (Brewer's yeast) (2)

Scer\SET6

2 of 15

Yes

Scer\SET5

1 of 15

Schizosaccharomyces pombe (Fission yeast) (2)

Spom\set5

1 of 12

Yes

Spom\set6

1 of 12

Yes

Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG091904PB )

Organism

Common Name

Gene

AAA Syntenic Ortholog

Multiple Dmel Genes in this Orthologous Group

Drosophila suzukii

Spotted wing Drosophila

Drosophila simulans

Drosophila sechellia

Drosophila erecta

Drosophila yakuba

Drosophila ananassae

Drosophila pseudoobscura pseudoobscura

Dpse\GA22855

Drosophila persimilis

Dper\GL13396

Drosophila willistoni

Dwil\GK16970

Drosophila virilis

Dvir\GJ16480

Drosophila mojavensis

Dmoj\GI21459

Drosophila grimshawi

Dgri\GH12314

Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091505EC )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Musca domestica

House fly

Mdoa\17011884

Musca domestica

House fly

Mdoa\17009502

Musca domestica

House fly

Mdoa\17011885

Musca domestica

House fly

Mdoa\17009501

Musca domestica

House fly

Mdoa\17007727

Musca domestica

House fly

Mdoa\17006815

Glossina morsitans

Tsetse fly

Gmor\GMOY004217

Glossina morsitans

Tsetse fly

Gmor\GMOY004216

Lucilia cuprina

Australian sheep blowfly

Lcup\FF38_08622

Aedes aegypti

Yellow fever mosquito

Aaeg\AAEL008032

Anopheles darlingi

American malaria mosquito

Adar\ADAC000669

Anopheles gambiae

Malaria mosquito

Agam\AGAP000041

Culex quinquefasciatus

Southern house mosquito

Cqui\CPIJ018500

Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W03LN )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Bombyx mori

Silkmoth

Bmor\BGIBMGA003139

Danaus plexippus

Monarch butterfly

Dple\DPOGS211153-PA

Heliconius melpomene

Postman butterfly

Hmel\HMEL017192

Apis florea

Little honeybee

Aflo\2833311652

Apis mellifera

Western honey bee

Amel\GB49416

Bombus impatiens

Common eastern bumble bee

Bimp\BIMP19146

Bombus terrestris

Buff-tailed bumblebee

Bter\15213082

Linepithema humile

Argentine ant

Lhum\LH21230

Megachile rotundata

Alfalfa leafcutting bee

Mrot\MROTU:000769

Nasonia vitripennis

Parasitic wasp

Nvit\Nasvi2EG003811

Nasonia vitripennis

Parasitic wasp

Nvit\Nasvi2EG003809

Tribolium castaneum

Red flour beetle

Tcas\TC014347

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI44442

Zootermopsis nevadensis

Nevada dampwood termite

Znev\Znev_07333

Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X03II )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Stegodyphus mimosarum

African social velvet spider

Smim\KFM72222.1

Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( None identified )

No non-Arthropod Metazoa orthologies identified

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v8.0)

Drosophila melanogaster (Fruit fly) (16)

Gene Symbol

Score

Source

Alignment

5 of 10

5 of 10

5 of 10

4 of 10

4 of 10

4 of 10

4 of 10

4 of 10

4 of 10

dao

2 of 10

2 of 10

2 of 10

2 of 10

1 of 10

1 of 10

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

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?

SMYD1; SET and MYND domain containing 1

5 of 15

606846

SMYD2; SET and MYND domain containing 2

4 of 15

610663

SMYD3; SET and MYND domain containing 3

4 of 15

608783

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

SmydA-8 - CAP

two hybrid

(Hu et al., 2017.6.13)

SmydA-8 - CG10209

two hybrid

(Hu et al., 2017.6.13)

SmydA-8 - CG15772

two hybrid

(Hu et al., 2017.6.13)

SmydA-8 - CG44250

two hybrid

(Hu et al., 2017.6.13)

SmydA-8 - Gsc

two hybrid

(Hu et al., 2017.6.13)

SmydA-8 - Hsp67Bc

two hybrid

(Hu et al., 2017.6.13)

SmydA-8 - 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

BioGRID - A database of protein and genetic interactions.

57739

DroID - A comprehensive database of gene and protein interactions.

FBgn0053548

InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.

31200

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

SmydA-8

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

1-0.8

Cytogenetic map

2E2-2E2

Sequence location

X:2,205,515..2,213,809 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

2E2-2E2

Limits computationally determined from genome sequence between P{EP}Actn^EP1193&P{EP}CG4322^EP1631 and P{EP}EP1460&P{EP}CG2924^EP1596 Limits computationally determined from genome sequence between P{lacW}l(2)k11206^k11206 and P{lacW}tkv^k16713&P{lacW}l(2)k01302^k01302

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

2E-2E

(Alatortsev, 1999.4.29)

Experimentally Determined Recombination Data

Location

1-0.8

(FlyBase, 2016)

1-0.2

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (2)

Bloomington

22935

Mi{ET1}SmydA-8^MB00924 w¹¹¹⁸

VDRC

v33042

w¹¹¹⁸ P{GD9503}v33042

Genomic Clones (8)

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

cDNA Clones (50)

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

IP12582

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.

FBgn0053548

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0053548

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

31200

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Other Information

Relationship to Other Genes

Source for database identify of

Source for identity of: SmydA-8 msta

(Calpena et al., 2015)

Source for database merge of

Source for merge of: msta CG32799

(FlyBase Genome Annotators, 2005)

Additional comments

FlyBase curator comment: Renamed from 'msta' to 'SmydA-8' as part of the systematic Smyd gene nomenclature review (FBrf0229184), and because the 'msta' symbol appears to be based solely on a sequence record (FBrf0112438) with unknown etymology and hasn't been widely used since.

(Calpena et al., 2015)

Annotations CG32799 and CG32800 merged as CG33548 (which corresponds to msta) in release 4.1 of the genome annotation.

(FlyBase Genome Annotators, 2005)

Annotation CG18033 split into CG32799 and CG32800 (msta) in release 3 of the genome annotation.

(FlyBase Genome Annotators, 2002-2003)

Other Comments

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.

31200

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.