FlyBase Gene Report: Dmel\Syx6

General Information

Symbol

Dmel\Syx6

Species

D. melanogaster

Name

Syntaxin 6

Annotation Symbol

CG7736

Feature Type

protein_coding_gene

FlyBase ID

FBgn0037084

Gene Model Status

Current

Stock Availability

8 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Gene Group
Interactive Fly

Also Known As

Syntaxin

Key Links

Genomic Location

Cytogenetic map

47D7-47E1

Sequence location

2R:11,219,539..11,222,480 [+]

Recombination map

2-64

RefSeq locus

NT_033778 REGION:11219539..11222480

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 (14 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 SNAP receptor activity

inferred from biological aspect of ancestor with PANTHER:PTN000461349

(GO Reference Genome Project, 2011-)

inferred from sequence or structural similarity

(Littleton, 2000)

non-traceable author statement

(Littleton et al., 1999)

enables SNARE binding

inferred from biological aspect of ancestor with PANTHER:PTN000461349

(GO Reference Genome Project, 2011-)

Biological Process (7 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (7 terms)

CV Term

Evidence

References

involved_in Golgi vesicle transport

inferred from electronic annotation with InterPro:IPR015260

(InterPro Project Members, 2004-)

involved_in intracellular protein transport

inferred from biological aspect of ancestor with PANTHER:PTN000461349

(GO Reference Genome Project, 2011-)

involved_in retrograde transport, endosome to Golgi

inferred from biological aspect of ancestor with PANTHER:PTN008572346

(GO Reference Genome Project, 2011-)

involved_in synaptic vesicle docking

inferred from sequence or structural similarity

(Littleton, 2000)

involved_in vesicle docking

inferred from biological aspect of ancestor with PANTHER:PTN000461349

(GO Reference Genome Project, 2011-)

involved_in vesicle fusion

inferred from biological aspect of ancestor with PANTHER:PTN000461349

(GO Reference Genome Project, 2011-)

involved_in vesicle-mediated transport

inferred from electronic annotation with InterPro:IPR010989

(InterPro Project Members, 2004-)

Cellular Component (5 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (5 terms)

CV Term

Evidence

References

is_active_in endomembrane system

inferred from biological aspect of ancestor with PANTHER:PTN000461349

(GO Reference Genome Project, 2011-)

located_in membrane

inferred from electronic annotation with InterPro:IPR010989, InterPro:IPR015260

(InterPro Project Members, 2004-)

located_in plasma membrane

non-traceable author statement

(Littleton et al., 1999)

inferred from sequence or structural similarity

(Littleton, 2000)

part_of SNARE complex

inferred from biological aspect of ancestor with PANTHER:PTN000461349

(GO Reference Genome Project, 2011-)

is_active_in synaptic vesicle membrane

inferred from biological aspect of ancestor with PANTHER:PTN000272438

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

Qc-SNAREs

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Group (FlyBase)

Qc-SNAREs -: Q-SNAREs are members of the SNARE (soluble N-ethylmaleimide-sensitive factor-attachment protein (SNAP) receptor) family that mediate vesicle-fusion. SNAREs are cytoplasmic, membrane-anchored proteins that contain a 60 amino acid SNARE domain. Three Q-SNAREs domains from the target membrane and one R-SNARE domain from the vesicle interact to form a four four-helix bundle that pulls the two membranes in close proximity and promotes fusion. After fusion, the complexes are dissembled by NSF (N-ethylmaleimide-sensitive factor) and SNAPs (Soluble NSF Attachment Proteins). Q-SNAREs are named from their contribution of a conserved Glutamine (Q) residue to the helix bundle. Q-SNARE domains are designated a, b or c, depending on their position within the helix bundle. (Adapted from PMID:15893389 and FBrf0216182).

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Syx6 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 Q7JY00)

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 5.44

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

Gene model reviewed during 5.49

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Syx6-RB

FBtr0088103

NM_206093

1361

226

Syx6-RD

FBtr0088104

NM_206092

1982

323

Syx6-RE

FBtr0088102

NM_206094

1945

339

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

Syx6-PB

FBpp0087204

25.1

226

6.57

FBpp0087205

36.6

323

6.02

FBpp0087203

38.2

339

6.39

Q7JY00

NP_995816

AAM68721

Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

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

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\Syx6 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

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).

2.62

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 3

organism

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 13 -- 16

embryonic brain

(Fisher et al., 2012)

larval nervous system

(Fisher et al., 2012)

larval ventral nerve cord

(Fisher et al., 2012)

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\Syx6 in JBrowse

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

View exonic expression by developmental stage for Dmel\Syx6

View exonic expression by tissue for Dmel\Syx6

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

FBgn0037084

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

40373/tissue=All

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

FBgn0037084

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0037084

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

FBgn0037084

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

CG7736

Flygut - An atlas of the Drosophila adult midgut

FBgn0037084

Images

FlyExpress - Embryonic expression images (BDGP data)

Show all FlyExpress processed images for Dmel\Syx6

Stages(s) 1-3
Stages(s) 13-16

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 4 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 7 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Syx6

Transgenic constructs containing regulatory region of Syx6

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(2R)Exel6060

(Ryder, 2004.4.26)

Inferred from location ( 11 )

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

Syx6^EY14508

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

Syx6^GD422

viable, with Scer\GAL4^Mef2.PR

Syx6^GD422

viable, with Scer\GAL4^pnr-MD237

Syx6^GD422

viable, with Scer\GAL4^tin.CΔ4

Syx6^GD422

Sterility

Allele

fertile

Syx6^EY14508

Phenotype manifest in

Allele

nurse cell | oogenesis stage S13, with Scer\GAL4^GR1

Syx6^JF03125

nurse cell | oogenesis stage S14 | increased number, with Scer\GAL4^GR1

Syx6^JF03125

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) (13)

Hsap\STX6

14 of 14

Yes

Hsap\STX10

13 of 14

Yes

3 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

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) (4)

Rnor\Stx6

13 of 14

Yes

Rnor\Stx8

3 of 14

Rnor\Bet1l

1 of 14

Rnor\Bet1

1 of 14

Mus musculus (laboratory mouse) (4)

Mmus\Stx6

13 of 14

Yes

Mmus\Stx8

3 of 14

Mmus\Bet1l

1 of 14

Mmus\Bet1

1 of 14

Xenopus tropicalis (Western clawed frog) (12)

Xtro\stx10

10 of 13

Yes

Xtro\stx6

7 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Danio rerio (Zebrafish) (8)

Drer\stx6

14 of 14

Yes

Drer\stx10

13 of 14

Yes

Drer\LOC110440104

2 of 14

Yes

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (5)

Cele\syx-6

8 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

Anopheles gambiae (African malaria mosquito) (5)

Agam\AgaP_AGAP006251

12 of 12

Yes

2 of 12

1 of 12

1 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (20)

Atha\SYP61

10 of 13

Yes

2 of 13

2 of 13

1 of 13

1 of 13

1 of 13

Yes

Atha\AT2G18860

1 of 13

Yes

Atha\AT4G14600

1 of 13

Atha\AT4G30240

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

Atha\SYP72

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (6)

Scer\TLG1

7 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Schizosaccharomyces pombe (Fission yeast) (5)

Spom\tlg1

9 of 12

Yes

2 of 12

1 of 12

1 of 12

1 of 12

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Syx6. 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) (4)

2 of 13

1 of 13

1 of 13

1 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 ( 1 )

Allele

Disease

Interaction

References

Syx6^EY14508

ameliorates amyotrophic lateral sclerosis type 8

modeled by Vap33^{P58S.UAS.Tag:FLAG}

(Sanhueza et al., 2015)

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?

14 of 14

13 of 14

3 of 14

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

Syx6 - Antdh

experimental knowledge based

(Guruharsha et al., 2011)

Syx6 - EbpIII

experimental knowledge based

(Guruharsha et al., 2011)

Syx6 - Obp19d

experimental knowledge based

(Guruharsha et al., 2011)

Syx6 - Snap24

experimental knowledge based

(Guruharsha et al., 2011)

Syx6 - Syb

experimental knowledge based

(Guruharsha et al., 2011)

Syx6 - Tpi

experimental knowledge based

(Guruharsha et al., 2011)

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.

65620

DroID - A comprehensive database of gene and protein interactions.

FBgn0037084

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

40373

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

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

SNARE interactions in vesicular transport

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

2-64

Cytogenetic map

47D7-47E1

Sequence location

2R:11,219,539..11,222,480 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

47D7-47E1

Limits computationally determined from genome sequence between P{EP}shn^EP2359&P{EP}shn^EP644 and P{PZ}rM547

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

2-64

(FlyBase, 2016)

2-64.1

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (8)

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

Bloomington

28505

y¹ v¹; P{TRiP.JF03125}attP2/TM3, Sb¹

93788

y¹ w^*; TI{CRIMIC.TG4.1}Syx6^{CR02419-TG4.1}/CyO

84244

y¹ sc^* v¹ sev²¹; P{TKO.GS04342}attP40

NIG-Fly

7736R-3

P{NIG.7736R}3

2RG-1375

y² VhaAC39-1^cho-1 v¹; P{U6-Syx6.NIG.sgRNA}attP40/CyO

VDRC

v104795

P{KK109340}VIE-260B

v1501

w¹¹¹⁸; P{GD422}v1501

v342068

P{hsFLP}1, y¹ w¹¹¹⁸; P{HD_CFD01491}attP40/CyO-GFP

Genomic Clones (29)

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

cDNA Clones (35)

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

Other clones

DPiM_RE48509

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.

FBgn0037084

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0037084

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

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)

Relationship to Other Genes

Source for database merge of

Additional comments

Nomenclature History

Source for database identify of

Source for identity of: Syx6 CG7736

(McLennan, 2001.5.22)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (12)

Reported As

Symbol Synonym

CG7736

(National Institute of Genetics Fly Stocks, 2022-, Harris et al., 2016, Hosono et al., 2015, Garcia et al., 2013, Praveen et al., 2012, Lin et al., 2010, Pessa et al., 2010, Keleman et al., 2009.8.5, Perkins et al., 2009, Dorer et al., 2006, Whitfield et al., 2002, Robertson, 2001.7.7, Bock, 2000.10.26)

CT23545

(Otake et al., 2002)

Dm Syx6

(Littleton, 2000)

DmSyx6

(McLennan, 2001.5.22)

SYN6

(Dorer et al., 2006)

SYX6/10

(Lloyd et al., 2000)

Syx

(Wagh et al., 2006)

Syx6

(Hofbauer et al., 2024, Ochi et al., 2024, Bourne et al., 2022, Li et al., 2020, Mondragon et al., 2019, Gene Disruption Project members, 2018-, Gerards et al., 2018, Transgenic RNAi Project members, 2017-, Ng and Jackson, 2015, Sanhueza et al., 2015, Borner et al., 2014, Garcia et al., 2013, Kwon et al., 2013, Japanese National Institute of Genetics, 2012.5.21, Guruharsha et al., 2011, Pessa et al., 2010, Kloepper et al., 2008)

syx6

(Jay et al., 2021)

Name Synonyms

Syntaxin

(Hossain et al., 2008, Kittel et al., 2006, Pereanu and Hartenstein, 2006, Wagh et al., 2006)

Syntaxin 6

(Saadin and Starz-Gaiano, 2018, Harris et al., 2016, Guruharsha et al., 2011, McLennan, 2001.5.22)

syntaxin

(Dumstrei et al., 2003)

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 ( 51 )

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.

40373

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.

Q7JY00

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.

Q7JY00

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0037084

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

40373/tissue=All

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

FBgn0037084

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

FBgn0037084

FlyMine - An integrated database for Drosophila genomics

FBgn0037084

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

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

dme:Dmel_CG7736

MARRVEL_MODEL - MARRVEL (model organism gene)

40373

Linkouts

BioGRID - A database of protein and genetic interactions.

65620

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

FBgn0037084

DroID - A comprehensive database of gene and protein interactions.

FBgn0037084

DRSC - Results frm RNAi screens

FBgn0037084

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

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0037084

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0037084

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

CG7736

Flygut - An atlas of the Drosophila adult midgut

FBgn0037084

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

FBgn0037084

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

TC032340

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

SNARE interactions in vesicular transport

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

40373

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

References (72)

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

2.62

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