FlyBase Gene Report: Dmel\Sdc

General Information

Symbol

Dmel\Sdc

Species

D. melanogaster

Name

Syndecan

Annotation Symbol

CG10497

Feature Type

protein_coding_gene

FlyBase ID

FBgn0010415

Gene Model Status

Current

Stock Availability

25 publicly available

Gene Summary

Syndecan (Sdc) encodes a transmembrane heparan sulfate proteoglycan. It binds to the products of sli and robo1 to regulate axon guidance at the CNS midline, and it cooperates with the product of Lar to promote synapse growth at the larval neuromuscular junction. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
UniProtKB
Interactive Fly

Also Known As

l(2)10608, CT27296, dSdc, Dsyndecan

Key Links

Genomic Location

Cytogenetic map

57E1-57E6

Sequence location

2R:21,392,402..21,481,176 [-]

Recombination map

2-95

RefSeq locus

NT_033778 REGION:21392402..21481176

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 (12 terms)

Molecular Function (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (6 terms)

Terms Based on Experimental Evidence (5 terms)

CV Term

Evidence

References

involved_in axon guidance

inferred from mutant phenotype

(Chanana et al., 2009, Rawson et al., 2005, Johnson et al., 2004, Steigemann et al., 2004)

involved_in epithelial cell migration, open tracheal system

inferred from mutant phenotype

(Schulz et al., 2011)

involved_in glial cell development

inferred from mutant phenotype

(Stork et al., 2014)

involved_in motor neuron axon guidance

inferred from mutant phenotype

(Fox and Zinn, 2005)

involved_in positive regulation of synaptic assembly at neuromuscular junction

inferred from mutant phenotype

(Johnson et al., 2006)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

involved_in cell migration

inferred from biological aspect of ancestor with PANTHER:PTN000099415

(GO Reference Genome Project, 2011-)

Cellular Component (6 terms)

Terms Based on Experimental Evidence (4 terms)

CV Term

Evidence

References

located_in axon

inferred from direct assay

(Johnson et al., 2004)

located_in neuromuscular junction

inferred from mutant phenotype

(Ren et al., 2009)

inferred from direct assay

(Friedman et al., 2013, Johnson et al., 2006)

located_in perivitelline space

inferred from high throughput direct assay

(Lye et al., 2014)

located_in synapse

inferred from direct assay

(Johnson et al., 2006)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

is_active_in cell surface

inferred from biological aspect of ancestor with PANTHER:PTN000099415

(GO Reference Genome Project, 2011-)

located_in membrane

inferred from electronic annotation with InterPro:IPR001050

(InterPro Project Members, 2004-)

Gene Group (FlyBase)

GLYPICANS

Protein Family (UniProt)

Belongs to the syndecan proteoglycan family. (P49415)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

Gene Group (FlyBase)

GLYPICANS -: Glypicans are glycosylphosphatidylinositol (GPI) anchored heparan sulfate proteoglycans. Glypicans can bind growth factors and morphogens, regulating their extracellular distribution. (Adapted from FBrf0138451).

Protein Function (UniProtKB)

Cell surface proteoglycan that bears heparan sulfate. Required for axonal and myotube guidance, is a necessary component of slit/robo signaling and is required in the slit target cells.

(UniProt, P49415)

Summary (Interactive Fly)

a heparan sulfate proteoglycan - a necessary component of Slit/Robo signaling required in Slit target cells - a crucial regulator of synapse development and growth

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Sdc 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 P49415)

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

Annotated transcripts do not represent all possible combinations of alternative exons and/or alternative promoters.

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

Gene model reviewed during 5.51

Stop-codon suppression (UGA) postulated; FBrf0234051.

Gene model reviewed during 6.25

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Sdc-RA

FBtr0071706

NM_057617

2482

399

Sdc-RB

FBtr0071707

NM_166449

1985

226

Sdc-RD

FBtr0273206

NM_001144256

1869

398

FBtr0305897

2944

FBtr0342892

2245

266

Sdc-RI

FBtr0342893

NM_001144257

3982

494

Sdc-RJ

FBtr0342894

NM_001169767

2770

495

Sdc-RK

FBtr0342895

NM_166450

3466

322

Sdc-RL

FBtr0474169

NM_001369961

2482

408

Additional Transcript Data and Comments

Reported size (kB)

3.9, 2.3 (northern blot)

(Spring et al., 1994)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

UniProt

RefSeq ID

GenBank

Sdc-PA

FBpp0071623

42.1

399

4.05

FBpp0071624

24.0

226

4.82

NP_726071

AAM70897

Sdc-PD

FBpp0271714

42.0

398

4.05

FBpp0297065

8.3

8.46

FBpp0309693

28.2

266

3.86

FBpp0309694

52.2

494

4.21

FBpp0309695

52.3

495

4.21

FBpp0309696

34.2

322

5.68

NP_726072

AAM70898

Sdc-PL

FBpp0423168

43.1

408

4.08

QCD26204

Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments

Reported size (kDa)

395 (aa); 39 (kD predicted)

(Spring et al., 1994)

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\Sdc using the Feature Mapper tool.

External Data

Crossreferences

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

Sdc_1
Sdc_2

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).

-0.83

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage

larval tracheal system

(Staudt et al., 2005)

larval central nervous system

Comment: axons

(Staudt et al., 2005)

mesoderm

(Staudt et al., 2005)

embryonic stage 1 -- 3

organism

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 4 -- 6

organism | ubiquitous

• cytoplasm | basal

Comment: apically cleared

(Fisher et al., 2012)

embryonic stage 7

mesoderm

(Knox et al., 2011)

embryonic stage 7 -- 8

antennal anlage

Comment: reported as procephalic ectoderm anlage

(Fisher et al., 2012)

central brain anlage

Comment: reported as procephalic ectoderm anlage

(Fisher et al., 2012)

dorsal head epidermis anlage

Comment: reported as procephalic ectoderm anlage

(Fisher et al., 2012)

visual anlage

Comment: reported as procephalic ectoderm anlage

(Fisher et al., 2012)

anterior endoderm anlage

(Fisher et al., 2012)

head mesoderm

(Fisher et al., 2012)

organism | ubiquitous

(Fisher et al., 2012)

posterior endoderm

(Fisher et al., 2012)

trunk mesoderm

(Fisher et al., 2012)

ventral ectoderm

(Fisher et al., 2012)

embryonic stage 9 -- 10

antennal primordium

Comment: reported as procephalic ectoderm primordium

(Fisher et al., 2012)

central brain primordium

Comment: reported as procephalic ectoderm primordium

(Fisher et al., 2012)

visual primordium

Comment: reported as procephalic ectoderm primordium

(Fisher et al., 2012)

dorsal head epidermis primordium

Comment: reported as procephalic ectoderm primordium

(Fisher et al., 2012)

lateral head epidermis primordium

Comment: reported as procephalic ectoderm primordium

(Fisher et al., 2012)

ventral head epidermis primordium

Comment: reported as procephalic ectoderm primordium

(Fisher et al., 2012)

anterior endoderm

(Fisher et al., 2012)

foregut primordium

(Fisher et al., 2012)

head mesoderm

(Fisher et al., 2012)

posterior endoderm

(Fisher et al., 2012)

trunk mesoderm

(Fisher et al., 2012)

ventral ectoderm

(Fisher et al., 2012)

ventral nerve cord primordium

(Fisher et al., 2012)

embryonic stage 13 -- 15

cardial cell

(Knox et al., 2011)

embryonic stage 13 -- 16

Bolwig organ

(Fisher et al., 2012)

embryonic brain

(Fisher et al., 2012)

embryonic central brain neuron

(Fisher et al., 2012)

embryonic dorsal apodeme

(Fisher et al., 2012)

embryonic dorsal epidermis

(Fisher et al., 2012)

embryonic foregut

(Fisher et al., 2012)

embryonic hindgut

(Fisher et al., 2012)

embryonic large intestine

(Fisher et al., 2012)

embryonic Malpighian tubule

(Fisher et al., 2012)

embryonic stomatogastric nervous system

(Fisher et al., 2012)

embryonic ventral apodeme

(Fisher et al., 2012)

embryonic ventral epidermis

(Fisher et al., 2012)

embryonic/larval corpus allatum

(Fisher et al., 2012)

embryonic/larval lymph gland

(Fisher et al., 2012)

embryonic/larval midgut

(Fisher et al., 2012)

larval nervous system

(Fisher et al., 2012)

larval visceral muscle cell

(Fisher et al., 2012)

lateral cord neuron

(Fisher et al., 2012)

larval ventral nerve cord

(Fisher et al., 2012)

larval apodeme

(Staudt et al., 2005)

northern blot

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 11 -- 16

Comment: reference states 7-15 hr AEL

(Spring et al., 1994)

Additional Descriptive Data

Sdc is expressed broadly in embryos but is enriched in the mesoderm during gastrulation and in cardial cells during germ band retraction.

(Knox et al., 2011)

Sdc is expressed in the mesoderm, the tracheal system, the axons of the CNS, in segment border cells, and in the differentiated apodemes.

(Staudt et al., 2005)

The 3.9kb Sdc transcript is detected in 7-15hr embryos (only stage tested).

(Spring et al., 1994)

The 2.3kb Sdc transcript is a minor transcript detected in 7-15hr embryos (only stage tested).

(Spring et al., 1994)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

No Assay Recorded

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 16

presumptive embryonic/larval central nervous system & motor neuron

• axon

(Johnson et al., 2004)

lateral longitudinal fascicle & medial longitudinal fascicle

• axon

(Johnson et al., 2004)

symmetrical commissure & fascicle

• axon

(Johnson et al., 2004)

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 16

larval longitudinal connective

Comment: 13-16 hr AEL

(Spring et al., 1994)

larval anterior commissure

Comment: reference states 13-16 hr AEL

(Spring et al., 1994)

embryonic/larval hindgut

(Spring et al., 1994)

embryonic/larval midgut

Comment: reference states 13-16 hr AEL

(Spring et al., 1994)

embryonic/larval pharynx

Comment: reference states 13-16 hr AEL

(Spring et al., 1994)

embryonic/larval lymph gland

Comment: reference states 13-16 hr AEL

(Spring et al., 1994)

peripheral nervous system

Comment: reference states 13-16 hr AEL

(Spring et al., 1994)

larval posterior commissure

Comment: reference states 13-16 hr AEL

(Spring et al., 1994)

ventral midline of embryo

Comment: reference states 13-16 hr AEL

(Spring et al., 1994)

wandering third instar larval stage

embryonic/larval neuromuscular junction

• type I terminal bouton

(Dani et al., 2012)

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

adult head

• membrane

(Aradska et al., 2015)

day 7 of adulthood -- day 49 of adulthood

adult heart

(Cammarato et al., 2011)

Additional Descriptive Data

At the larval neuromuscular junction, Sdc protein shows a punctate expression pattern strongly concentrated in a halo-like array around the presynaptic membrane.

(Dani et al., 2012)

also expressed at muscle insertions sites of embryonic CNS in stage 16 embryos

(Johnson et al., 2004)

In 13-16hr embryos, Sdc protein is prominant in the lymph glands, in the peripheral and central nervous systems, and along the basal surfaces of the gut epithelia. In the central nervous system, it is found in the commissures and longitudinal connectives and along the midline.

(Spring et al., 1994)

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in axon

inferred from direct assay

(Johnson et al., 2004)

located_in neuromuscular junction

inferred from mutant phenotype

(Ren et al., 2009)

inferred from direct assay

(Friedman et al., 2013, Johnson et al., 2006)

located_in perivitelline space

inferred from high throughput direct assay

(Lye et al., 2014)

located_in synapse

inferred from direct assay

(Johnson et al., 2006)

Expression Deduced from Reporters

Reporter: PBac{754.P.FSVS-0}Sdc^CPTI002578

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

adult brain

(Knowles-Barley, 2011.8.24)

adult brain cell body rind

(Knowles-Barley, 2011.8.24)

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Sdc in JBrowse

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

View exonic expression by developmental stage for Dmel\Sdc

View exonic expression by tissue for Dmel\Sdc

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

FBgn0010415

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

37447/tissue=All

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

FBgn0010415

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0010415

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

FBgn0010415

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

CG10497

Flygut - An atlas of the Drosophila adult midgut

FBgn0010415

Images

FlyExpress - Embryonic expression images (BDGP data)

Show all FlyExpress processed images for Dmel\Sdc

Stages(s) 4-6
Stages(s) 7-8
Stages(s) 9-10
Stages(s) 11-12

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 62 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 27 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Sdc

Transgenic constructs containing regulatory region of Sdc

Aberrations (Deficiencies and Duplications) ( 8 )

Inferred from experimentation ( 8 )

Gene partially disrupted in

Df(2R)AA21

(Fox and Zinn, 2005)

Df(2R)Sara¹²

(Bokel et al., 2006)

Gene disrupted in

Df(2R)48

(Johnson et al., 2004)

Df(2R)E3578

(BDGP Project Members, 1994-1999)

Df(2R)Exel6076

(Ryder, 2004.4.26)

Df(2R)Pu-D17

(Spradling et al., 1999, BDGP Project Members, 1994-1999)

Df(2R)XE3030

(Spradling et al., 1999, BDGP Project Members, 1994-1999)

Gene not disrupted in

Df(2R)C4

(Fox and Zinn, 2005)

Inferred from location ( 5 )

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

lethal (with Df(2R)Exel6067)

Sdc⁴⁸

lethal (with Df(2R)Exel6076)

Sdc^{MI03925-TG4.0}

lethal | recessive

lethal - all die before end of larval stage

Sdc²³

partially lethal - majority die

partially lethal - majority die, with Scer\GAL4^btl.PS

Sdc²⁶³⁹

partially lethal - majority die (with Df(2R)Exel6067)

partially lethal - majority die (with Df(2R)PK1)

partially lethal - majority die (with Sdc²³)

partially lethal - majority die (with Sdc⁴⁸)

partially lethal - majority die (with Sdc⁹⁷)

partially lethal - majority die (with Sdc²⁴⁵¹)

Sdc²⁶³⁹

partially lethal - majority die (with Sdc²⁵²³)

Sdc²⁶³⁹

partially lethal - majority die (with Sdc²⁵²⁷)

Sdc²⁶³⁹

partially lethal - majority die (with Sdc²⁶²²)

Sdc²⁶³⁹

partially lethal - majority die (with Sdc²⁶²⁶)

Sdc²⁶³⁹

partially lethal - majority die (with Sdc²⁶³⁹)

partially lethal - majority die | recessive

partially lethal - majority live (with Df(2R)PI12)

Sdc²³

viable

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

Sdc^GD4545

viable (with Df(2R)PI12)

viable (with Df(2R)XE-2900)

Sterility

Allele

female semi-fertile

Sdc^BG02774

fertile

Other Phenotypes

Allele

abnormal immune response

Sdc^k10215

abnormal neuroanatomy

abnormal neuroanatomy, with Scer\GAL4^elav-C155

Sdc^EY04602

abnormal neuroanatomy, with Scer\GAL4^how-24B

Sdc^UAS.cJa

abnormal neuroanatomy (with Sdc⁴⁸)

Sdc¹⁰⁶⁰⁸

abnormal neuroanatomy (with Sdc¹⁰⁶⁰⁸)

Sdc⁴⁸

abnormal neuroanatomy | cell non-autonomous | third instar larval stage, with Scer\GAL4^hh-Gal4

Sdc^RNAi.WIZ.UAS

abnormal neuroanatomy | embryonic stage

abnormal neuroanatomy | embryonic stage, with Scer\GAL4^Ntan1-Mz97

Sdc^{PA.UAS.Tag:FLAG,GFP}

abnormal neuroanatomy | larval stage

abnormal neuroanatomy | larval stage, with Scer\GAL4^elav.PU

Sdc^UAS.cJa

abnormal neuroanatomy | larval stage, with Scer\GAL4^how-24B

Sdc^UAS.cJa

abnormal neuroanatomy | larval stage (with Sdc⁴⁸), with Sara^Ubi.PJ

Sdc¹⁰⁶⁰⁸

abnormal neuroanatomy | larval stage (with Sdc¹⁰⁶⁰⁸), with Sara^Ubi.PJ

Sdc⁴⁸

abnormal neuroanatomy | third instar larval stage, with Scer\GAL4^elav.PU

abnormal neuroanatomy | third instar larval stage, with Scer\GAL4^how-24B

abnormal neuroanatomy | third instar larval stage (with Df(2R)48)

Sdc¹⁰⁶⁰⁸

abnormal neurophysiology (with Sdc⁴⁸)

Sdc¹⁰⁶⁰⁸

abnormal neurophysiology (with Sdc¹⁰⁶⁰⁸)

Sdc⁴⁸

abnormal size | adult stage | female limited

Sdc^BG02774

abnormal sleep | adult stage

Sdc^BG02774

abnormal starvation stress response | adult stage

Sdc^BG02774

decreased rate of movement | adult stage | male limited

Sdc^BG02774

short lived

Sdc^BG02774

some die during larval stage

Sdc²³

Phenotype manifest in

Allele

adult dorsal tracheal branch

Sdc²³

adult dorsal tracheal branch, with Scer\GAL4^btl.PS

Sdc^RNAi.UAS.cSa

anterior fascicle & axon | ectopic

astrocyte-like glial cell | embryonic stage

Sdc²⁶³⁹

astrocyte-like glial cell | embryonic stage, with Scer\GAL4^Ntan1-Mz97

Sdc^{PA.UAS.Tag:FLAG,GFP}

dendritic tree | cell non-autonomous | third instar larval stage, with Scer\GAL4^hh-Gal4

Sdc^RNAi.WIZ.UAS

distal dendrite | cell non-autonomous | third instar larval stage, with Scer\GAL4^hh-Gal4

Sdc^RNAi.WIZ.UAS

embryonic/larval dorsal tracheal branch | third instar larval stage

embryonic/larval dorsal tracheal branch | third instar larval stage, with Scer\GAL4^btl.PS

Sdc^RNAi.UAS.cSa

embryonic/larval dorsal tracheal branch | third instar larval stage, with Scer\GAL4^esg-p127

Sdc^RNAi.UAS.cSa

embryonic/larval dorsal tracheal branch | third instar larval stage (with Sdc²³)

Sdc²⁶³⁹

embryonic/larval dorsal tracheal branch | third instar larval stage (with Sdc²⁶³⁹)

Sdc²³

embryonic/larval ganglionic tracheal branch | third instar larval stage

Sdc²⁶³⁹

embryonic/larval salivary gland, with Scer\GAL4^fkh.PH

Sdc^EP2047

embryonic somatic muscle cell | ventral

eye photoreceptor cell & axon (with Sdc⁴⁸)

Sdc¹⁰⁶⁰⁸

eye photoreceptor cell & axon (with Sdc¹⁰⁶⁰⁸)

Sdc⁴⁸

fascicle | ectopic | embryonic stage

Sdc²³

glial cell projection | embryonic stage

Sdc²⁶³⁹

glial cell projection | embryonic stage, with Scer\GAL4^Ntan1-Mz97

Sdc^{PA.UAS.Tag:FLAG,GFP}

lamina plexus (with Sdc⁴⁸)

Sdc¹⁰⁶⁰⁸

lamina plexus (with Sdc¹⁰⁶⁰⁸)

Sdc⁴⁸

larval abdominal segmental nerve, with Scer\GAL4^how-24B

Sdc^UAS.cJa

larval multidendritic class IV neuron | cell non-autonomous | third instar larval stage, with Scer\GAL4^hh-Gal4

Sdc^RNAi.WIZ.UAS

lateral transverse muscle cell

Sdc²³

medulla (with Sdc⁴⁸)

Sdc¹⁰⁶⁰⁸

medulla (with Sdc¹⁰⁶⁰⁸)

Sdc⁴⁸

NMJ bouton | increased number | third instar larval stage, with Scer\GAL4^elav.PU

NMJ bouton | increased number | third instar larval stage, with Scer\GAL4^how-24B

NMJ bouton | larval stage

NMJ bouton | larval stage, with Scer\GAL4^elav.PU

Sdc^UAS.cJa

NMJ bouton | larval stage, with Scer\GAL4^how-24B

Sdc^UAS.cJa

NMJ bouton | larval stage (with Sdc⁴⁸), with Sara^Ubi.PJ

Sdc¹⁰⁶⁰⁸

NMJ bouton | larval stage (with Sdc¹⁰⁶⁰⁸), with Sara^Ubi.PJ

Sdc⁴⁸

NMJ bouton | third instar larval stage, with Scer\GAL4^how-24B

NMJ bouton | third instar larval stage (with Df(2R)48)

Sdc¹⁰⁶⁰⁸

presumptive embryonic/larval central nervous system

synapse, with Scer\GAL4^elav-C155

Sdc^EY04602

terminal tracheal cell | third instar larval stage

Sdc²⁶³⁹

tracheal fusion cell | third instar larval stage

Sdc²⁶³⁹

visceral muscle fiber

Sdc²³

wing vein, with Scer\GAL4^A9

Sdc^RNAi.UAS.cYa

wing vein, with Scer\GAL4^Bx-MS1096

Sdc^RNAi.UAS.cYa

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) (4)

Hsap\SDC4

6 of 14

Yes

Hsap\SDC1

5 of 14

Yes

Hsap\SDC2

5 of 14

Yes

Hsap\SDC3

5 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) (4)

Rnor\Sdc1

7 of 14

Yes

Rnor\Sdc3

6 of 14

Yes

Rnor\Sdc4

6 of 14

Yes

Rnor\Sdc2

5 of 14

Yes

Mus musculus (laboratory mouse) (4)

Mmus\Sdc1

6 of 14

Yes

Mmus\Sdc2

6 of 14

Yes

Mmus\Sdc3

5 of 14

Yes

Mmus\Sdc4

5 of 14

Yes

Xenopus tropicalis (Western clawed frog) (3)

Xtro\sdc3

5 of 13

Yes

Xtro\sdc2

3 of 13

Yes

Xtro\sdc1

2 of 13

Yes

Danio rerio (Zebrafish) (3)

Drer\sdc2

6 of 14

Yes

Drer\sdc3

5 of 14

Yes

Drer\sdc4

5 of 14

Yes

Caenorhabditis elegans (Nematode, roundworm) (1)

Cele\sdn-1

8 of 14

Yes

Anopheles gambiae (African malaria mosquito) (1)

Agam\AgaP_AGAP007657

8 of 12

Yes

Arabidopsis thaliana (thale-cress) (0)

Saccharomyces cerevisiae (Brewer's yeast) (0)

Schizosaccharomyces pombe (Fission yeast) (0)

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Sdc. 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) (0)

Human Disease Associations

FlyBase Human Disease Model Reports

insulin signaling, regulation of fat storage, Drosophila fat body model

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 0 )

Allele

Disease

Evidence

References

Potential Models Based on Orthology ( 1 )

Human Ortholog

Disease

Evidence

References

SDC3; syndecan 3

model of obesity

IEA

(FlyBase, 2019-)

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?

6 of 14

5 of 14

5 of 14

5 of 14

OBESITY

obesity

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.

Dmel gene

Ortholog showing functional complementation

Supporting References

Sdc

Hsap\SDC2

(Chanana et al., 2009)

Interactions

Summary of Physical Interactions

esyN Network Diagram

Show neighbor-neighbor interactions:

Off

Show/hide secondary interactors
(data from AllianceMine provided by esyN)

Select Layout:

Force Directed

Circle

Concentric

Legend:

Protein

RNA

Selected Interactor(s)

Other 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

Sdc - Lar

affinity technology, inferred by author, tag visualisation, pull down, enzyme linked immunosorbent assay

(Johnson et al., 2006, Fox and Zinn, 2005)

Sdc - Mtpβ

experimental knowledge based

(Guruharsha et al., 2011)

Sdc - Sidpn

anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based

(Rhee et al., 2014)

Sdc - robo1

anti bait coimmunoprecipitation, western blot

(Johnson et al., 2004)

Sdc - sli

anti bait coimmunoprecipitation, western blot

(Johnson et al., 2004)

RNA-protein

Physical Interaction

Assay

References

Sdc - B52

electrophoretic mobility shift assay, autoradiography, systematic evolution of ligands by exponential enrichment, full identification by DNA sequencing

(Kim et al., 2003)

Summary of Genetic Interactions

esyN Network Diagram

Show/hide secondary interactors
(data from AllianceMine provided by esyN)

esyN Network Key:

Suppression

Enhancement

Other 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

enhanceable

(Poe et al., 2017)

suppressible

(Chanana et al., 2009, Rawson et al., 2005, Johnson et al., 2004)

Sdc

enhanceable

dlp

(Chanana et al., 2009)

Sdc

suppressible

Lar

(Fox and Zinn, 2005)

Sara|Sdc

enhanceable

Lar

(Johnson et al., 2006)

Sdc

enhanceable

robo1

(Steigemann et al., 2004)

Sdc

enhanceable

robo2

(Steigemann et al., 2004)

Sdc

suppressible

Sdc::Hsap\PDGFRB

(Nguyen et al., 2016)

Sdc

suppressible

sli

(Schulz et al., 2011)

Sdc

enhanceable

sli

(Steigemann et al., 2004)

Sdc

enhanceable

ttv

(Chanana et al., 2009)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

brm

suppressible

Sdc

(Tegeder et al., 2019)

comm

suppressible

Sdc

(Schulz et al., 2011)

dally

enhanceable

Sdc

(Poe et al., 2017)

enhanceable

Sdc

(Kucherenko et al., 2008)

Dys

suppressible

Sdc

(Kucherenko et al., 2008)

Fmr1

suppressible

dlp|Sdc

(Friedman et al., 2013)

Hsepi

suppressible

Sdc

(Dejima et al., 2013)

Jra|kay

suppressible

Sdc

(Franciscovich et al., 2008)

kay

enhanceable

Sdc

(Franciscovich et al., 2008)

Lar

enhanceable

Sdc

(Fox and Zinn, 2005)

robo1

suppressible

Sdc

(Schulz et al., 2011)

robo1

enhanceable

Sdc

(Schulz et al., 2011)

robo2

suppressible

Sdc

(Schulz et al., 2011)

robo2

enhanceable

Sdc

(Schulz et al., 2011, Steigemann et al., 2004)

sli

enhanceable

Sdc

(Steigemann et al., 2004)

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

63077

DroID - A comprehensive database of gene and protein interactions.

FBgn0010415

MIST (genetic) - An integrated Molecular Interaction Database

37447

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

37447

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

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

External Data

Linkouts

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

Class of Gene

gene_with_stop_codon_read_through

(Jungreis et al., 2016)

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-95

Cytogenetic map

57E1-57E6

Sequence location

2R:21,392,402..21,481,176 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

57E1-57E6

Limits computationally determined from genome sequence between P{PZ}tmx¹&P{EP}MESK2^EP2347 and P{PZ}Egfr⁰⁵³⁵¹

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

57E2-57E2

(Spring, 1993.11.8)

57E1-57E2

(determined by in situ hybridisation)

(Spradling et al., 1999, BDGP Project Members, 1994-1999)

Experimentally Determined Recombination Data

Location

2-95

(FlyBase, 2016)

2-101.4

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (25)

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

Bloomington

8564

y¹ w^*; P{UAS-Sdc.J}3

23972

w¹¹¹⁸; Mi{ET1}Sdc^MB02461

77601

w¹¹¹⁸; PBac{IT.GAL4}Sdc^1247-G4

77596

w¹¹¹⁸; PBac{IT.GAL4}Sdc^1057-G4/CyO

19695

y¹ w^67c23; P{EPgy2}Sdc^EY04602

36954

y¹ w^*; Mi{MIC}Sdc^MI03925/SM6a

Korea

11063

P{EP}Sdc^G8270

Kyoto

123145

w¹¹¹⁸; P{RS3}Sdc^CB-0371-3

123398

w¹¹¹⁸; P{RS3}Sdc^CB-0988-3

115567

w¹¹¹⁸; PBac{768.FSVS-0}Sdc^CPTI002735

VDRC

v107320

P{KK108799}VIE-260B

v13322

w¹¹¹⁸; P{GD4545}v13322

More stocks available...

Genomic Clones (64)

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

cDNA Clones (140)

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

LP21789

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.

FBgn0010415

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0010415

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Hayashi et al., 2021, Johnson et al., 2004, Spring et al., 1994)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Mutant embryos show defects in midline axon guidance in the central nervous system.

(Johnson et al., 2004)

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)

Sdc gene product is a heparan sulfate proteoglycan expressed at the cell surface. The single Sdc gene product is expressed in embryonic tissues equivalent to mammalian tissues that express distinct members of the syndecan family.

(Spring et al., 1994)

Relationship to Other Genes

Source for database merge of

Source for merge of: Sdc l(2)10608

(Lincecum et al., 2000)

Additional comments

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (15)

Reported As

Symbol Synonym

CG10497

(Aradska et al., 2015, Yamamoto-Hino et al., 2015, Cammarato et al., 2011, Ni et al., 2010.12.1, Keleman et al., 2009.8.5, Grieder et al., 2007, Molnar et al., 2006, Gonzalez-Aguero et al., 2005, Spring, 2000.5.4)

CT27296

(Hynes and Zhao, 2000, Hynes and Zhao, 2000)

Dsyn

(Princivalle and de Agostini, 2002)

Sdc

(Corthals et al., 2023, Liu et al., 2022, Saha et al., 2022, Anqueira-González et al., 2021, Cattenoz et al., 2021, Hayes and Melrose, 2021, Kamimura and Maeda, 2021, Semaniuk et al., 2021, Chou et al., 2020, Dorogova et al., 2020, Nishihara, 2020, Samuels et al., 2020, Statzer and Ewald, 2020, Sun et al., 2020, Thuveson et al., 2019, Lee et al., 2018, Bonneaud et al., 2017, Hughes and Jacobs, 2017, Kamimura and Maeda, 2017, Poe et al., 2017, Warren et al., 2017, Carbone et al., 2016, Clandinin and Owens, 2016-, Gene Disruption Project members, 2016-, Jungreis et al., 2016, Nakato and Li, 2016, Nguyen et al., 2016, Duff et al., 2015, Gene Disruption Project members, 2015-, Jambor et al., 2015, Ashwal-Fluss et al., 2014, Kim et al., 2014, Montgomery et al., 2014, Stork et al., 2014, Friedman et al., 2013, Muha and Müller, 2013, Ozkan et al., 2013, Wilson et al., 2013, Cho et al., 2012, Dani et al., 2012, Knox et al., 2011, Smart et al., 2011, Cook et al., 2010.2.12, Wallace et al., 2010, Chanana et al., 2009, Ren et al., 2009, Franciscovich et al., 2008, Kucherenko et al., 2008, Vyas et al., 2008, Buszczak et al., 2007, Furrer et al., 2007, Grieder et al., 2007, Schulz et al., 2007, Bokel et al., 2006, Johnson et al., 2006, Liebl et al., 2006, Molnar et al., 2006, Häcker et al., 2005, Staudt et al., 2005)

Syd

Syn

(Brunner et al., 2006)

dSdc

(Yamamoto-Hino et al., 2015, De Luca et al., 2010)

l(2)10608

(Spradling et al., 1999, BDGP Project Members, 1994-1999)

syd

(Yan et al., 2009)

syn

(Princivalle and de Agostini, 2002)

Name Synonyms

Dsyndecan

(Nybakken and Perrimon, 2002, Park et al., 2000)

dSyndecan

(Martin et al., 2002)

syndecan

(Weigelt et al., 2020, Kamimura and Maeda, 2017, Maybeck and Röper, 2009, Schulz et al., 2009, Yan et al., 2009, Yan and Lin, 2007, Brunner et al., 2006, Yamashita et al., 2004, Bellaiche et al., 1998, Spring, 1993.11.8)

Secondary FlyBase IDs

FBgn0010667

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 107 )

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.

37447

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.

P49415

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

P49415

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.

P49415

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0010415

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

37447/tissue=All

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

FBgn0010415

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

FBgn0010415

FlyMine - An integrated database for Drosophila genomics

FBgn0010415

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

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

dme:Dmel_CG10497

MARRVEL_MODEL - MARRVEL (model organism gene)

37447

Linkouts

BioGRID - A database of protein and genetic interactions.

63077

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

FBgn0010415

DroID - A comprehensive database of gene and protein interactions.

FBgn0010415

DRSC - Results frm RNAi screens

FBgn0010415

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

Sdc_1
Sdc_2

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0010415

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0010415

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

CG10497

Flygut - An atlas of the Drosophila adult midgut

FBgn0010415

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

FBgn0010415

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

TC010796

Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution

Interactive Fly

MIST (genetic) - An integrated Molecular Interaction Database

37447

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

37447

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

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

References (204)

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

-0.83

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