FlyBase Gene Report: Dmel\ssp2

General Information

Symbol

Dmel\ssp2

Species

D. melanogaster

Name

short spindle 2

Annotation Symbol

CG9028

Feature Type

protein_coding_gene

FlyBase ID

FBgn0036389

Gene Model Status

Current

Stock Availability

10 publicly available

Gene Summary

short spindle 2 (ssp2) encodes a microtubule plus-end-tracking protein that binds to the product of Eb1 and the microtubule polymerase encoded by msps. It contributes to dynamic microtubule behaviour, spindle size and kinetochore-microtubule interaction. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Interactive Fly

Also Known As

sentin

Key Links

Genomic Location

Cytogenetic map

70C7-70C9

Sequence location

3L:13,965,203..13,973,067 [+]

Recombination map

3-41

RefSeq locus

NT_037436 REGION:13965203..13973067

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 (4 terms)

Molecular Function (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (2 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

involved_in microtubule cytoskeleton organization

inferred from direct assay

(Li et al., 2011)

involved_in spindle attachment to meiosis I kinetochore

inferred from mutant phenotype

(Głuszek et al., 2015)

Terms Based on Predictions or Assertions (0 terms)

Cellular Component (2 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

located_in centrosome

inferred from high throughput direct assay

(Lye et al., 2014)

located_in meiotic spindle pole

inferred from direct assay

(Głuszek et al., 2015)

Terms Based on Predictions or Assertions (0 terms)

Gene Group (FlyBase)

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\ssp2 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 Q9VUA5)

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 5.56

Gene model reviewed during 5.46

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

Complete overlap: transcripts of this gene are completely overlapped by those of a second gene on the same strand.

Gene model reviewed during 5.57

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

ssp2-RA

FBtr0075759

NM_140415

3435

982

ssp2-RC

FBtr0346645

NM_001300136

4496

982

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

ssp2-PA

FBpp0075501

106.6

982

5.25

FBpp0312225

106.6

982

5.25

Q9VUA5

NP_001287065

AHN58090

Polypeptides with Identical Sequences

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

982 aa isoforms: ssp2-PA, ssp2-PC

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Crossreferences

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Q9VUA5

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\ssp2 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).

NA

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 3

organism

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 4 -- 6

organism

(Fisher et al., 2012)

embryonic stage 7 -- 8

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 9 -- 10

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 11 -- 12

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 13 -- 16

organism | ubiquitous

(Fisher et al., 2012)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in centrosome

inferred from high throughput direct assay

(Lye et al., 2014)

located_in meiotic spindle pole

inferred from direct assay

(Głuszek et al., 2015)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\ssp2 in JBrowse

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

View exonic expression by developmental stage for Dmel\ssp2

View exonic expression by tissue for Dmel\ssp2

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

FBgn0036389

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

39540/tissue=All

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

FBgn0036389

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0036389

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

FBgn0036389

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

CG9028

Flygut - An atlas of the Drosophila adult midgut

FBgn0036389

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 15 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 6 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of ssp2

Transgenic constructs containing regulatory region of ssp2

Aberrations (Deficiencies and Duplications) ( 4 )

Inferred from experimentation ( 4 )

Gene partially disrupted in

Df(3L)ssp2³²

(Głuszek et al., 2015)

Df(3L)ssp2¹³⁶

(Głuszek et al., 2015)

Df(3L)ssp2^Δ19

(Głuszek et al., 2015)

Df(3L)ssp2^ΔB

(Głuszek et al., 2015)

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

viable

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

ssp2^GD14520

viable, with Scer\GAL4^Mef2.PR

ssp2^GD14520

viable, with Scer\GAL4^pnr-MD237

ssp2^GD14520

Sterility

Allele

female sterile

Other Phenotypes

Allele

abnormal meiotic cell cycle

abnormal stress response

ssp2^BG01472

Phenotype manifest in

Allele

kinetochore

meiotic spindle

oocyte

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) (2)

Hsap\NXF2

1 of 14

Yes

Hsap\NXF3

1 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\Nxf1

1 of 14

Yes

Rnor\Nxf2

1 of 14

Yes

Rnor\Nxf3

1 of 14

Yes

Rnor\Nxf7

1 of 14

Yes

Mus musculus (laboratory mouse) (4)

Mmus\Nxf1

1 of 14

Yes

Mmus\Nxf2

1 of 14

Yes

Mmus\Nxf3

1 of 14

Yes

Mmus\Nxf7

1 of 14

Yes

Xenopus tropicalis (Western clawed frog) (0)

Danio rerio (Zebrafish) (2)

Drer\nxf1a

1 of 14

Yes

Drer\nxf1b

1 of 14

Yes

Caenorhabditis elegans (Nematode, roundworm) (1)

Cele\nxf-2

1 of 14

Yes

Anopheles gambiae (African malaria mosquito) (4)

Agam\AgaP_AGAP005606

6 of 12

Yes

Agam\AgaP_AGAP005607

5 of 12

Yes

Agam\AgaP_AGAP002004

1 of 12

Agam\AgaP_AGAP002193

1 of 12

Arabidopsis thaliana (thale-cress) (0)

Saccharomyces cerevisiae (Brewer's yeast) (1)

Scer\MEX67

1 of 13

Yes

Schizosaccharomyces pombe (Fission yeast) (1)

Spom\mex67

1 of 12

Yes

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:ssp2. 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) (3)

nxf2

1 of 13

nxf4

1 of 13

sbr

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 ( 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?

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

ssp2 - Eb1

pull down, western blot, anti bait coimmunoprecipitation, anti tag western blot

(Li et al., 2011)

ssp2 - mael

anti bait coimmunoprecipitation, peptide massfingerprinting

(Sato et al., 2011)

ssp2 - msps

anti tag coimmunoprecipitation, anti tag western blot

(Li et al., 2012)

ssp2 - polo

protein kinase assay, molecular weight estimation by staining

(Moriwaki and Goshima, 2016)

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

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

lok

suppressible

ssp2

(Park and Song, 2008)

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

64880

DroID - A comprehensive database of gene and protein interactions.

FBgn0036389

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

39540

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-41

Cytogenetic map

70C7-70C9

Sequence location

3L:13,965,203..13,973,067 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

70C7-70C9

Limits computationally determined from genome sequence between P{EP}EP3561^EP3561 and P{PZ}l(3)70Da⁰²⁴⁰²&P{PZ}btl⁰⁰²⁰⁸

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-41

(FlyBase, 2016)

3-35.4

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (10)

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

Bloomington

41837

y¹ v¹; P{TRiP.GL01265}attP2

14850

y¹ w^67c23; P{EPgy2}ssp2^EY00443

15345

y¹ w^67c23; P{EPgy2}ssp2^EY01356

28498

y¹ w^*; P{EP}ssp2^G8836 Nxf3^G8836

65664

w¹¹¹⁸; PBac{IT.GAL4}Nxf3^1311-G4 ssp2^1311-G4

51079

y¹ w^*; Mi{MIC}ssp2^MI08368/TM3, Sb¹ Ser¹

91308

y¹ w^*; TI{CRIMIC.TG4.1}ssp2^{CR01804-TG4.1} Nxf3^{CR01804-TG4.1-X}/TM3, Sb¹ Ser¹

Kyoto

115115

w¹¹¹⁸; PBac{602.P.SVS-1}ssp2^CPTI000635

VDRC

v105723

P{KK107135}VIE-260B

v47774

w¹¹¹⁸; P{GD14520}v47774

Genomic Clones (15)

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

cDNA Clones (72)

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

LD42058

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.

FBgn0036389

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0036389

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Głuszek et al., 2015, Li et al., 2011)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

RNAi screen using dsRNA made from templates generated with primers directed against this gene results in aberrantly short spindles when assayed in S2 cells. This phenotype can be observed when the screen is performed with or without Cdc27 dsRNA.

(Goshima et al., 2007)

Relationship to Other Genes

Source for database merge of

Additional comments

Nomenclature History

Source for database identify of

Source for identity of: ssp2 CG9028

(Goshima et al., 2007)

Nomenclature comments

Etymology

Called 'sentin' from the Japanese word "Sentan", which means "tip".

(Li et al., 2011)

Synonyms and Secondary IDs (7)

Reported As

Symbol Synonym

CG9028

(Li et al., 2011, Ni et al., 2010.12.1, Keleman et al., 2009.8.5, Goshima et al., 2007)

Sentin

(Hughes et al., 2018)

Ssp2

(Goshima et al., 2007)

sentin

(Głuszek et al., 2015)

ssp2

(Gene Disruption Project members, 2018-, Hughes et al., 2018, Clandinin and Owens, 2016-, Das et al., 2016, Litovchenko and Laurent, 2016, Jambor et al., 2015, Lye et al., 2014, Kwon et al., 2013, Li et al., 2011, Sato et al., 2011)

Name Synonyms

CG9028

Sentin

(Costa and Ohkura, 2019)

sentin

(Li et al., 2011)

short spindle

(Park and Song, 2008)

short spindle 2

(Park and Song, 2008)

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 ( 37 )

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.

39540

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.

Q9VUA5

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

Q9VUA5

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.

Q9VUA5

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0036389

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

39540/tissue=All

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

FBgn0036389

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

FBgn0036389

FlyMine - An integrated database for Drosophila genomics

FBgn0036389

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

dme:Dmel_CG9028

MARRVEL_MODEL - MARRVEL (model organism gene)

39540

Linkouts

BioGRID - A database of protein and genetic interactions.

64880

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

FBgn0036389

DroID - A comprehensive database of gene and protein interactions.

FBgn0036389

DRSC - Results frm RNAi screens

FBgn0036389

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0036389

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0036389

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

CG9028

Flygut - An atlas of the Drosophila adult midgut

FBgn0036389

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

39540

References (43)

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

NA

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