FlyBase Gene Report: Dmel\SKIP

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\SKIP 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).

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Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 9 -- 10

inclusive hindgut primordium

(Fisher et al., 2012)

embryonic stage 11 -- 12

anterior midgut primordium

(Fisher et al., 2012)

central brain primordium

(Fisher et al., 2012)

dorsal epidermis primordium

(Fisher et al., 2012)

embryonic central brain neuron

(Fisher et al., 2012)

hindgut proper primordium

(Fisher et al., 2012)

posterior midgut primordium

(Fisher et al., 2012)

ventral nerve cord primordium

(Fisher et al., 2012)

embryonic stage 13 -- 16

embryonic brain

(Fisher et al., 2012)

embryonic dorsal epidermis

(Fisher et al., 2012)

embryonic hindgut

(Fisher et al., 2012)

embryonic/larval midgut

(Fisher et al., 2012)

larval nervous system

(Fisher et al., 2012)

larval ventral nerve cord

(Fisher et al., 2012)

embryonic stage 16

larval brain

(Diao et al., 2009)

larval ventral nerve cord

(Diao et al., 2009)

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

Reporter: P{GT1}SKIP^BG00076

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

olfactory receptor neuron | subset

(Tunstall et al., 2012)

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\SKIP in JBrowse

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

View exonic expression by developmental stage for Dmel\SKIP

View exonic expression by tissue for Dmel\SKIP

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

FBgn0051163

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

42601/tissue=All

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

FBgn0051163

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0051163

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

FBgn0051163

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

CG31163

Flygut - An atlas of the Drosophila adult midgut

FBgn0051163

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 46 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 5 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of SKIP

Transgenic constructs containing regulatory region of SKIP

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene not disrupted in

Df(3R)Exel6190

(Diao et al., 2009)

Gene disrupted in

Df(3R)Exel6190

(Ryder, 2004.4.26)

Inferred from location ( 7 )

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 - all die before end of P-stage | recessive

SKIP^BG00076

viable

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

SKIP^GD10184

viable, with Scer\GAL4^Mef2.PR

SKIP^GD10184

viable, with Scer\GAL4^pnr-MD237

SKIP^GD10184

viable, with Scer\GAL4^tin.CΔ4

SKIP^GD10184

Sterility

Allele

fertile

Other Phenotypes

Allele

abnormal smell perception

SKIP^BG00076

Phenotype manifest in

Allele

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (20)

Hsap\SAMD5

7 of 14

Yes

Hsap\SAMSN1

6 of 14

Yes

Hsap\SASH1

6 of 14

Yes

Hsap\SASH3

5 of 14

Yes

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

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) (18)

Rnor\Samd5

7 of 14

Yes

Rnor\Samsn1

5 of 14

Yes

Rnor\Sash1

5 of 14

Yes

Rnor\Sash3

5 of 14

Yes

2 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

Mus musculus (laboratory mouse) (20)

Mmus\Samd5

7 of 14

Yes

Mmus\Samsn1

6 of 14

Yes

Mmus\Sash1

5 of 14

Yes

Mmus\Sash3

5 of 14

Yes

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

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Xenopus tropicalis (Western clawed frog) (11)

Xtro\samsn1

4 of 13

Yes

Xtro\sash1

4 of 13

Yes

Xtro\sash3

4 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

Xtro\kiaa1217

1 of 13

Xtro\klhl17

1 of 13

Danio rerio (Zebrafish) (24)

Drer\samsn1a

6 of 14

Yes

Drer\sash1b

6 of 14

Yes

Drer\samsn1b

5 of 14

Yes

Drer\sash1a

5 of 14

Yes

Drer\sash3

5 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

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (1)

Cele\C46H3.2

1 of 14

Yes

Anopheles gambiae (African malaria mosquito) (2)

Agam\AgaP_AGAP004106

9 of 12

Yes

Agam\AgaP_AGAP000961

2 of 12

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:SKIP. 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)

CG34377

7 of 13

CG17625

4 of 13

ckn

2 of 13

CG4393

1 of 13

CG34384

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 ( 2 )

Human Ortholog

Disease

Evidence

References

SASH1; SAM and SH3 domain containing 1

model of dyschromatosis universalis hereditaria

IEA

(FlyBase, 2019-)

SASH3; SAM and SH3 domain containing 3

model of immunodeficiency 102

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?

SAMD5; sterile alpha motif domain containing 5

7 of 14

620517

SAMSN1; SAM domain, SH3 domain and nuclear localization signals 1

6 of 14

607978

SASH1; SAM and SH3 domain containing 1

6 of 14

607955

dyschromatosis universalis hereditaria

SASH3; SAM and SH3 domain containing 3

5 of 14

300441

IMMUNODEFICIENCY 102; IMD102

immunodeficiency 102

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

SKIP - Shal

pull down, western blot, two hybrid

(Diao et al., 2009)

Summary of Genetic Interactions

Interaction Browsers

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

67562

DroID - A comprehensive database of gene and protein interactions.

FBgn0051163

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

42601

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

gene_with_edited_transcript

(Rodriguez et al., 2012)

gene_with_stop_codon_read_through

(Jungreis et al., 2011)

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-74

Cytogenetic map

94A2-94A4

Sequence location

3R:22,133,830..22,296,126 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

94A2-94A4

Limits computationally determined from genome sequence between P{lacW}how^j5B5&P{EP}EP738 and P{lacW}l(3)L3560^L3560

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-74

(FlyBase, 2016)

3-76.7

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (146)

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

Korea

11945

P{VT045603-GAL4}attP2

11946

P{VT045608-GAL4}attP2

11947

P{VT045623-GAL4}attP2

11948

P{VT045646-GAL4}attP2

11949

P{VT045654-GAL4}attP2

11950

P{VT045658-GAL4}attP2

11951

P{VT045661-GAL4}attP2

11952

P{VT045667-GAL4}attP2

12198

P{VT045669-GAL4}attP2

12769

P{VT045595-GAL4}attP2

7086R-1

v109892

More stocks available...

Genomic Clones (83)

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

cDNA Clones (187)

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

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.

FBgn0051163

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0051163

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Amourda and Saunders, 2020, Diao et al., 2009)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Relationship to Other Genes

Source for database merge of

Source for merge of: CG13864 CG13863 CG5736 CG7087 CG7086

(FlyBase Genome Annotators, 2002-2003)

Additional comments

One of the introns of CG31163 has the sequence and structural characteristics of a "mirtron"- mirtrons are encoded as an intron of another gene which accumulate as a lariats after splicing and require debranching enzyme for conversion into a functional miRNA. The mirtron encoded by the CG31163 intron is referred to as mir-1010.

(Ruby et al., 2007)

Annotations CG13864, CG13863, CG5736, CG7087 and CG7086 merged as CG31163 in release 3 of the genome annotation.

(FlyBase Genome Annotators, 2002-2003)

Nomenclature History

Source for database identify of

Source for identity of: SKIP CG31163

(Diao et al., 2009)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (10)

Reported As

Symbol Synonym

CG13863

CG13864

CG31163

(Ashwal-Fluss et al., 2014, Hadar et al., 2012, Japanese National Institute of Genetics, 2012.5.21, Chung et al., 2011, Jungreis et al., 2011, Diao et al., 2009, Keleman et al., 2009.8.5, Lebo et al., 2009, González et al., 2008, Firth and Baker, 2007, Ruby et al., 2007, Burgler and Macdonald, 2005, Burnette et al., 2005, Kim et al., 2005)

CG5736

CG7086

CG7087

Name Synonyms

Shal K+ Channel Interacting Protein

(Diao et al., 2009)

Shal K+ channel interacting protein

Skal K+ channel interacting protein

(Chen et al., 2014)

Secondary FlyBase IDs

FBgn0038933
FBgn0038935
FBgn0038936
FBgn0038937
FBgn0040583

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 93 )

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.

42601

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.

A0A0B4KHV7

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.

A0A0B4KHV7

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0051163

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

42601/tissue=All

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

FBgn0051163

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

FBgn0051163

FlyMine - An integrated database for Drosophila genomics

FBgn0051163

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

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

dme:Dmel_CG31163

MARRVEL_MODEL - MARRVEL (model organism gene)

42601

Linkouts

BioGRID - A database of protein and genetic interactions.

67562

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

FBgn0051163

DroID - A comprehensive database of gene and protein interactions.

FBgn0051163

DRSC - Results frm RNAi screens

FBgn0051163

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

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0051163

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0051163

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

CG31163

Flygut - An atlas of the Drosophila adult midgut

FBgn0051163

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

TC031001

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

42601

References (87)

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

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