FlyBase Gene Report: Dmel\sqd

General Information

Symbol

Dmel\sqd

Species

D. melanogaster

Name

squid

Annotation Symbol

CG16901

Feature Type

protein_coding_gene

FlyBase ID

FBgn0263396

Gene Model Status

Stock Availability

17 publicly available

Gene Summary

squid (sqd) encodes a member of the hnRNPA family of RNA binding proteins. It is involved in the localization and translational regulation of grk mRNA in oogenesis. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
UniProtKB
Interactive Fly

Also Known As

hrp40, l(3)j4B4, hnRNP A, l(3)EP3631, RRM3

Key Links

Genomic Location

Cytogenetic map

Sequence location

3R:13,634,862..13,646,304 [-]

Recombination map

3-54

RefSeq locus

NT_033777 REGION:13634862..13646304

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse GBrowse

Other Genome Views

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

Function

GO Summary Ribbons

Gene Ontology (GO) Annotations (29 terms)

Molecular Function (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

enables mRNA 3'-UTR binding

traceable author statement

(Johnstone and Lasko, 2001, Cooperstock and Lipshitz, 1997)

enables RNA binding

inferred from biological aspect of ancestor with PANTHER:PTN002689978

(assigned by GO_Central )

(Gaudet et al., 2011)

Biological Process (19 terms)

Terms Based on Experimental Evidence (12 terms)

CV Term

Evidence

References

involved_in dorsal/ventral axis specification, ovarian follicular epithelium

inferred from mutant phenotype

(Kelley, 1993)

involved_in dorsal/ventral pattern formation

inferred from mutant phenotype

(Clouse et al., 2008)

involved_in germarium-derived egg chamber formation

inferred from mutant phenotype

(Steinhauer and Kalderon, 2005)

involved_in negative regulation of RNA splicing

inferred from mutant phenotype

(Ji and Tulin, 2009)

involved_in oocyte anterior/posterior axis specification

inferred from mutant phenotype

(Steinhauer and Kalderon, 2005)

involved_in oocyte localization involved in germarium-derived egg chamber formation

inferred from mutant phenotype

(Steinhauer and Kalderon, 2005)

involved_in oocyte microtubule cytoskeleton organization

inferred from mutant phenotype

(Steinhauer and Kalderon, 2005)

involved_in oogenesis

inferred from mutant phenotype

(Steinhauer and Kalderon, 2005)

involved_in ovarian follicle cell migration

inferred from mutant phenotype

(Kelley, 1993)

involved_in pole plasm mRNA localization

inferred from mutant phenotype

(Herpers and Rabouille, 2004)

involved_in pole plasm oskar mRNA localization

inferred from expression pattern

(Norvell et al., 2005)

involved_in regulation of alternative mRNA splicing, via spliceosome

inferred from high throughput mutant phenotype

(Park et al., 2004)

Terms Based on Predictions or Assertions (9 terms)

CV Term

Evidence

References

involved_in dorsal/ventral pattern formation

traceable author statement

(Farina and Singer, 2002, Cooperstock and Lipshitz, 1997)

involved_in intracellular mRNA localization

non-traceable author statement

(Tekotte and Davis, 2002)

traceable author statement

(Farina and Singer, 2002, Johnstone and Lasko, 2001, Cooperstock and Lipshitz, 1997)

involved_in mRNA export from nucleus

non-traceable author statement

(Tekotte and Davis, 2002)

involved_in mRNA splicing, via spliceosome

inferred by curator from GO:0071011,GO:0071013

(Herold et al., 2009)

involved_in negative regulation of translation

traceable author statement

(Cooperstock and Lipshitz, 1997)

involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay

traceable author statement

(Farina and Singer, 2002)

involved_in oogenesis

traceable author statement

(Farina and Singer, 2002)

involved_in regulation of gene expression

inferred from biological aspect of ancestor with PANTHER:PTN002689978

(assigned by GO_Central )

(Gaudet et al., 2011)

involved_in RNA export from nucleus

traceable author statement

(Cooperstock and Lipshitz, 1997)

Cellular Component (8 terms)

Terms Based on Experimental Evidence (6 terms)

CV Term

Evidence

References

part_of catalytic step 2 spliceosome

inferred from high throughput direct assay

(Herold et al., 2009)

located_in chromatin

inferred from direct assay

(Prasanth et al., 2000)

located_in nucleus

inferred from direct assay

(Prasanth et al., 2000, Matunis et al., 1992)

inferred from high throughput direct assay

(Lye et al., 2014)

located_in omega speckle

inferred from direct assay

(Prasanth et al., 2000)

located_in polytene chromosome puff

inferred from direct assay

(Ji and Tulin, 2009, Matunis et al., 1992)

part_of precatalytic spliceosome

inferred from high throughput direct assay

(Herold et al., 2009)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

located_in cytoplasm

traceable author statement

(Johnstone and Lasko, 2001)

is_active_in nucleoplasm

inferred from biological aspect of ancestor with PANTHER:PTN002689978

(assigned by GO_Central )

(Gaudet et al., 2011)

located_in nucleus

traceable author statement

(Johnstone and Lasko, 2001, Cooperstock and Lipshitz, 1997)

inferred by curator from GO:0000381

(Park et al., 2004)

Gene Group (FlyBase)

SPLICEOSOME COMPLEX A

Protein Family (UniProt)

-

Protein Signatures (InterPro)

Summaries

Gene Snapshot

squid (sqd) encodes a member of the hnRNPA family of RNA binding proteins. It is involved in the localization and translational regulation of grk mRNA in oogenesis. [Date last reviewed: 2019-03-14]

Gene Group (FlyBase)

SPLICEOSOME COMPLEX A -: Nuclear pre-mRNA splicing is catalyzed by the spliceosome which assembles in a step-wise manner. Complex A, the pre-spliceosome, is composed of U1 and U2 snRNPs and proteins involved in recognition of the 5' splice site and branch point. (Adapted from PMID:24452469 and PMID:23118483).

Protein Function (UniProtKB)

This protein is a component of ribonucleosomes. Could be needed to organize a concentration gradient of a dorsalizing morphogen (Dm) originating in the germinal vesicle. At least one of the isoforms is essential in somatic tissues.

(UniProt, Q08473)

Summary (Interactive Fly)

RNA-binding protein, hnRNP D homolog - mRNA localization and translation are coupled by an interaction between Sqd and the translational repressor protein Bruno - Squid promotes apical cytoplasmic transport and localization of transcripts

Interactive Fly

Gene Model and Products

Number of Transcripts

5

Number of Unique Polypeptides

4

Please see the JBrowse view of Dmel\sqd 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 New Section

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry Q08473)

If you don't see the viewer to the right, 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.

Comments on Gene Model

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

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

Gene model reviewed during 5.47

Sequence Ontology: Class of Gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

FBtr0082854

5551

321

FBtr0082855

2115

344

FBtr0082856

2239

308

FBtr0082857

1983

178

FBtr0309094

2844

308

Additional Transcript Data and Comments

Reported size (kB)

4.8, 3.5, 2.3, 1.9, 1.7, 1.5 (northern blot)

(Kelley, 1993)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

UniProt

RefSeq ID

GenBank

FBpp0082319

35.0

321

6.54

FBpp0082320

36.2

344

7.62

FBpp0082321

33.1

308

6.96

FBpp0089309

18.3

178

9.97

FBpp0301102

33.1

308

6.96

Polypeptides with Identical Sequences

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

308 aa isoforms: sqd-PC, sqd-PE

Additional Polypeptide Data and Comments

Reported size (kDa)

321, 308 (aa)

(Kelley, 1993)

40 (kD observed)

(Matunis et al., 1992)

345, 321 (aa); 40 (kD observed); 36, 35 (kD predicted)

(Matunis et al., 1992)

Comments

External Data

Crossreferences

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

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

Mapped Features

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

Expression Summary Ribbons

Colored tiles in ribbon indicate that the Fly Cell Atlas project found the gene expressed in that cell type. Darker colors mean that more cells of that cell type express the gene:

low

high

Colorless tiles indicate that there is no scRNAseq data for the gene in that cell type.

Colored tiles in ribbon indicate that expression data (RNA and/or protein) has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.

Colored tiles in the ribbon indicate the average RNA expression level of the gene at the indicated stages:

low

high

as determined by RNA-seq (RPKM) using whole organism samples modENCODE, Brown et al., 2014. For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 3

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 4 -- 6

organism | intense | ubiquitous

(Fisher et al., 2012)

embryonic stage 7 -- 8

organism | intense | ubiquitous

(Fisher et al., 2012)

embryonic stage 9 -- 10

organism | intense | ubiquitous

(Fisher et al., 2012)

embryonic stage 11 -- 12

organism | intense | ubiquitous

(Fisher et al., 2012)

embryonic stage 13 -- 16

organism | intense | ubiquitous

(Fisher et al., 2012)

embryonic/larval midgut

(Fisher et al., 2012)

northern blot

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage | female

(Kelley, 1993)

oogenesis & adult stage | female

(Kelley, 1993)

RT-PCR

Stage

Tissue/Position (including subcellular localization)

Reference

oogenesis stage S8 -- S14 & adult stage | female

(Van Buskirk and Schupbach, 2002)

(Van Buskirk and Schupbach, 2002)

Additional Descriptive Data

Isoform-specific expression patterns are observed. Sex-specific expression of alternative transcripts observed.

(Telonis-Scott et al., 2009)

1.5kb sqd transcripts are expressed predominantly in ovaries.

(Kelley, 1993)

2.3kb sqd transcripts are expressed predominantly in non-ovarian tissues.

(Kelley, 1993)

1.9kb sqd transcripts are expressed predominantly in ovaries.

(Kelley, 1993)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

(Cáceres and Nilson, 2009)

(Cáceres and Nilson, 2009)

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

• membrane

(Aradska et al., 2015)

day 7 of adulthood -- day 49 of adulthood

(Cammarato et al., 2011)

western blot

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage | female

(Goodrich et al., 2004)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

part_of catalytic step 2 spliceosome

inferred from high throughput direct assay

(Herold et al., 2009)

located_in chromatin

inferred from direct assay

(Prasanth et al., 2000)

located_in nucleus

inferred from direct assay

(Prasanth et al., 2000, Matunis et al., 1992)

inferred from high throughput direct assay

(Lye et al., 2014)

located_in omega speckle

inferred from direct assay

(Prasanth et al., 2000)

located_in polytene chromosome puff

inferred from direct assay

(Ji and Tulin, 2009, Matunis et al., 1992)

part_of precatalytic spliceosome

inferred from high throughput direct assay

(Herold et al., 2009)

Expression Deduced from Reporters

Reporter: P{PZ}sqd⁰⁰⁰⁴⁸

Stage

Tissue/Position (including subcellular localization)

Reference

oogenesis & adult stage | female

(Kelley, 1993)

adult stage | female & oogenesis

(Kelley, 1993)

Reporter: PBac{602.P.SVS-1}sqd^CPTI000239

Stage

Tissue/Position (including subcellular localization)

Reference

adult brain cell body rind

(Knowles-Barley, 2011.8.24)

spermatogenesis

primary spermatocyte

(Lowe et al., 2014)

Y chromosome loop

(Lowe et al., 2014)

High-Throughput Expression Data

Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\sqd in GBrowse 2

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

View exonic expression by developmental stage for Dmel\sqd

View exonic expression by tissue for Dmel\sqd

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

FBgn0263396

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

41666/tissue=All

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

FBgn0263396

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

FBgn0263396

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

CG16901

Images

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 35 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 15 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of sqd

Transgenic constructs containing regulatory region of sqd

Aberrations (Deficiencies and Duplications) ( 7 )

Inferred from experimentation ( 7 )

Gene not disrupted in

(Spradling et al., 1999, Peng and Mount, 1995, BDGP Project Members, 1994-1999)

(Peng and Mount, 1995)

(BDGP Project Members, 1994-1999)

(Francis-Lang, 1999.8.10)

Gene disrupted in

(Peng and Mount, 1995)

(Ryder, 2004.4.26)

(Francis-Lang, 1999.8.10, Peng and Mount, 1995)

(Norvell et al., 2005, Peng and Mount, 1995)

Inferred from location ( 0 )

Alleles Representing Disease-Implicated Variants

Phenotypes

For more details about a specific phenotype click on the relevant allele symbol.

Lethality

Allele

lethal, with Scer\GAL4^Mef2.PR

sqd^GD8593

lethal (with Df(3R)l26c)

sqd^j4B4

lethal (with Df(3R)urd)

lethal | recessive

lethal | recessive, with Scer\GAL4^- :

sqd^EP3631

lethal - all die before end of pupal stage, with Scer\GAL4^pnr-MD237

sqd^GD8593

lethal - all die during embryonic stage | maternal effect

sqd^K12

partially lethal

sqd^GS18188

partially lethal - majority die (with Df(3R)urd)

sqd^ix77

partially lethal - majority die (with sqd^ix50)

sqd^j4B4

partially lethal - majority die (with sqd^ix77)

sqd^j4B4

partially lethal - majority die (with sqd^j4B4)

sqd^CB02655

viable, with Scer\GAL4^tin.CΔ4

sqd^GD8593

Sterility

Allele

female sterile, with Scer\GAL4^VP16.otu

sqd^HMC03848

female sterile (with sqd¹)

female sterile (with sqd^ix50)

sqd¹

female sterile (with sqd^ix77)

sqd¹

female sterile | recessive

sqd⁰⁰⁰⁴⁸

semi-sterile | recessive

Other Phenotypes

Allele

increased occurrence of cell division | spermatogenesis, with Scer\GAL4^VP16.nos.UTR

sqd^EP746

short lived | heat sensitive, with Scer\GAL4^tin.CΔ4

sqd^GD8593

some die during embryonic stage | maternal effect

sqd^K12

some die during pupal stage, with Scer\GAL4^pnr-MD237

sqd^GD8593

visible, with Scer\GAL4^GMR.PF

sqd^GD8593

Phenotype manifest in

Allele

border follicle cell | germline clone

sqd^j4B4

centripetal follicle cell | germline clone

sqd^j4B4

cyst cell of ovary | germline clone

sqd^j4B4

dorsal appendage

sqd¹

dorsal appendage (with sqd¹)

sqd^K12

dorsal appendage (with sqd^K12)

sqd¹

dorsal appendage | germline clone

sqd^j4B4

dorsal appendage | maternal effect

sqd^K12

sqd^j6E3

egg (with sqd¹)

sqd^K12

egg (with sqd^K12)

sqd¹

egg | germline clone

sqd^j4B4

egg | maternal effect | ventral

sqd¹

egg chamber | germline clone

sqd^j4B4

sqd¹

egg chorion (with sqd¹)

sqd^K12

egg chorion (with sqd^K12)

sqd¹

egg chorion | dorsal

sqd^K12

egg operculum (with sqd¹)

sqd^K12

egg operculum (with sqd^K12)

sqd¹

filzkorper | maternal effect

sqd^K12

follicle cell | germline clone

sqd^j4B4

interommatidial bristle, with Scer\GAL4^GMR.PF

sqd^GD8593

microtubule organizing center & oocyte | germ-line clone

sqd^j4B4

nurse cell & nuclear chromosome

nurse cell | germline clone

sqd^j4B4

oocyte (with Df(3R)urd)

oocyte (with sqd¹)

sqd^j4B4

oocyte (with sqd^ix50)

sqd^j4B4

oocyte (with sqd^ix77)

sqd^j4B4

oocyte (with sqd^j4B4)

oocyte & microtubule | germ-line clone

sqd^j4B4

oocyte | germline clone

sqd^j4B4

ovariole | germline clone

sqd^j4B4

spermatogonium, with Scer\GAL4^ptc-559.1

sqd^EP746

stalk follicle cell | germline clone

sqd^j4B4

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v8.0)

Homo sapiens (Human) (7)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

11 of 15

Yes

Yes

9 of 15

No

Yes

9 of 15

No

Yes

4

3 of 15

No

No

1

3 of 15

No

No

1

1 of 15

No

No

1 of 15

No

Yes

Model Organism Orthologs (via DIOPT v8.0)

Mus musculus (laboratory mouse) (11)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

12 of 15

Yes

Yes

10 of 15

No

Yes

9 of 15

No

Yes

4 of 15

No

Yes

3 of 15

No

No

3 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

Yes

1 of 15

No

No

1 of 15

No

Yes

Rattus norvegicus (Norway rat) (9)

9 of 13

Yes

Yes

9 of 13

Yes

Yes

Rnor\LOC103689931

7 of 13

No

Yes

5 of 13

No

Yes

3 of 13

No

No

2 of 13

No

No

2 of 13

No

Yes

1 of 13

No

No

1 of 13

No

No

Xenopus tropicalis (Western clawed frog) (6)

8 of 12

Yes

Yes

7 of 12

No

Yes

6 of 12

No

Yes

2 of 12

No

No

1 of 12

No

No

1 of 12

No

No

Danio rerio (Zebrafish) (10)

10 of 15

Yes

Yes

10 of 15

Yes

Yes

9 of 15

No

Yes

9 of 15

No

Yes

3 of 15

No

No

3 of 15

No

No

2 of 15

No

No

Drer\zgc:110796

2 of 15

No

No

1 of 15

No

No

Drer\LOC100537556

1 of 15

No

No

Caenorhabditis elegans (Nematode, roundworm) (4)

6 of 15

Yes

Yes

2 of 15

No

No

1 of 15

No

Yes

1 of 15

No

No

Arabidopsis thaliana (thale-cress) (17)

3 of 9

Yes

No

2 of 9

No

No

1 of 9

No

Yes

1 of 9

No

No

1 of 9

No

Yes

1 of 9

No

No

1 of 9

No

No

1 of 9

No

No

1 of 9

No

No

1 of 9

No

Yes

1 of 9

No

Yes

1 of 9

No

No

1 of 9

No

No

1 of 9

No

No

1 of 9

No

No

1 of 9

No

No

1 of 9

No

Yes

Saccharomyces cerevisiae (Brewer's yeast) (5)

4 of 15

Yes

No

1 of 15

No

No

1 of 15

No

Yes

1 of 15

No

Yes

1 of 15

No

Yes

Schizosaccharomyces pombe (Fission yeast) (3)

2 of 12

Yes

Yes

Spom\SPBC660.15

2 of 12

Yes

No

1 of 12

No

Yes

Other Organism Orthologs (via OrthoDB)

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v8.0)

Drosophila melanogaster (Fruit fly) (18)

Gene Symbol

Score

Source

Alignment

5 of 10

5 of 10

4 of 10

3 of 10

3 of 10

2 of 10

2 of 10

2 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

Human Disease Associations

FlyBase Human Disease Model Reports

muscular dystrophy, limb-girdle, autosomal dominant 3

Disease Model Summary Ribbon

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

HNRNPDL; heterogeneous nuclear ribonucleoprotein D like

model of autosomal dominant limb-girdle muscular dystrophy type 3

IEA

(FlyBase, 2019-)

Modifiers Based on Experimental Evidence ( 1 )

Allele

Disease

Interaction

References

exacerbates neurodegenerative disease

modeled by TBPH^Δ23, TBPH^{dsRNA.UAS.cUa}

(Appocher et al., 2017)

Disease Associations of Human Orthologs (via DIOPT v8.0 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?

HNRNPAB; heterogeneous nuclear ribonucleoprotein A/B

11 of 15

HNRNPD; heterogeneous nuclear ribonucleoprotein D

9 of 15

HNRNPDL; heterogeneous nuclear ribonucleoprotein D like

9 of 15

MUSCULAR DYSTROPHY, LIMB-GIRDLE, AUTOSOMAL DOMINANT 3; LGMDD3

autosomal dominant limb-girdle muscular dystrophy type 3

MSI1; musashi RNA binding protein 1

3 of 15

MSI2; musashi RNA binding protein 2

3 of 15

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

Interactions Browser

View in Interactions Browser

Please see the Physical Interaction reports below for full details

RNA-protein

Physical Interaction

Assay

References

anti bait coimmunoprecipitation, nucleotide sequence identification

(Olson et al., 2007)

electrophoretic mobility shift assay, autoradiography, anti bait coimmunoprecipitation, western blot, peptide massfingerprinting

(Hansen et al., 2015, Clouse et al., 2008, Geng and Macdonald, 2006)

anti bait coimmunoprecipitation, quantitative reverse transcription pcr

(Mihailovich et al., 2012)

anti tag coimmunoprecipitation, primer specific pcr

(McDermott and Davis, 2013, McDermott et al., 2012)

anti tag coimmunoprecipitation, primer specific pcr, anti bait coimmunoprecipitation, quantitative reverse transcription pcr, nucleic acid uv cross-linking assay, autoradiography, pull down, peptide massfingerprinting, phage display

(Li et al., 2014, McDermott and Davis, 2013, McDermott et al., 2012, Rom et al., 2007, Norvell et al., 1999)

sqd - lncRNA:Hsrω

anti bait coimmunoprecipitation, primer specific pcr, southern blot, pull down, anti tag western blot

(Onorati et al., 2011, Prasanth et al., 2000)

anti tag coimmunoprecipitation, primer specific pcr

(McDermott and Davis, 2013, McDermott et al., 2012)

coimmunoprecipitation, quantitative reverse transcription pcr

(Olesnicky et al., 2018)

protein-protein

Physical Interaction

Assay

References

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

methyltransferase assay, autoradiography

(Boulanger et al., 2004)

anti tag coimmunoprecipitation, peptide massfingerprinting

(Friedman et al., 2011)

anti tag coimmunoprecipitation, peptide massfingerprinting

(Friedman et al., 2011)

anti bait coimmunoprecipitation, peptide massfingerprinting, molecular weight estimation by autoradiography, two hybrid, western blot, molecular weight estimation by staining

(Clouse et al., 2008, Goodrich et al., 2004, Amero et al., 1993, Matunis et al., 1992)

anti bait coimmunoprecipitation, western blot, molecular weight estimation by autoradiography, molecular weight estimation by staining

(Prasanth et al., 2000, Amero et al., 1993, Matunis et al., 1992)

anti bait coimmunoprecipitation, molecular weight estimation by autoradiography, molecular weight estimation by staining

(Amero et al., 1993, Matunis et al., 1992)

anti bait coimmunoprecipitation, molecular weight estimation by staining

(Amero et al., 1993)

anti bait coimmunoprecipitation, molecular weight estimation by staining

(Amero et al., 1993)

anti bait coimmunoprecipitation, molecular weight estimation by staining

(Amero et al., 1993)

anti bait coimmunoprecipitation, molecular weight estimation by staining

(Amero et al., 1993)

anti bait coimmunoprecipitation, molecular weight estimation by staining

(Amero et al., 1993)

electrophoretic mobility shift assay, autoradiography, anti bait coimmunoprecipitation, western blot, peptide massfingerprinting

(Hansen et al., 2015, Clouse et al., 2008, Geng and Macdonald, 2006)

anti tag coimmunoprecipitation, anti tag western blot

(Tang et al., 2021)

anti tag coimmunoprecipitation, anti tag western blot, Identification by mass spectrometry

(Dold et al., 2020)

anti tag coimmunoprecipitation, western blot

(Ji and Tulin, 2009)

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

anti bait coimmunoprecipitation, western blot

(Amero et al., 1993)

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

anti tag coimmunoprecipitation, peptide massfingerprinting

(Friedman et al., 2011)

anti tag coimmunoprecipitation, multidimensional protein identification technology, western blot, anti bait coimmunoprecipitation

(Ahlander and Bosco, 2009)

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

anti bait coimmunoprecipitation, western blot

(McDermott et al., 2012)

far western blotting, Identification by mass spectrometry, anti bait coimmunoprecipitation, western blot

(Lo Piccolo et al., 2018, Romano et al., 2014)

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

pull down, autoradiography

(Norvell et al., 1999)

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

pull down, autoradiography, anti bait coimmunoprecipitation, western blot

(Norvell et al., 1999)

anti tag coimmunoprecipitation, peptide massfingerprinting

(Friedman et al., 2011)

anti bait coimmunoprecipitation, peptide massfingerprinting, western blot, anti tag coimmunoprecipitation

(Clouse et al., 2008)

anti tag coimmunoprecipitation, anti tag western blot

(Tang et al., 2021)

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

pull down, autoradiography

(Norvell et al., 1999)

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

anti tag coimmunoprecipitation, anti tag western blot

(Tang et al., 2021)

anti tag coimmunoprecipitation, western blot

(Khan et al., 2015, Majumdar et al., 2012)

anti bait coimmunoprecipitation, western blot, peptide massfingerprinting, anti tag coimmunoprecipitation

(Clouse et al., 2008)

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

Summary of Genetic Interactions

esyN Network Diagram

esyN Network Key:

Suppression

Enhancement

View in Interactions Browser

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

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

enhanceable

(Goodrich et al., 2004)

suppressible

(Goodrich et al., 2004)

enhanceable

(Ahlander and Bosco, 2009)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

enhanceable

(Geng and MacDonald, 2007)

enhanceable

(Ahlander and Bosco, 2009)

suppressible

(Molla-Herman et al., 2015)

enhanceable

(Appocher et al., 2017)

External Data

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0263396

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

sqd

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

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

FBgn0263396

External Data

Linkouts

KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.

Dorso-ventral axis formation

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

Genomic Location and Detailed Mapping Data

Chromosome (arm)

3R

Recombination map

3-54

Cytogenetic map

Sequence location

3R:13,634,862..13,646,304 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

87F5-87F6

Limits computationally determined from genome sequence between P{PZ}CtBP⁰³⁴⁶³ and P{lacW}B52^s2249&P{lacW}flfl^L4179

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

87F2-87F3

(determined by in situ hybridisation) 87F3--4 (determined by in situ hybridisation)

(Spradling et al., 1999)

87F3-87F4

(determined by in situ hybridisation) 87F2--3 (determined by in situ hybridisation)

(Perrimon et al., 1996)

87F3-87F4

(BDGP Project Members, 1994-1999)

87F-87F

(determined by in situ hybridisation)

(Kelley, 1993, Matunis et al., 1992)

87F4-87F10

(determined by in situ hybridisation)

(Kelley, 1992)

Experimentally Determined Recombination Data

Location

3-54

(FlyBase, 2016)

3-51.0

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (17)

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

31302

y¹ v¹; P{TRiP.JF01248}attP2

31686

y¹ v¹; P{TRiP.JF01479}attP2

53891

y¹ v¹; P{TRiP.HMJ21209}attP40

62572

w¹¹¹⁸; PBac{IT.GAL4}sqd^0005-G4

38552

y¹ w^*; Mi{MIC}sqd^MI02237

85056

w¹¹¹⁸; PBac{PB}sqd^c04803/TM6B, Tb¹

35627

y¹ sc^* v¹ sev²¹; P{TRiP.GL00473}attP2

124361

w¹¹¹⁸; P{RS3}sqd^UM-8129-3

125596

w¹¹¹⁸; P{RS5}sqd^5-HA-2313

115104

w¹¹¹⁸; PBac{602.P.SVS-1}sqd^CPTI000239

v330425

P{VSH330425}attP40

v32395

w¹¹¹⁸; P{GD8593}v32395

More stocks available...

Genomic Clones (18)

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

cDNA Clones (832)

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 GBrowse 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.

FBgn0263396

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

41666

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Blanchette et al., 2009)

monoclonal antibody

(Goodrich et al., 2004)

monoclonal

(Matunis et al., 1992)

Commercially Available Antibodies

Developmental Studies Hybridoma Bank - Monoclonal antibodies for use in research

Other Information

Relationship to Other Genes

Source for database identify of

Source for identity of: sqd CG17791

(Gabrielian, 1999.11)

Source for database merge of

Source for merge of: CR33328 BcDNA:GM03761

(Rana, 2004.7.2)

Source for merge of: sqd l(3)j4B4

(FlyBase, 1996-)

Source for merge of: sqd Rbp3

(Misra, 2000.7.28)

Source for merge of: CG16901 CG17791

(FlyBase Genome Annotators, 2002-2003)

Source for merge of: sqd CR33328

(FlyBase Genome Annotators, 2011)

Additional comments

Annotation CG16901 merged with annotation CR33328 in release 5.40 of the genome annotation; CR33328 corresponds to 3' UTR of CG16901.

(FlyBase Genome Annotators, 2011)

Annotations CG16901 and CG17791 merged as sqd in release 3 of the genome annotation.

(FlyBase Genome Annotators, 2002-2003)

Other Comments

Nonsense-mediated mRNA decay (NMD) down-regulates a distinct splice isoform(s) of this gene.

(Hansen et al., 2009)

Identified as a potential component of the hh signalling pathway in a genome-wide RNAi screen. dsRNA made from templates generated with primers directed affects the extent of expression of a hh signaling reporter construct in Clone 8 cells.

(Nybakken et al., 2005)

New annotation (CR33328) in release 3.2 of the genome annotation.

(FlyBase Genome Annotators, 2004)

ftz transcript localization in blastoderm embryos involves sqd, which selectively binds to the ftz 3' UTR.

(Lall et al., 1999)

Sxl does not form an immunoprecipitable complex with sqd.

(Deshpande et al., 1996)

The autosomal "FLP-DFS" technique (using the P{ovoD1-18} P{FRT(w^hs)} P{hsFLP} chromosomes) has been used to identify the specific maternal effect phenotype for the zygotic lethal mutation. sqd is required for germ cell viability or early oogenesis.

(Perrimon et al., 1996)

sqd expression patterns in wild type and mutant ovaries demonstrates an essential role of sqd gene product in the germ line during oogenesis.

(Matunis et al., 1994)

Phenotypic and molecular characterisation of sqd demonstrates that the RNA-binding gene product plays a central role in establishing egg polarity.

(Kelley, 1993)

A sequence comparison and numerical analysis of the RRM-containing (RNA recognition motif) proteins suggests that functionally related RRM-containing proteins have significant sequence similarities in their RRMs.

(Kim and Baker, 1993)

The distribution of the hnRNP protein sqd on nascent transcripts from polytene chromosomes has been studied.

(Matunis et al., 1993)

A sqd cDNA clone has been isolated and sequenced.

(Matunis et al., 1992)

Origin and Etymology

Discoverer

Etymology

Identification

External Crossreferences and Linkouts ( 96 )

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.

41666

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.

Q08473

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

Q08473

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

A0A0B4K6U6

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.

Q08473

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0263396

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

FBgn0263396

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

41666/tissue=All

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

FBgn0263396

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

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

FBgn0263396

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

CG16901

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

FBgn0263396

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

41666

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

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

Dmel_CG16901

MARRVEL_MODEL - MARRVEL (model organism gene)

41666

Linkouts

ApoDroso - Functional genomic database for photoreceptor development, survival and function

12133-sqd[j6E3]

DroID - A comprehensive database of gene and protein interactions.

FBgn0263396

Developmental Studies Hybridoma Bank - Monoclonal antibodies for use in research

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

Interactive Fly

KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.

Dorso-ventral axis formation

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

sqd

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

Synonyms and Secondary IDs (27)

Reported As

Symbol Synonym

BcDNA:GM03761

CG17791

(Labourier et al., 2002)

CR33328

HRP40

(Nakamura et al., 1994)

Hrb87

(Kim and Baker, 1993)

Hrb87Fb

Hrp40

(Ustaoglu et al., 2019, Jansen and Niessing, 2012, Kuan et al., 2009, Jolly and Lakhotia, 2006, Lakhotia, 2003, Rajendra et al., 2001, Hovemann et al., 2000, Prasanth et al., 2000)

RRM3

(Kim, 1993.3.10)

Rbp3

SQD

(Rom et al., 2007, Sofola et al., 2007)

Sqd

(Dold et al., 2020, Appocher et al., 2017, McDermott and Davis, 2013, O'Sullivan et al., 2013, McDermott et al., 2012, Vazquez-Pianzola and Suter, 2012, Onorati et al., 2011, Shimada et al., 2011, Ji and Tulin, 2009, Norvell et al., 2008, Puri et al., 2008, Meigh et al., 2007, Rasmussen and Kellis, 2007, Minakhina and Steward, 2005)

Squid

(Layalle et al., 2021, Lo Piccolo et al., 2018, Jansen and Niessing, 2012, Izaurralde, 1999)

fs(3)00048

hnRNP 1

(Kiebler and DesGroseillers, 2000)

hnRNP A

(Jolly and Lakhotia, 2006, Lakhotia, 2003)

hrp40

(Horan et al., 2015, Hartmann et al., 2011, Blanchette et al., 2009, Olson et al., 2007, Lakhotia et al., 1999, Reim et al., 1999, Deshpande et al., 1996, Matunis et al., 1994, Samuels et al., 1994, Amero et al., 1993, Matunis et al., 1993, Weeks et al., 1993, Matunis et al., 1992, Matunis et al., 1992)

l(3)EP3631

(Francis-Lang, 1999.8.10)

l(3)j4B4

(Spradling et al., 1999, Perrimon et al., 1996, BDGP Project Members, 1994-1999)

l(3)j6E3

l(3)j8E7

rrm3

(Kim and Baker, 1993)

sqd

(Kim et al., 2021, Lindsey et al., 2021, Ramesh et al., 2020, Samuels et al., 2020, Sapiro et al., 2020, Fingerhut et al., 2019, Park et al., 2019, Bonneaud et al., 2017, Transgenic RNAi Project members, 2017-, Clandinin and Owens, 2016-, Davidson et al., 2016, Lee et al., 2016, Lefebvre et al., 2016, Mao et al., 2016, Brooks et al., 2015, Dent et al., 2015, Fear et al., 2015, Hansen et al., 2015, Horan et al., 2015, Khan et al., 2015, Ashwal-Fluss et al., 2014, Li et al., 2014, Olesnicky et al., 2014, Baumgartner et al., 2013, Kwon et al., 2013, Mihailovich et al., 2012, Baxley et al., 2011, FlyBase Genome Annotators, 2011, Friedman et al., 2011, Serbus et al., 2011, Arancio et al., 2010, Ellis and Carney, 2010, Klusza and Deng, 2010, Ahlander and Bosco, 2009, Dworkin et al., 2009, Hansen et al., 2009, Herold et al., 2009, Kalifa et al., 2009, Telonis-Scott et al., 2009, Clouse et al., 2008, Jaramillo et al., 2008, Jaramillo et al., 2008, Akdemir et al., 2007, Buszczak et al., 2007, Delanoue et al., 2007, Geng and MacDonald, 2007, Quinones-Coello, 2007, Sofola et al., 2007, Geng and Macdonald, 2006, McIntyre et al., 2006, Norvell et al., 2005, Nybakken et al., 2005, Gim et al., 2001)

squid

(Cáceres and Nilson, 2009)

Name Synonyms

RNA-binding protein 3

heterogeneous-nuclear-ribonucleoprotein-87Fb

lethal (3) j4B4

squid

(Schüpbach, 2019, Cammarato et al., 2011, Hartmann et al., 2011, Klusza and Deng, 2010, Kalifa et al., 2009, Chen and Schupbach, 2006)

Secondary FlyBase IDs

FBgn0053328
FBgn0047283
FBgn0086897
FBgn0003498
FBgn0010257
FBgn0010299
FBgn0011398
FBgn0011413
FBgn0027643
FBgn0040556
FBgn0011363

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

References (267)