FlyBase Gene Report: Dmel\Sk1

General Information

Symbol

Dmel\Sk1

Species

D. melanogaster

Name

Sphingosine kinase 1

Annotation Symbol

CG1747

Feature Type

protein_coding_gene

FlyBase ID

FBgn0030300

Gene Model Status

Current

Stock Availability

7 publicly available

Enzyme Name (EC)

sphingosine kinase (2.7.1.91)

Gene Summary

Sphingosine kinase 1 (Sk1) encodes an enzyme that catalyzes the phosphorylation of sphingosine to sphingosine 1-phosphate, a bioactive lipid mediator. It regulates cell proliferation, differentiation, endolysosomal trafficking and muscle cell repair. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
Interactive Fly

Also Known As

Sphk1

Key Links

Genomic Location

Cytogenetic map

10B13-10B13

Sequence location

X:11,442,539..11,446,012 [+]

Recombination map

1-34

RefSeq locus

NC_004354 REGION:11442539..11446012

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 (10 terms)

Molecular Function (2 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

enables D-erythro-sphingosine kinase activity

inferred from direct assay

(Herr et al., 2004)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

enables D-erythro-sphingosine kinase activity

inferred from biological aspect of ancestor with PANTHER:PTN000270645

(GO Reference Genome Project, 2011-)

enables kinase activity

inferred from electronic annotation with InterPro:IPR001206

(InterPro Project Members, 2004-)

Biological Process (3 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

involved_in phosphorylation

inferred from direct assay

(Herr et al., 2004)

involved_in sphingolipid metabolic process

inferred from direct assay

(Herr et al., 2004)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

involved_in sphingosine biosynthetic process

inferred from biological aspect of ancestor with PANTHER:PTN000270644

(GO Reference Genome Project, 2011-)

Cellular Component (5 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

located_in cytosol

inferred from direct assay

(Yonamine et al., 2011)

located_in plasma membrane

inferred from direct assay

(Yonamine et al., 2011)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

is_active_in cytoplasm

inferred from biological aspect of ancestor with PANTHER:PTN000270644

(GO Reference Genome Project, 2011-)

is_active_in intracellular membrane-bounded organelle

inferred from biological aspect of ancestor with PANTHER:PTN000270644

(GO Reference Genome Project, 2011-)

is_active_in membrane

inferred from biological aspect of ancestor with PANTHER:PTN000270644

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

SPHINGOSINE KINASES

Protein Family (UniProt)

Protein Signatures (InterPro)

Catalytic Activity (EC/Rhea)

D-erythro-sphingosine kinase activity

a sphingoid base + ATP = a sphingoid 1-phosphate + ADP + H(+) (2.7.1.91)

RHEA 35847:

Summaries

Gene Snapshot

Gene Group (FlyBase)

SPHINGOSINE KINASES -: Sphingosine kinases catalyze the phosphorylation of the primary hydroxyl of sphingosine to form sphingosine 1-phosphate. (Adapted from FBrf0161471).

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Sk1 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 Q9VYY8)

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 5.45

Sequence Ontology: Class of Gene

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Sk1-RA

FBtr0073498

NM_132489

2680

641

Sk1-RB

FBtr0073497

NM_167286

2616

641

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

Sk1-PA

FBpp0073347

71.4

641

7.43

FBpp0073346

71.4

641

7.43

Q9VYY8

NP_727528

AAN09634

Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

641 aa isoforms: Sk1-PA, Sk1-PB

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Crossreferences

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

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Q9VYY8

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Sk1 using the Feature Mapper tool.

External Data

Crossreferences

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

Sk1_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).

-0.78

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 6 -- 11

anterior midgut primordium

(Herr and Harris, 2004)

posterior midgut primordium

(Herr and Harris, 2004)

mesoderm

(Herr and Harris, 2004)

embryonic stage 13 -- 16

embryonic midgut chamber

(Fisher et al., 2012)

embryonic/larval midgut

(Fisher et al., 2012)

embryonic stage 15 -- 16

embryonic/larval midgut primordium

(Herr and Harris, 2004)

embryonic hindgut

(Herr and Harris, 2004)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

adult head

• membrane

(Aradska et al., 2015)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in cytosol

inferred from direct assay

(Yonamine et al., 2011)

located_in plasma membrane

inferred from direct assay

(Yonamine et al., 2011)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Sk1 in JBrowse

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

View exonic expression by developmental stage for Dmel\Sk1

View exonic expression by tissue for Dmel\Sk1

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

FBgn0030300

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

32089/tissue=All

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

FBgn0030300

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0030300

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

FBgn0030300

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

CG1747

Flygut - An atlas of the Drosophila adult midgut

FBgn0030300

Images

FlyExpress - Embryonic expression images (BDGP data)

Show all FlyExpress processed images for Dmel\Sk1

Stages(s) 13-16

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 3 )

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 Sk1

Transgenic constructs containing regulatory region of Sk1

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene partially disrupted in

Df(1)CRIMIC-CR70046

(Gene Disruption Project members, 2018-)

Inferred from location ( 0 )

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

Sk1^GD9386

viable, with Scer\GAL4^Mef2.PR

Sk1^GD9386

viable, with Scer\GAL4^pnr-MD237

Sk1^GD9386

viable, with Scer\GAL4^tin.CΔ4

Sk1^GD9386

viable, with Scer\GAL4^Tub.PU

Sk1^GD9386

Sterility

Allele

fertile

Phenotype manifest in

Allele

rhabdomere, with Scer\GAL4^GMR.PF

Sk1^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) (8)

Hsap\SPHK2

13 of 14

Yes

11 of 14

4 of 14

4 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) (5)

Rnor\Sphk2

14 of 14

Yes

11 of 14

4 of 14

2 of 14

1 of 14

Mus musculus (laboratory mouse) (5)

Mmus\Sphk2

14 of 14

Yes

9 of 14

4 of 14

3 of 14

2 of 14

Xenopus tropicalis (Western clawed frog) (8)

Xtro\sphk1

9 of 13

Yes

Xtro\sphk2

7 of 13

Yes

Xtro\cerk

2 of 13

Xtro\XB5892679

2 of 13

Xtro\cerkl

1 of 13

Yes

Xtro\kxd1

1 of 13

Xtro\LOC100498520

1 of 13

Xtro\mbd3

1 of 13

Danio rerio (Zebrafish) (6)

Drer\sphk2

13 of 14

Yes

11 of 14

4 of 14

4 of 14

4 of 14

2 of 14

Caenorhabditis elegans (Nematode, roundworm) (6)

Cele\sphk-1

12 of 14

Yes

3 of 14

2 of 14

1 of 14

1 of 14

1 of 14

Anopheles gambiae (African malaria mosquito) (6)

Agam\AgaP_AGAP006995

8 of 12

Yes

2 of 12

2 of 12

1 of 12

1 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (8)

Atha\SPHK1

11 of 13

Yes

Atha\SPHK2

11 of 13

Yes

Atha\ACD5

3 of 13

Atha\LCBK1

2 of 13

Atha\LCBK2

2 of 13

Yes

Atha\APC4

1 of 13

Atha\DGK3

1 of 13

Atha\DGK7

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (3)

Scer\LCB4

11 of 13

Yes

Scer\LCB5

11 of 13

Yes

Scer\TIM54

1 of 13

Yes

Schizosaccharomyces pombe (Fission yeast) (2)

Spom\SPAC4A8.07c

10 of 12

Yes

Spom\tim54

1 of 12

Yes

Escherichia coli (enterobacterium) (1)

Ecol\yegS

3 of 11

Yes

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Sk1. 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) (5)

Sk2

12 of 13

5 of 13

5 of 13

1 of 13

1 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

lipotoxic cardiomyopathy, ceramide/sphingolipid-related

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 1 )

Allele

Disease

Evidence

References

Sk1^GD9386

model of cardiomyopathy

CEA

(Walls et al., 2018)

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?

SPHK2; sphingosine kinase 2

13 of 14

607092

SPHK1; sphingosine kinase 1

11 of 14

603730

CERK; ceramide kinase

4 of 14

610307

CERKL; ceramide kinase like

4 of 14

608381

RETINITIS PIGMENTOSA 26; RP26

retinitis pigmentosa 26

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

esyN Network Diagram

Other Interaction Browsers

Summary of Genetic Interactions

esyN Network Diagram

Other 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.

58500

DroID - A comprehensive database of gene and protein interactions.

FBgn0030300

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

32089

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyCyc Pathways - Pathways from a BioCyc PGDB for Dmel

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

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

Sphingolipid de novo biosynthesis

External Data

Linkouts

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

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

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

1-34

Cytogenetic map

10B13-10B13

Sequence location

X:11,442,539..11,446,012 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

10B13-10B13

Limits computationally determined from genome sequence between P{EP}CG11756^EP1610 and P{EP}CG32666^EP1452

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

1-34

(FlyBase, 2016)

1-36.3

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (7)

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

Bloomington

94956

Df(1)CRIMIC-CR70046, y¹ w^* TI{KozakGAL4}Sk1^{CR70046-KO-kG4}

36747

y¹ sc^* v¹ sev²¹; P{TRiP.HMS03007}attP2/TM3, Sb¹

NIG-Fly

HMS03007

y¹ sc^* v¹ sev²¹; P{TRiP.HMS03007}attP2/TM3, Sb¹

VDRC

v330054

P{VSH330054}attP40

v32932

w¹¹¹⁸; P{GD9386}v32932

v342779

P{hsFLP}1, y1 w1118; P{HD_CFD01812}attP40/CyO-GFP

v342841

P{hsFLP}1, y1 w1118; P{HD_CFD02219}attP40/CyO-GFP

Genomic Clones (13)

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

cDNA Clones (7)

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

RE64552

Other clones

DPiM_RE64552

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.

FBgn0030300

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0030300

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Yonamine et al., 2011)

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

The Sk1 gene may have been derived from the Sk2 gene by retroposition.

(Pan and Zhang, 2009)

Nomenclature History

Source for database identify of

Source for identity of: Sphk1 CG1747

(Herr, 2002.10.4)

Source for identity of: Sk1 CG1747

(Dobrosotskaya et al., 2002)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (8)

Reported As

Symbol Synonym

CG1747

(Meadows, 2017.1.11, Ni et al., 2011.7.19, Pan and Zhang, 2009, Dobrosotskaya et al., 2002, Herr, 2002.10.4, Renault et al., 2002, Renault et al., 2002, Morrison et al., 2000)

SK1

(Pantoja et al., 2013, Dobrosotskaya et al., 2002)

Sk1

(Fleck et al., 2024, Yin et al., 2023, Ding et al., 2022, Kanca et al., 2022, Khan et al., 2021, Walls et al., 2020, Gene Disruption Project members, 2018-, Walls et al., 2018, Sanchez-Alvarez et al., 2015, dos Santos, 2014, Pogson et al., 2014, Japanese National Institute of Genetics, 2012.5.21, Langley et al., 2012, Yonamine et al., 2011, Reddy et al., 2010)

SphK1

(Kraut, 2011)

Sphk1

(Giot et al., 2003, Herr, 2002.10.4)

sk1

(Boumard and Bardin, 2021)

Name Synonyms

Sphingosine kinase 1

(Yonamine et al., 2011, Dobrosotskaya et al., 2002)

Sphingosine kinase I

(Dobrosotskaya et al., 2002)

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 ( 49 )

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.

32089

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.

Q9VYY8

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

Q9VYY8

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.

Q9VYY8

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0030300

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

32089/tissue=All

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

FBgn0030300

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

FBgn0030300

FlyMine - An integrated database for Drosophila genomics

FBgn0030300

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

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

dme:Dmel_CG1747

MARRVEL_MODEL - MARRVEL (model organism gene)

32089

Linkouts

BioGRID - A database of protein and genetic interactions.

58500

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

FBgn0030300

DroID - A comprehensive database of gene and protein interactions.

FBgn0030300

DRSC - Results frm RNAi screens

FBgn0030300

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

Sk1_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0030300

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0030300

FlyCyc Pathways - Pathways from a BioCyc PGDB for Dmel

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

CG1747

Flygut - An atlas of the Drosophila adult midgut

FBgn0030300

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

FBgn0030300

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

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

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

32089

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.

Sphingolipid de novo biosynthesis

References (54)

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

-0.78

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