FlyBase Gene Report: Dmel\Spt3

General Information

Symbol

Dmel\Spt3

Species

D. melanogaster

Name

Spt3

Annotation Symbol

CG3169

Feature Type

protein_coding_gene

FlyBase ID

FBgn0037981

Gene Model Status

Current

Stock Availability

5 publicly available

Gene Summary

Spt3 (Spt3) encodes a encodes a subunit of the SAGA chromatin modifying complex. [Date last reviewed: 2019-08-01] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
UniProtKB
Interactive Fly

Also Known As

dSpt3

Key Links

Genomic Location

Cytogenetic map

87A5-87A5

Sequence location

3R:12,017,156..12,018,550 [+]

Recombination map

3-51

RefSeq locus

NT_033777 REGION:12017156..12018550

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 (6 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 protein heterodimerization activity

inferred from electronic annotation with InterPro:IPR009072

(InterPro Project Members, 2004-)

enables transcription coactivator activity

inferred from biological aspect of ancestor with PANTHER:PTN000890146

(GO Reference Genome Project, 2011-)

Biological Process (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

involved_in transcription by RNA polymerase II

inferred from electronic annotation with InterPro:IPR003195

(InterPro Project Members, 2004-)

Cellular Component (3 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

located_in nucleus

inferred from direct assay

(Weake et al., 2011, Guelman et al., 2006)

part_of SAGA complex

inferred from direct assay

(Weake et al., 2011, Guelman et al., 2006)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

part_of histone acetyltransferase complex

inferred from sequence or structural similarity with SGD:S000002800

(Aoyagi and Wassarman, 2000)

inferred from sequence or structural similarity with UniProtKB:O75486

(Aoyagi and Wassarman, 2000)

Gene Group (FlyBase)

SAGA COMPLEX

Protein Family (UniProt)

Belongs to the SPT3 family. (Q9VGE2)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

Spt3 (Spt3) encodes a encodes a subunit of the SAGA chromatin modifying complex. [Date last reviewed: 2019-08-01]

Gene Group (FlyBase)

SAGA COMPLEX -: The Spt-Ada-Gcn5 Acetyltransferase (SAGA) complex is a chromatin modifying complex. SAGA can acetylate and deubiquitinate histone residues. Also SAGA has been shown to regulate the transcriptional activation of a subset of genes. (Adapted from FBrf0228923, FBrf0219841 and FBrf0233349).

Protein Function (UniProtKB)

Component of the transcription regulatory complex SAGA, a multiprotein complex that activates transcription by remodeling chromatin and mediating histone acetylation and deubiquitination (PubMed:12697829, PubMed:16980620, PubMed:18188155, PubMed:21764853, PubMed:24493646, PubMed:30559249). The SAGA complex predominantly acetylates histone H3 (PubMed:12697829, PubMed:30559249). Required for oogenesis; involved in transcriptional activation (PubMed:34807910).

(UniProt, Q9VGE2)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Spt3 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 Q9VGE2)

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

Gene model reviewed during 5.47

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Spt3-RA

FBtr0082537

NM_141889

1395

384

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

Spt3-PA

FBpp0082011

43.5

384

9.36

Q9VGE2

NP_650146

AAF54741

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

Subunit Structure (UniProtKB)

Component of the Spt-Ada-Gcn5 acetyltransferase (SAGA) complex consisting of wda/Taf5L, Saf6, Taf9, Taf10b, Taf12, Ada1, Spt3, Spt7, Spt20, Sf3b3, Sf3b5, Nipped-A/Tra1, a histone acetyltransferase (HAT) module made up of Gcn5, Ada2b (Isoform B), Ada3 and Sgf29, and a deubiquitinase (DUB) module made up of not/nonstop, Sgf11 and e(y)2 tethered to SAGA by Atxn7 (PubMed:12697829, PubMed:16980620, PubMed:18188155, PubMed:21764853, PubMed:24493646, PubMed:30559249). Taf5 and Taf10, which has partially redundant properties with Taf10b, may also be part of this complex (PubMed:12697829).

(UniProt, Q9VGE2)

Crossreferences

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

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Q9VGE2

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Spt3 using the Feature Mapper tool.

External Data

Crossreferences

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

Spt3_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).

0.28

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in nucleus

inferred from direct assay

(Weake et al., 2011, Guelman et al., 2006)

part_of SAGA complex

inferred from direct assay

(Weake et al., 2011, Guelman et al., 2006)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Spt3 in JBrowse

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

View exonic expression by developmental stage for Dmel\Spt3

View exonic expression by tissue for Dmel\Spt3

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

FBgn0037981

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

41461/tissue=All

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

FBgn0037981

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0037981

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

FBgn0037981

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

CG3169

Flygut - An atlas of the Drosophila adult midgut

FBgn0037981

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 ( 4 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Spt3

Transgenic constructs containing regulatory region of Spt3

Aberrations (Deficiencies and Duplications) ( 6 )

Inferred from experimentation ( 6 )

Gene disrupted in

Df(3R)Δ87A5-1

(Patrón et al., 2019)

Df(3R)Exel6162

(Ryder, 2004.4.26)

Df(3R)Exel7312

(Ryder, 2004.4.26)

Df(3R)Exel8155

(Ryder, 2004.4.26)

Gene not disrupted in

Df(3R)Δ87A4-1

(Patrón et al., 2019)

Df(3R)Δ87A4-2

(Patrón et al., 2019)

Inferred from location ( 10 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

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

Spt3^GD4391

viable, with Scer\GAL4^Mef2.PR

Spt3^GD4391

viable, with Scer\GAL4^pnr-MD237

Spt3^GD4391

viable, with Scer\GAL4^tin.CΔ4

Spt3^GD4391

Other Phenotypes

Allele

short lived | heat sensitive, with Scer\GAL4^tin.CΔ4

Spt3^GD4391

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) (1)

Hsap\SUPT3H

11 of 14

Yes

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (1)

Rnor\Supt3h

6 of 14

Yes

Mus musculus (laboratory mouse) (1)

Mmus\Supt3

10 of 14

Yes

Xenopus tropicalis (Western clawed frog) (1)

Xtro\supt3h

5 of 13

Yes

Danio rerio (Zebrafish) (2)

Drer\supt3h

9 of 14

Yes

Drer\taf13

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (1)

Cele\tag-342

2 of 14

Yes

Anopheles gambiae (African malaria mosquito) (1)

Agam\AgaP_AGAP011670

12 of 12

Yes

Arabidopsis thaliana (thale-cress) (1)

Atha\TAF13

1 of 13

Yes

Saccharomyces cerevisiae (Brewer's yeast) (1)

Scer\SPT3

6 of 13

Yes

Schizosaccharomyces pombe (Fission yeast) (1)

Spom\spt3

8 of 12

Yes

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Spt3. 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) (1)

Taf13

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?

SUPT3H; SPT3 homolog, SAGA and STAGA complex component

11 of 14

602947

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

View in FlyBase Interactions Browser View in MIST tool (external link)

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

Spt3

anti tag coimmunoprecipitation, peptide massfingerprinting

(Stegeman et al., 2016)

Spt3 - Ada1-2

anti tag coimmunoprecipitation, peptide massfingerprinting

(Stegeman et al., 2016, Weake et al., 2009)

Spt3 - Ada2b

anti tag coimmunoprecipitation, peptide massfingerprinting, anti bait coimmunoprecipitation, western blot, two hybrid, multidimensional protein identification technology

(Torres-Zelada et al., 2019, Stegeman et al., 2016, Weake et al., 2011, Weake et al., 2009, Weake et al., 2008, Guelman et al., 2006, Kusch et al., 2003)

Spt3 - Ada3

anti bait coimmunoprecipitation, western blot, anti tag coimmunoprecipitation, peptide massfingerprinting

(Stegeman et al., 2016, Guelman et al., 2006, Kusch et al., 2003)

Spt3 - Atxn7

anti tag coimmunoprecipitation, peptide massfingerprinting

(Stegeman et al., 2016, Mohan et al., 2014)

Spt3 - CG12112

anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based

(Rhee et al., 2014)

Spt3 - Gcn5

anti tag coimmunoprecipitation, peptide massfingerprinting, anti bait coimmunoprecipitation, western blot

(Stegeman et al., 2016, Guelman et al., 2006, Kusch et al., 2003)

Spt3 - Nipped-A

anti bait coimmunoprecipitation, western blot, anti tag coimmunoprecipitation, peptide massfingerprinting

(Stegeman et al., 2016, Kusch et al., 2003)

Spt3 - Saf6

anti tag coimmunoprecipitation, peptide massfingerprinting

(Stegeman et al., 2016, Weake et al., 2009)

Spt3 - Sf3b3

anti tag coimmunoprecipitation, peptide massfingerprinting

(Stegeman et al., 2016)

Spt3 - Sf3b5

anti tag coimmunoprecipitation, peptide massfingerprinting, two hybrid

(Stegeman et al., 2016)

Spt3 - Sgf11

anti tag coimmunoprecipitation, peptide massfingerprinting

(Stegeman et al., 2016)

Spt3 - Sgf29

anti tag coimmunoprecipitation, peptide massfingerprinting

(Stegeman et al., 2016, Weake et al., 2009)

Spt3 - SmB

anti tag coimmunoprecipitation, peptide massfingerprinting

(Stegeman et al., 2016)

Spt3 - SmD1

anti tag coimmunoprecipitation, peptide massfingerprinting

(Stegeman et al., 2016)

Spt3 - SmE

anti tag coimmunoprecipitation, peptide massfingerprinting

(Stegeman et al., 2016)

Spt3 - Spt20

anti tag coimmunoprecipitation, peptide massfingerprinting

(Stegeman et al., 2016)

Spt3 - Spt7

anti tag coimmunoprecipitation, peptide massfingerprinting

(Stegeman et al., 2016)

Spt3 - Taf10

anti bait coimmunoprecipitation, western blot

(Kusch et al., 2003)

Spt3 - Taf10b

anti tag coimmunoprecipitation, peptide massfingerprinting

(Stegeman et al., 2016)

Spt3 - Taf12

anti tag coimmunoprecipitation, peptide massfingerprinting

(Stegeman et al., 2016)

Spt3 - Taf5

anti bait coimmunoprecipitation, western blot

(Kusch et al., 2003)

Spt3 - Taf9

anti tag coimmunoprecipitation, peptide massfingerprinting, anti bait coimmunoprecipitation, western blot

(Stegeman et al., 2016, Kusch et al., 2003)

Spt3 - U2A

anti tag coimmunoprecipitation, peptide massfingerprinting

(Stegeman et al., 2016)

Spt3 - e(y)2

anti tag coimmunoprecipitation, peptide massfingerprinting

(Stegeman et al., 2016)

Spt3 - not

anti tag coimmunoprecipitation, anti tag western blot, peptide massfingerprinting

(Stegeman et al., 2016, Weake et al., 2008)

Spt3 - wda

anti tag coimmunoprecipitation, peptide massfingerprinting

(Stegeman et al., 2016, Weake et al., 2009)

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

Subunit Structure (UniProtKB)

(UniProt, Q9VGE2 )

Linkouts

BioGRID - A database of protein and genetic interactions.

66578

DroID - A comprehensive database of gene and protein interactions.

FBgn0037981

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

41461

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-51

Cytogenetic map

87A5-87A5

Sequence location

3R:12,017,156..12,018,550 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

87A5-87A5

Limits computationally determined from genome sequence between P{EP}Lk6^EP886 and P{PZ}svp⁰⁷⁸⁴²

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-51

(FlyBase, 2016)

3-49.0

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (5)

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

Bloomington

35148

y¹ sc^* v¹ sev²¹; P{TRiP.GL00016}attP2

80239

y¹ sc^* v¹ sev²¹; P{TOE.GS02704}attP40

57733

y¹ sc^* v¹ sev²¹; P{TRiP.HMC04922}attP40

NIG-Fly

GL00016

y¹ sc^* v¹ sev²¹; P{TRiP.GL00016}attP2

VDRC

v10818

w¹¹¹⁸; P{GD4391}v10818

Genomic Clones (26)

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

cDNA Clones (13)

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

RE50415

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.

FBgn0037981

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

RE48528

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0037981

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Li et al., 2017, Kusch et al., 2003)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

wda, Spt3 and Ada2b associate in a complex.

(Guelman et al., 2006)

dsRNA has been made from templates generated with primers directed against this gene.

(Marr et al., 2006)

Relationship to Other Genes

Source for database merge of

Additional comments

Nomenclature History

Source for database identify of

Source for identity of: Spt3 CG3169

(Aoyagi and Wassarman, 2000)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (5)

Reported As

Symbol Synonym

CG3169

(Stegeman et al., 2016, Mohan et al., 2014, Spedale et al., 2012, Ni et al., 2011.7.19, Ni et al., 2010.12.1, Weake et al., 2009, Aoyagi and Wassarman, 2000)

SPT3

(Marr et al., 2006, Aoyagi and Wassarman, 2000)

TFIID

(Butler and Kadonaga, 2002)

dSpt3

(Spedale et al., 2012, Weake et al., 2008, Guelman et al., 2006, Guelman et al., 2006, Kusch et al., 2003)

Name Synonyms

Spt3

Secondary FlyBase IDs

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 30 )

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.

41461

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.

Q9VGE2

UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information

Q9VGE2

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.

Q9VGE2

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0037981

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

41461/tissue=All

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

FBgn0037981

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

FBgn0037981

FlyMine - An integrated database for Drosophila genomics

FBgn0037981

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

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

dme:Dmel_CG3169

MARRVEL_MODEL - MARRVEL (model organism gene)

41461

Linkouts

BioGRID - A database of protein and genetic interactions.

66578

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

FBgn0037981

DroID - A comprehensive database of gene and protein interactions.

FBgn0037981

DRSC - Results frm RNAi screens

FBgn0037981

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

Spt3_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0037981

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0037981

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

CG3169

Flygut - An atlas of the Drosophila adult midgut

FBgn0037981

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

TC002852

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

41461

References (56)

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

0.28

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