FlyBase Gene Report: Dmel\Syt4

General Information

Symbol

Dmel\Syt4

Species

D. melanogaster

Name

Synaptotagmin 4

Annotation Symbol

CG10047

Feature Type

protein_coding_gene

FlyBase ID

FBgn0028400

Gene Model Status

Current

Stock Availability

35 publicly available

Gene Summary

Synaptotagmin 4 (Syt4) encodes a vesicular calcium binding protein implicated in retrograde signaling at synapses. It is proposed to regulate calcium-dependent cargo trafficking within the postsynaptic compartment. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
Interactive Fly

Also Known As

SytIV, Synaptotagmin IV, syt 4

Key Links

Genomic Location

Cytogenetic map

84D3-84D3

Sequence location

3R:7,266,065..7,270,809 [+]

Recombination map

3-48

RefSeq locus

NT_033777 REGION:7266065..7270809

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 (23 terms)

Molecular Function (4 terms)

Terms Based on Experimental Evidence (3 terms)

CV Term

Evidence

References

enables calcium-dependent phospholipid binding

inferred from direct assay

(Wang and Chapman, 2010)

enables phosphatidylserine binding

inferred from direct assay

(Wang and Chapman, 2010)

enables SNARE binding

inferred from physical interaction with FLYBASE:Snap25; FB:FBgn0011288,FLYBASE:Syx1A; FB:FBgn0013343

(Wang and Chapman, 2010)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

enables calcium ion sensor activity

inferred from biological aspect of ancestor with PANTHER:PTN000001283

(GO Reference Genome Project, 2011-)

enables calcium-dependent phospholipid binding

non-traceable author statement

(Lloyd et al., 2000)

inferred from biological aspect of ancestor with PANTHER:PTN000001283

(GO Reference Genome Project, 2011-)

enables SNARE binding

inferred from biological aspect of ancestor with PANTHER:PTN000001283

(GO Reference Genome Project, 2011-)

Biological Process (9 terms)

Terms Based on Experimental Evidence (3 terms)

CV Term

Evidence

References

involved_in positive regulation of vesicle fusion

inferred from direct assay

(Wang and Chapman, 2010)

involved_in regulation of neurotransmitter secretion

inferred from mutant phenotype

(Barber et al., 2009)

involved_in regulation of synaptic plasticity

inferred from mutant phenotype

(Barber et al., 2009)

Terms Based on Predictions or Assertions (6 terms)

CV Term

Evidence

References

involved_in calcium-dependent activation of synaptic vesicle fusion

inferred from biological aspect of ancestor with PANTHER:PTN004120656

(GO Reference Genome Project, 2011-)

involved_in neurotransmitter secretion

non-traceable author statement

(Lloyd et al., 2000)

involved_in regulation of calcium ion-dependent exocytosis

inferred from biological aspect of ancestor with PANTHER:PTN000001283

(GO Reference Genome Project, 2011-)

involved_in synaptic vesicle exocytosis

inferred from sequence or structural similarity

(Littleton, 2000)

involved_in vesicle fusion

inferred from biological aspect of ancestor with PANTHER:PTN001597973

(GO Reference Genome Project, 2011-)

involved_in vesicle-mediated transport

inferred from biological aspect of ancestor with PANTHER:PTN000001283

(GO Reference Genome Project, 2011-)

non-traceable author statement

(Lloyd et al., 2000)

Cellular Component (10 terms)

Terms Based on Experimental Evidence (4 terms)

CV Term

Evidence

References

located_in apical plasma membrane

inferred from direct assay

(Singari et al., 2014)

located_in neuromuscular junction

inferred from direct assay

(Adolfsen et al., 2004)

located_in postsynaptic membrane

inferred from direct assay

(Barber et al., 2009)

located_in vesicle

inferred from direct assay

(Adolfsen et al., 2004)

Terms Based on Predictions or Assertions (6 terms)

CV Term

Evidence

References

is_active_in axon

inferred from biological aspect of ancestor with PANTHER:PTN004120656

(GO Reference Genome Project, 2011-)

is_active_in exocytic vesicle

inferred from biological aspect of ancestor with PANTHER:PTN000001283

(GO Reference Genome Project, 2011-)

located_in membrane

inferred from electronic annotation with InterPro:IPR001565

(InterPro Project Members, 2004-)

inferred from sequence model

(FlyBase Curators, 2011-)

is_active_in plasma membrane

inferred from biological aspect of ancestor with PANTHER:PTN000001283

(GO Reference Genome Project, 2011-)

is_active_in synapse

inferred from biological aspect of ancestor with PANTHER:PTN004120656

(GO Reference Genome Project, 2011-)

located_in synaptic vesicle

inferred from sequence or structural similarity

(Littleton, 2000)

Gene Group (FlyBase)

SYNAPTOTAGMINS & SYNAPTOTAGMIN-LIKE PROTEINS

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

Gene Group (FlyBase)

SYNAPTOTAGMINS & SYNAPTOTAGMIN-LIKE PROTEINS -: Synaptotagmins are a family of membrane-trafficking proteins characterized by an N-terminal transmembrane region and tandem cytoplasmic C2 domains which mediate specific interactions. Some of the family can interact with lipids in a Ca²⁺-dependent manner, leading to Ca²⁺-regulated release of neurotransmitters and hormones in the nervous and endocrine system. (Adapted from PMID:24065953 and FBrf0210023).

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Syt4 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 Q9U6P7)

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 5.49

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Syt4-RA

FBtr0081578

NM_058116

3103

474

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

Syt4-PA

FBpp0081097

52.2

474

9.09

Q9U6P7

NP_477464

AAF54037

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)

474 (aa)

(Littleton et al., 1999)

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\Syt4 using the Feature Mapper tool.

External Data

Crossreferences

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).

-0.76

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage

neuron

(Littleton et al., 1999)

presumptive embryonic/larval central nervous system

(Littleton et al., 1999)

embryonic stage 13 -- 16

dorsal sensory complex proper primordium

Comment: reported as dorsal/lateral sensory complexes

(Fisher et al., 2012)

embryonic brain

(Fisher et al., 2012)

embryonic head sensory system

(Fisher et al., 2012)

larval nervous system

(Fisher et al., 2012)

sensory nervous system primordium

(Fisher et al., 2012)

ventral midline of embryo

(Fisher et al., 2012)

larval ventral nerve cord

(Fisher et al., 2012)

ventral sensory complex primordium

(Fisher et al., 2012)

larval midline neuron

(Kearney et al., 2004)

embryonic stage 13 -- 17

larval central nervous system

(Kang et al., 2009)

larval ventral nerve cord

(Kang et al., 2009)

embryonic midline of ventral nerve cord

(Kang et al., 2009)

Additional Descriptive Data

Syt4 is initially expressed in embryonic stage 13 in the CNS, ventral nerve cord, and ventral midline and expression persists into late embryonic stages.

(Kang et al., 2009)

Syt4 transcripts are expressed ubiquitously and specifically in the embryonic central nervous system. They are expressed in most or all neurons.

(Littleton et al., 1999)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

neuron

• synaptic vesicle

(Littleton et al., 1999)

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

adult head

• membrane

(Aradska et al., 2015)

Additional Descriptive Data

Syt4 protein localizes to synaptic vesicles.

(Littleton et al., 1999)

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in apical plasma membrane

inferred from direct assay

(Singari et al., 2014)

located_in neuromuscular junction

inferred from direct assay

(Adolfsen et al., 2004)

located_in postsynaptic membrane

inferred from direct assay

(Barber et al., 2009)

located_in vesicle

inferred from direct assay

(Adolfsen et al., 2004)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Syt4 in JBrowse

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

View exonic expression by developmental stage for Dmel\Syt4

View exonic expression by tissue for Dmel\Syt4

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

FBgn0028400

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

40876/tissue=All

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

FBgn0028400

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0028400

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

FBgn0028400

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

CG10047

Flygut - An atlas of the Drosophila adult midgut

FBgn0028400

Images

FlyExpress - Embryonic expression images (BDGP data)

Show all FlyExpress processed images for Dmel\Syt4

Stages(s) 13-16

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 8 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 20 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Syt4

Transgenic constructs containing regulatory region of Syt4

Aberrations (Deficiencies and Duplications) ( 2 )

Inferred from experimentation ( 2 )

Gene disrupted in

Df(3R)Exel6146

(Ryder, 2004.4.26)

Df(3R)rn¹⁶

(Yoshihara et al., 2005)

Inferred from location ( 6 )

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

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

Syt4^GD2842

viable, with Scer\GAL4^Mef2.PR

Syt4^GD2842

viable, with Scer\GAL4^pnr-MD237

Syt4^GD2842

viable, with Scer\GAL4^tin.CΔ4

Syt4^GD2842

Sterility

Allele

fertile

Other Phenotypes

Allele

abnormal neuroanatomy

Syt4^BA1

abnormal neuroanatomy | recessive | third instar larval stage

Syt4^BA1

abnormal neuroanatomy | third instar larval stage (with Df(3R)rn¹⁶)

Syt4^BA1

abnormal neurophysiology

Syt4^BA1

abnormal neurophysiology, with Scer\GAL4^Mhc.PW

Syt4^wt.UAS

abnormal neurophysiology | larval stage, with Scer\GAL4^elav.PLu

Syt4^UAS.cLa

abnormal neurophysiology | third instar larval stage

Syt4^BA1

abnormal neurophysiology | third instar larval stage (with Df(3R)rn¹⁶)

Syt4^BA1

visible, with Scer\GAL4^Bx-MS1096-KE

Syt4^GYB

Phenotype manifest in

Allele

embryonic/larval neuromuscular junction | third instar larval stage (with Df(3R)rn¹⁶)

Syt4^BA1

hypodermal muscle cell of A1-7 | third instar larval stage (with Df(3R)rn¹⁶)

Syt4^BA1

motor neuron

Syt4^BA1

neuromuscular junction

Syt4^BA1

neuromuscular junction, with Scer\GAL4^elav.PLu

Syt4^UAS.cLa

neuromuscular junction, with Scer\GAL4^Mhc.PW

neuromuscular junction (with Df(3R)rn¹⁶)

Syt4^BA1

NMJ bouton

Syt4^BA1

NMJ bouton, with Scer\GAL4^Mhc.PW

NMJ bouton (with Df(3R)rn¹⁶)

Syt4^BA1

NMJ bouton | third instar larval stage

Syt4^BA1

NMJ bouton | third instar larval stage | chemical conditional

Syt4^BA1

wing vein, with Scer\GAL4^Bx-MS1096-KE

Syt4^GYB

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) (54)

Hsap\SYT4

11 of 14

Yes

Hsap\SYT11

11 of 14

Yes

Hsap\SYT1

5 of 14

Hsap\SYT2

5 of 14

Hsap\SYT3

5 of 14

Yes

Hsap\SYT5

5 of 14

Hsap\SYT6

5 of 14

Yes

Hsap\SYT7

5 of 14

Hsap\SYT8

5 of 14

Yes

Hsap\SYT9

5 of 14

Yes

Hsap\SYT10

5 of 14

Yes

Hsap\SYT13

5 of 14

Yes

Hsap\SYT17

5 of 14

Yes

Hsap\LOC102724488

4 of 14

Yes

Hsap\SYT15

4 of 14

Yes

3 of 14

3 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

Yes

Hsap\RPH3A

2 of 14

Hsap\SYT14

2 of 14

Hsap\SYTL3

2 of 14

Yes

Hsap\SYTL4

2 of 14

Hsap\SYTL5

2 of 14

Hsap\TC2N

2 of 14

Yes

Hsap\C2CD4A

1 of 14

Yes

Hsap\C2CD4B

1 of 14

Yes

Hsap\C2CD4C

1 of 14

Yes

Hsap\C2CD4D

1 of 14

Yes

Hsap\FER1L6

1 of 14

Hsap\JMJD7-PLA2G4B

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Hsap\PLA2G4F

1 of 14

Yes

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

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) (40)

Rnor\Syt4

11 of 14

Yes

Rnor\Syt11

11 of 14

Yes

Rnor\Syt1

5 of 14

Rnor\Syt2

5 of 14

Rnor\Syt3

5 of 14

Yes

Rnor\Syt5

5 of 14

Rnor\Syt6

5 of 14

Yes

Rnor\Syt7

5 of 14

Rnor\Syt8

5 of 14

Yes

Rnor\Syt9

5 of 14

Yes

Rnor\Syt10

5 of 14

Yes

Rnor\Syt13

5 of 14

Yes

Rnor\Syt17

5 of 14

Yes

Rnor\Doc2b

3 of 14

Rnor\Syt12

3 of 14

Rnor\Syt15

3 of 14

Yes

2 of 14

2 of 14

2 of 14

2 of 14

Yes

2 of 14

2 of 14

2 of 14

2 of 14

Yes

Rnor\C2cd4a

1 of 14

Yes

Rnor\C2cd4b

1 of 14

Yes

Rnor\C2cd4c

1 of 14

Yes

Rnor\C2cd4d

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Rnor\Pla2g4d

1 of 14

Yes

Rnor\Pla2g4e

1 of 14

Yes

Rnor\Pla2g4f

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

Mus musculus (laboratory mouse) (42)

Mmus\Syt4

11 of 14

Yes

Mmus\Syt11

11 of 14

Yes

Mmus\Syt1

5 of 14

Mmus\Syt3

5 of 14

Yes

Mmus\Syt5

5 of 14

Mmus\Syt6

5 of 14

Yes

Mmus\Syt7

5 of 14

Mmus\Syt8

5 of 14

Yes

Mmus\Syt9

5 of 14

Yes

Mmus\Syt10

5 of 14

Yes

Mmus\Syt13

5 of 14

Yes

Mmus\Syt17

5 of 14

Yes

Mmus\Syt2

4 of 14

Mmus\Syt15

4 of 14

Yes

3 of 14

3 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

Yes

2 of 14

2 of 14

2 of 14

2 of 14

Yes

Mmus\C2cd4a

1 of 14

Yes

Mmus\C2cd4b

1 of 14

Yes

Mmus\C2cd4c

1 of 14

Yes

Mmus\C2cd4d

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Mmus\Pla2g4d

1 of 14

Yes

Mmus\Pla2g4e

1 of 14

Yes

Mmus\Pla2g4f

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Xenopus tropicalis (Western clawed frog) (42)

Xtro\syt4

9 of 13

Yes

Xtro\LOC100493529

4 of 13

Xtro\syt1

4 of 13

Xtro\syt3

4 of 13

Yes

Xtro\syt6

4 of 13

Yes

Xtro\syt7

4 of 13

Xtro\syt13

4 of 13

Yes

Xtro\syt17

4 of 13

Yes

3 of 13

3 of 13

3 of 13

3 of 13

Yes

Xtro\syt11

3 of 13

Yes

Xtro\syt15

3 of 13

Yes

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

Yes

Xtro\c2cd4c

1 of 13

Yes

1 of 13

1 of 13

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

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

Danio rerio (Zebrafish) (50)

Drer\syt4

10 of 14

Yes

Drer\syt11a

10 of 14

Yes

Drer\syt11b

10 of 14

Yes

4 of 14

4 of 14

4 of 14

4 of 14

4 of 14

4 of 14

4 of 14

4 of 14

4 of 14

4 of 14

4 of 14

Yes

Drer\syt15

4 of 14

Yes

4 of 14

3 of 14

3 of 14

3 of 14

3 of 14

2 of 14

2 of 14

2 of 14

2 of 14

Drer\si:ch211-266g18.6

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

Yes

Drer\sytl2a

2 of 14

Yes

Drer\sytl2b

2 of 14

Drer\sytl3

2 of 14

Yes

Drer\sytl5

2 of 14

Drer\tc2n

2 of 14

Yes

Drer\c2cd4a

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Drer\LOC101884989

1 of 14

Drer\LOC103909492

1 of 14

Yes

Drer\pla2g4f.1

1 of 14

Yes

Drer\pla2g4f.2

1 of 14

Yes

Drer\rph3aa

1 of 14

Drer\syt8

1 of 14

Yes

Drer\syt14b

1 of 14

Drer\syt16

1 of 14

Drer\sytl4

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (18)

Cele\snt-4

12 of 14

Yes

4 of 14

4 of 14

4 of 14

4 of 14

3 of 14

3 of 14

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Cele\Y75B7AL.2

1 of 14

Anopheles gambiae (African malaria mosquito) (11)

Agam\AgaP_AGAP001800

10 of 12

Yes

4 of 12

4 of 12

4 of 12

3 of 12

2 of 12

2 of 12

1 of 12

1 of 12

1 of 12

Yes

Agam\AgaP_AGAP012252

1 of 12

Arabidopsis thaliana (thale-cress) (27)

Atha\AT2G21010

3 of 13

Yes

Atha\NTMC2T2.1

3 of 13

Yes

Atha\SYTB

3 of 13

Yes

Atha\SYTD

3 of 13

Yes

Atha\AT1G03370

2 of 13

Atha\AT2G21040

2 of 13

Yes

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (3)

Scer\TCB1

3 of 13

Yes

Scer\TCB2

3 of 13

Yes

Scer\TCB3

3 of 13

Yes

Schizosaccharomyces pombe (Fission yeast) (3)

Spom\SPCC962.01

2 of 12

Yes

Spom\syn1

2 of 12

Yes

Spom\mug190

1 of 12

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Syt4. 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) (12)

8 of 13

7 of 13

6 of 13

6 of 13

6 of 13

Rph

4 of 13

3 of 13

3 of 13

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

Syt4^HMS01934

ameliorates high grade glioma

modeled by Pi3K92E^{UAS.Tag:MYC,Tag:PM(hKRAS)}, btl::Egfr^λ.UAS

(Losada-Pérez et al., 2022)

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?

SYT4; synaptotagmin 4

11 of 14

600103

SYT11; synaptotagmin 11

11 of 14

608741

SYT1; synaptotagmin 1

5 of 14

185605

BAKER-GORDON SYNDROME; BAGOS

SYT2; synaptotagmin 2

5 of 14

SYNAPTOTAGMIN 2; SYT2

congenital myasthenic syndrome 7

SYT3; synaptotagmin 3

5 of 14

600327

SYT5; synaptotagmin 5

5 of 14

600782

SYT6; synaptotagmin 6

5 of 14

607718

SYT7; synaptotagmin 7

5 of 14

604146

SYT8; synaptotagmin 8

5 of 14

607719

SYT9; synaptotagmin 9

5 of 14

613528

SYT10; synaptotagmin 10

5 of 14

SYT13; synaptotagmin 13

5 of 14

607716

SYT17; synaptotagmin 17

5 of 14

Hsap\LOC102724488

4 of 14

SYT15; synaptotagmin 15

4 of 14

608081

DOC2B; double C2 domain beta

3 of 14

604568

SYT12; synaptotagmin 12

3 of 14

606436

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

Syt4 - Gtpbp2

two hybrid

(Hu et al., 2017.6.13)

Syt4 - Snap25

phenotype-based detection assay, inferred by author

(Wang and Chapman, 2010)

Syt4 - Syt1

pull down, molecular weight estimation by coomasie staining

(Littleton et al., 2001)

Syt4 - Syx1A

phenotype-based detection assay, inferred by author

(Wang and Chapman, 2010)

Syt4 - nSyb

phenotype-based detection assay, inferred by author

(Wang and Chapman, 2010)

Syt4 - wls

anti tag coimmunoprecipitation, anti tag western blot, anti bait coimmunoprecipitation

(Korkut et al., 2013)

Summary of Genetic Interactions

Interaction Browsers

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

Please look at the allele data for full details of the genetic interactions

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Syt4

suppressible

para

(Barber et al., 2009)

Syt4

enhanceable

Syx4

(Harris et al., 2016)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

suppressible

(Cho et al., 2015)

suppressible

(Barber et al., 2009)

sei

suppressible

Syt4

(Barber et al., 2009)

Syt1

suppressible

Syt4

(Robinson et al., 2002)

Syx1A

suppressible

Syt4

(Cho et al., 2015)

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

66071

DroID - A comprehensive database of gene and protein interactions.

FBgn0028400

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

40876

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

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

3-48

Cytogenetic map

84D3-84D3

Sequence location

3R:7,266,065..7,270,809 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

84D3-84D3

Limits computationally determined from genome sequence between P{EP}EP3060^EP3060 and P{PZ}grn⁰⁵⁹³⁰

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

84D-84D

(Lloyd et al., 2000)

Determined by comparing Celera genomic sequence with sequence from BDGP BAC and P1 clones.

(Lloyd et al., 2000)

Experimentally Determined Recombination Data

Location

3-48

(FlyBase, 2016)

3-44.2

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (35)

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

Bloomington

48238

w¹¹¹⁸; P{GMR10A09-GAL4}attP2

48270

w¹¹¹⁸; P{GMR10G01-GAL4}attP2

48435

w¹¹¹⁸; P{GMR10A07-GAL4}attP2

48447

w¹¹¹⁸; P{GMR11B07-GAL4}attP2

89616

w¹¹¹⁸; P{R11B07-p65.AD}JK22C

61506

w¹¹¹⁸; P{GMR10A09-lexA}attP40

69465

w¹¹¹⁸; P{R10A07-p65.AD}attP40

71186

w¹¹¹⁸; P{R10A09-p65.AD}attP40

69561

w¹¹¹⁸; P{R11B07-GAL4.DBD}attP2

NIG-Fly

10047R-1

P{NIG.10047R}1/SM6a, Duox^Cy

VDRC

v330273

P{VSH330273}attP40

v33317

w¹¹¹⁸; P{GD2842}v33317

More stocks available...

Genomic Clones (18)

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

cDNA Clones (80)

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

RE67111

Other clones

FI18813

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.

FBgn0028400

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0028400

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Korkut et al., 2013, Littleton et al., 1999)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Synaptic proliferation triggered by postsynaptic Syt4 overexpression at neuromuscular junctions occurs in an activity-dependent fashion.

(Barber et al., 2009)

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: Syt4 SytIV

(FlyBase, 1992-)

Nomenclature comments

FlyBase Curator comment: 'SytIV' has been renamed 'Syt4' to maintain conisistency in the nomenclature of the Synaptotagmin gene family.

(FlyBase, 1992-)

Etymology

Synonyms and Secondary IDs (14)

Reported As

Symbol Synonym

CG10047

(Meadows, 2017.1.11, Zhang et al., 2017, Ni et al., 2010.12.1, Perkins et al., 2009.3.31, Alias and Clark, 2007)

D.Syt IV

(Littleton et al., 1999)

SYT4

(Guan et al., 2020, Wang and Chapman, 2010, Lloyd et al., 2000)

Syt IV

(Adolfsen and Littleton, 2001)

SytIV

(Japanese National Institute of Genetics, 2012.5.21, Kang et al., 2009, Saraswati et al., 2007, Ostrin et al., 2006)

dsyt4

(Adolfsen et al., 2004)

syt 4

(Cho et al., 2015, Barber et al., 2009)

syt4

(Park et al., 2014, Saraswati et al., 2007, Adolfsen et al., 2004, Craxton, 2004)

sytIV

(Allen and Spradling, 2008, Robinson et al., 2002)

Name Synonyms

Synaptotagmin 4

(Singari et al., 2014, Wang and Chapman, 2010)

Synaptotagmin IV

(Kang et al., 2009, Ostrin et al., 2006, Littleton, 2000, Littleton et al., 1999)

synaptotagmin 4

(Lnenicka, 2020, Park et al., 2014, Singari et al., 2014)

synaptotagmin IV

(Littleton, 1999.8.26)

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 ( 38 )

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.

40876

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.

Q9U6P7

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.

Q9U6P7

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0028400

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

40876/tissue=All

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

FBgn0028400

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

FBgn0028400

FlyMine - An integrated database for Drosophila genomics

FBgn0028400

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

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

dme:Dmel_CG10047

MARRVEL_MODEL - MARRVEL (model organism gene)

40876

Linkouts

BioGRID - A database of protein and genetic interactions.

66071

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

FBgn0028400

DroID - A comprehensive database of gene and protein interactions.

FBgn0028400

DRSC - Results frm RNAi screens

FBgn0028400

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0028400

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0028400

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

CG10047

Flygut - An atlas of the Drosophila adult midgut

FBgn0028400

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

FBgn0028400

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

TC011462

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

40876

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

References (86)

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

-0.76

Report Sections