FlyBase Gene Report: Dmel\Smyd3

General Information

Symbol

Dmel\Smyd3

Species

D. melanogaster

Name

SET and MYND domain containing, class 3

Annotation Symbol

CG13761

Feature Type

protein_coding_gene

FlyBase ID

FBgn0011566

Gene Model Status

Current

Stock Availability

3 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Gene Group
Interactive Fly

Also Known As

EG:BACR7C10.4 , Bzd, Buzidau

Key Links

Genomic Location

Cytogenetic map

3A7-3A7

Sequence location

X:2,606,680..2,608,876 [-]

Recombination map

1-1

RefSeq locus

NC_004354 REGION:2606680..2608876

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

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

Function

Gene Ontology (GO) Annotations (3 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 methyltransferase activity

inferred from biological aspect of ancestor with PANTHER:PTN008534456

(GO Reference Genome Project, 2011-)

enables protein-lysine N-methyltransferase activity

inferred from biological aspect of ancestor with PANTHER:PTN008534456

(GO Reference Genome Project, 2011-)

inferred from sequence or structural similarity with UniProtKB:Q9NRG4

(Gene Ontology Curators, 2002-)

Biological Process (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Cellular Component (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

is_active_in nucleus

inferred from biological aspect of ancestor with PANTHER:PTN008534456

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

SET AND MYND DOMAIN FAMILY

Protein Family (UniProt)

Protein Signatures (InterPro)

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\Smyd3 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

Structure

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry Q9W4X8)

If you don't see a structure in the viewer, refresh your browser.

Model Confidence:

Very high (pLDDT > 90)
Confident (90 > pLDDT > 70)
Low (70 > pLDDT > 50)
Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures

Crossreferences

Comments on Gene Model

Low-frequency RNA-Seq exon junction(s) not annotated.

Gene model reviewed during 5.47

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Smyd3-RB

FBtr0070447

NM_080029

1762

468

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

UniProt

RefSeq ID

GenBank

Smyd3-PB

FBpp0070431

53.1

468

8.13

Q9W4X8

NP_524768

AAF45795

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

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\Smyd3 using the Feature Mapper tool.

External Data

Crossreferences

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

Bzd_1

Linkouts

Expression Data

Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

-0.43

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Smyd3 in JBrowse

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

View exonic expression by developmental stage for Dmel\Smyd3

View exonic expression by tissue for Dmel\Smyd3

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

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

44554/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0011566

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0011566

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0011566

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

CG13761

Flygut - An atlas of the Drosophila adult midgut

FBgn0011566

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 0 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 5 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Smyd3

Transgenic constructs containing regulatory region of Smyd3

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 13 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

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

Phenotype manifest in

Allele

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (7)

Hsap\SMYD3

14 of 14

Yes

Hsap\SMYD1

9 of 14

Yes

Hsap\SMYD2

9 of 14

Yes

Hsap\SMYD4

3 of 14

Hsap\SMYD5

2 of 14

Hsap\ZMYND15

2 of 14

Yes

Hsap\CBFA2T3

1 of 14

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (6)

Rnor\Smyd1

11 of 14

Yes

Rnor\Smyd2

11 of 14

Yes

Rnor\Smyd4

3 of 14

Rnor\Smyd3

2 of 14

Yes

Rnor\Smyd5

2 of 14

Rnor\Zmynd15

2 of 14

Yes

Mus musculus (laboratory mouse) (7)

Mmus\Smyd3

14 of 14

Yes

Mmus\Smyd1

9 of 14

Yes

Mmus\Smyd2

8 of 14

Yes

Mmus\Smyd4

3 of 14

Mmus\Smyd5

2 of 14

Mmus\Zmynd15

2 of 14

Yes

Mmus\Lonrf3

1 of 14

Xenopus tropicalis (Western clawed frog) (9)

Xtro\smyd3

7 of 13

Yes

Xtro\smyd1

5 of 13

Yes

Xtro\smyd2

5 of 13

Xtro\adhfe1

1 of 13

Xtro\mss51

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

Yes

Danio rerio (Zebrafish) (7)

Drer\smyd3

14 of 14

Yes

Drer\smyd2b

12 of 14

Yes

Drer\smyd1a

11 of 14

Yes

Drer\smyd1b

11 of 14

Yes

Drer\smyd2a

11 of 14

Yes

Drer\smyd4

3 of 14

Drer\smyd5

2 of 14

Caenorhabditis elegans (Nematode, roundworm) (5)

Cele\set-18

12 of 14

Yes

Cele\set-30

9 of 14

Yes

Cele\set-14

7 of 14

Yes

Cele\set-10

6 of 14

Yes

Cele\set-3

1 of 14

Anopheles gambiae (African malaria mosquito) (32)

Agam\AgaP_AGAP008954

12 of 12

Yes

3 of 12

3 of 12

3 of 12

3 of 12

3 of 12

3 of 12

3 of 12

3 of 12

3 of 12

3 of 12

3 of 12

3 of 12

3 of 12

3 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

1 of 12

1 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (9)

Atha\SDG37

13 of 13

Yes

Atha\ASHR2

4 of 13

Yes

Atha\SDG38

3 of 13

Yes

Atha\TPR9

2 of 13

Atha\AT1G26761

1 of 13

Yes

Atha\AT1G43245

1 of 13

Yes

Atha\AT4G21890

1 of 13

Yes

Atha\ATXR2

1 of 13

Atha\SDG35

1 of 13

Yes

Saccharomyces cerevisiae (Brewer's yeast) (2)

Scer\SET6

4 of 13

Yes

Scer\SET5

3 of 13

Schizosaccharomyces pombe (Fission yeast) (2)

Spom\set6

7 of 12

Yes

Spom\set5

2 of 12

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Smyd3. Refer to their site for version information.

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v9.1)

Gene Symbol

Score

Source

Alignment

Drosophila melanogaster (Fruit fly) (16)

4 of 13

4 of 13

4 of 13

4 of 13

4 of 13

dao

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

2 of 13

2 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

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 v9.1 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?

SMYD3; SET and MYND domain containing 3

14 of 14

608783

SMYD1; SET and MYND domain containing 1

9 of 14

606846

SMYD2; SET and MYND domain containing 2

9 of 14

610663

SMYD4; SET and MYND domain containing 4

3 of 14

619134

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

Interaction Browsers

Summary of Genetic Interactions

Interaction Browsers

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.

69131

DroID - A comprehensive database of gene and protein interactions.

FBgn0011566

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

KEGG Metabolic Pathways - A collection of manually drawn metabolic pathway maps representing knowledge of molecular interaction, reaction and relation networks.

External Data

Linkouts

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

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

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

1-1

Cytogenetic map

3A7-3A7

Sequence location

X:2,606,680..2,608,876 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

3A7-3A7

Limits computationally determined from genome sequence between P{EP}egh^EP804 and P{EP}sgg^EP1576

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

1-1

(FlyBase, 2016)

1-1.2

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (3)

Aberrations including deletions of this gene Aberrations including duplications of this gene

Bloomington

96739

y¹ v¹; P{TRiP.HMS06139}attP40

NIG-Fly

13761R-3

P{NIG.13761R}3

HMJ22440

y¹ v¹; P{TRiP.HMJ22440}attP40/CyO

Genomic Clones (11)

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

cDNA Clones (9)

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 JBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA clones, fully sequenced

BDGP DGC clones

SD20045

Other clones

MIP05435

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.

FBgn0011566

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0011566

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Relationship to Other Genes

Source for database merge of

Source for merge of: Bzd EG:BACR7C10.4

(FlyBase, 1996-)

Source for merge of: EG:BACR7C10.4 CG13761

(FlyBase, 1996-)

Additional comments

Source for merge of Bzd EG:BACR7C10.4 was sequence comparison ( date:000223 ).

(FlyBase, 1996-)

Source for merge of EG:BACR7C10.4 CG13761 was sequence comparison ( date:000425 ).

(FlyBase, 1996-)

Nomenclature History

Source for database identify of

Source for identity of: Smyd3 Bzd

(Calpena et al., 2015)

Nomenclature comments

FlyBase curator comment: Renamed from 'Bzd' to 'Smyd3' as part of the systematic Smyd gene nomenclature review (FBrf0229184), and because the 'Bzd/Buzidau' nomenclature is of unknown origin/meaning and hasn't been widely used.

(Calpena et al., 2015)

Etymology

Synonyms and Secondary IDs (6)

Reported As

Symbol Synonym

Bzd

(Neumüller et al., 2013, Japanese National Institute of Genetics, 2012.5.21)

CG13761

(National Institute of Genetics Fly Stocks, 2023-, Kurshakova et al., 2019, Calpena et al., 2015, Keleman et al., 2009.8.5, Perkins et al., 2009, Borras et al., 2003, Veraksa et al., 2002, Benos, 2000.12.13)

EG:BACR7C10.4

(Benos et al., 2001, Benos, 2000.12.13)

Smyd3

(Calpena et al., 2015)

Name Synonyms

Buzidau

(Calpena et al., 2015)

SET and MYND domain containing, class 3

Secondary FlyBase IDs

FBgn0029628

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 40 )

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.

44554

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/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.

Q9W4X8

UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information

Other crossreferences

AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.

Q9W4X8

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

44554/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0011566

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0011566

FlyMine - An integrated database for Drosophila genomics

FBgn0011566

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

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

dme:Dmel_CG13761

MARRVEL_MODEL - MARRVEL (model organism gene)

44554

Linkouts

BioGRID - A database of protein and genetic interactions.

69131

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

FBgn0011566

DroID - A comprehensive database of gene and protein interactions.

FBgn0011566

DRSC - Results frm RNAi screens

FBgn0011566

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

Bzd_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0011566

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0011566

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

CG13761

Flygut - An atlas of the Drosophila adult midgut

FBgn0011566

FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.

FBgn0011566

iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)

TC004426

KEGG Metabolic Pathways - A collection of manually drawn metabolic pathway maps representing knowledge of molecular interaction, reaction and relation networks.

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

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

References (31)

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

-0.43

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