FB2019_05, released Oct 15, 2019

Gene: Dmel\sqd

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General Information
Symbol
Dmel\sqd
Species
D. melanogaster
Name
squid
Annotation Symbol
CG16901
Feature Type
protein_coding_gene
FlyBase ID
FBgn0263396
Gene Model Status
Current
Stock Availability
19 publicly available
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]
Other Summaries
Also Known As
hrp40, l(3)j4B4, l(3)EP3631, RRM3, hnRNP A
Key Links
Genomic Location
Cytogenetic map
87F5-87F6
Sequence location
3R:13,634,862..13,646,304 [-]
Recombination map
3-54
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
GO Summary Ribbons
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Molecular Function (GO)
[Detailed GO annotations]
Experimental Evidence
-
Predictions / Assertions
mRNA 3'-UTR binding; mRNA binding; RNA binding; sequence-specific DNA binding; sequence-specific double-stranded DNA binding
Summaries
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
Gene Model and Products
Number of Transcripts
5
Number of Unique Polypeptides
4

Please see the GBrowse view of Dmel\sqd or 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
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
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
sqd-RA
FBtr0082854
NM_169529
5551
321
sqd-RB
FBtr0082855
NM_169528
2115
344
sqd-RC
FBtr0082856
NM_143952
2239
308
sqd-RD
FBtr0082857
NM_206481
1983
178
sqd-RE
FBtr0309094
NM_001260159
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
RefSeq ID
GenBank
sqd-PA
FBpp0082319
35.0
321
6.54
NP_731826
AAF54964
sqd-PB
FBpp0082320
36.2
344
7.62
NP_731825
AAF54963
sqd-PC
FBpp0082321
33.1
308
6.96
NP_652209
AAN13570
sqd-PD
FBpp0089309
18.3
178
9.97
NP_996203
AAS65146
sqd-PE
FBpp0301102
33.1
308
6.96
NP_001247088
AFH06406
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
hnRNP-specific mAbs were obtained and used to purify hnRNP complexes from S2 cells. hnRNP proteins were identified on the basis of nucleoplasmic localization, association with nascent transcripts, crosslinking to poly(A)-containing RNA in living cells, and amino acid sequence. Staining of polytene chromosomes reveals that sqd protein is associated with actively transcribing loci.
(Matunis et al., 1992)
sqd protein has two amino-terminal RNP-CS RNA-binding domains and a carboxy-terminal glycine-rich auxiliary domain.
(Matunis et al., 1992)
External Data
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Nucleotide / Polypeptide Records
 
UniProt
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\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
Gene Ontology (33 terms)
Molecular Function (5 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (5 terms)
CV Term
Evidence
References
mRNA 3'-UTR binding
traceable author statement
(Johnstone and Lasko, 2001, Cooperstock and Lipshitz, 1997)
mRNA binding
inferred from electronic annotation with InterPro:IPR037366
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
inferred from sequence or structural similarity
(Lasko, 2000)
RNA binding
inferred from biological aspect of ancestor with PANTHER:PTN002689974
(assigned by GO_Central )
(Gaudet et al., 2011)
sequence-specific DNA binding
inferred from biological aspect of ancestor with PANTHER:PTN002545010
(assigned by GO_Central )
(Gaudet et al., 2011)
sequence-specific double-stranded DNA binding
inferred from biological aspect of ancestor with PANTHER:PTN002545010
(assigned by GO_Central )
(Gaudet et al., 2011)
Biological Process (18 terms)
Terms Based on Experimental Evidence (12 terms)
CV Term
Evidence
References
dorsal/ventral axis specification, ovarian follicular epithelium
inferred from mutant phenotype
(Kelley, 1993)
dorsal/ventral pattern formation
inferred from mutant phenotype
(Clouse et al., 2008)
germarium-derived egg chamber formation
inferred from mutant phenotype
(Steinhauer and Kalderon, 2005)
negative regulation of RNA splicing
inferred from mutant phenotype
(Ji and Tulin, 2009)
oocyte anterior/posterior axis specification
inferred from mutant phenotype
(Steinhauer and Kalderon, 2005)
oocyte localization involved in germarium-derived egg chamber formation
inferred from mutant phenotype
(Steinhauer and Kalderon, 2005)
oocyte microtubule cytoskeleton organization
inferred from mutant phenotype
(Steinhauer and Kalderon, 2005)
oogenesis
inferred from mutant phenotype
(Steinhauer and Kalderon, 2005)
ovarian follicle cell migration
inferred from mutant phenotype
(Kelley, 1993)
pole plasm mRNA localization
inferred from mutant phenotype
(Herpers and Rabouille, 2004)
pole plasm oskar mRNA localization
inferred from expression pattern
(Norvell et al., 2005)
regulation of alternative mRNA splicing, via spliceosome
inferred from high throughput mutant phenotype
(Park et al., 2004)
Terms Based on Predictions or Assertions (8 terms)
CV Term
Evidence
References
dorsal/ventral pattern formation
traceable author statement
(Farina and Singer, 2002, Cooperstock and Lipshitz, 1997)
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)
mRNA export from nucleus
non-traceable author statement
(Tekotte and Davis, 2002)
mRNA splicing, via spliceosome
inferred by curator from GO:0071011,GO:0071013
(Herold et al., 2009)
negative regulation of translation
traceable author statement
(Cooperstock and Lipshitz, 1997)
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
traceable author statement
(Farina and Singer, 2002)
oogenesis
traceable author statement
(Farina and Singer, 2002)
RNA export from nucleus
traceable author statement
(Cooperstock and Lipshitz, 1997)
Cellular Component (10 terms)
Terms Based on Experimental Evidence (7 terms)
CV Term
Evidence
References
catalytic step 2 spliceosome
inferred from high throughput direct assay
(Herold et al., 2009)
chromatin
inferred from direct assay
(Prasanth et al., 2000)
NOT nucleolus
inferred from direct assay
(Matunis et al., 1992)
nucleus
inferred from direct assay
(Prasanth et al., 2000, Matunis et al., 1992)
inferred from high throughput direct assay
(Lye et al., 2014)
omega speckle
inferred from direct assay
(Prasanth et al., 2000)
polytene chromosome puff
inferred from direct assay
(Ji and Tulin, 2009, Matunis et al., 1992)
precatalytic spliceosome
inferred from high throughput direct assay
(Herold et al., 2009)
Terms Based on Predictions or Assertions (4 terms)
CV Term
Evidence
References
cytoplasm
traceable author statement
(Johnstone and Lasko, 2001)
nucleoplasm
inferred from biological aspect of ancestor with PANTHER:PTN002689978
(assigned by GO_Central )
(Gaudet et al., 2011)
nucleus
traceable author statement
(Johnstone and Lasko, 2001, Cooperstock and Lipshitz, 1997)
inferred from biological aspect of ancestor with PANTHER:PTN002309896
(assigned by GO_Central )
(Gaudet et al., 2011)
inferred by curator from GO:0000381
(Park et al., 2004)
ribonucleoprotein complex
inferred from biological aspect of ancestor with PANTHER:PTN002689974
(assigned by GO_Central )
(Gaudet et al., 2011)
Expression Data
Expression Summary Ribbons
Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
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
organism

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
ovary
(Kelley, 1993)
RT-PCR
Stage
Tissue/Position (including subcellular localization)
Reference
oogenesis stage S8 -- S14 & adult stage | female
egg chamber
(Van Buskirk and Schupbach, 2002)
oogenesis
egg chamber
(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
oogenesis
oocyte
(Cáceres and Nilson, 2009)
nurse cell
(Cáceres and Nilson, 2009)
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult head
(Aradska et al., 2015)
day 7 of adulthood -- day 49 of adulthood
adult heart
(Cammarato et al., 2011)
western blot
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage | female
ovary
(Goodrich et al., 2004)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
catalytic step 2 spliceosome
inferred from high throughput direct assay
(Herold et al., 2009)
chromatin
inferred from direct assay
(Prasanth et al., 2000)
NOT nucleolus
inferred from direct assay
(Matunis et al., 1992)
nucleus
inferred from direct assay
(Prasanth et al., 2000, Matunis et al., 1992)
inferred from high throughput direct assay
(Lye et al., 2014)
omega speckle
inferred from direct assay
(Prasanth et al., 2000)
polytene chromosome puff
inferred from direct assay
(Ji and Tulin, 2009, Matunis et al., 1992)
precatalytic spliceosome
inferred from high throughput direct assay
(Herold et al., 2009)
Expression Deduced from Reporters
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
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
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 33 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 14 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of sqd
Transgenic constructs containing regulatory region of sqd
Deletions and Duplications ( 7 )
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
lethal
lethal, with Scer\GAL4Mef2.PR
lethal (with Df(3R)l26c)
lethal (with Df(3R)urd)
lethal | recessive
lethal | recessive, with Scer\GAL4- :
lethal - all die before end of embryonic stage | maternal effect
lethal - all die before end of pupal stage, with Scer\GAL4pnr-MD237
partially lethal - majority die (with Df(3R)urd)
partially lethal - majority die (with sqdix50)
partially lethal - majority die (with sqdix77)
partially lethal - majority die (with sqdj4B4)
viable
viable, with Scer\GAL4tin.CΔ4
Sterility
Allele
female sterile
female sterile, with Scer\GAL4VP16.otu
female sterile (with sqd1)
female sterile (with sqdix50)
female sterile (with sqdix77)
female sterile | recessive
semi-sterile | recessive
Other Phenotypes
Allele
increased occurrence of cell division | spermatogenesis, with Scer\GAL4VP16.nos.UTR
short lived | heat sensitive, with Scer\GAL4tin.CΔ4
some die during embryonic stage | maternal effect
some die during pupal stage, with Scer\GAL4pnr-MD237
visible, with Scer\GAL4GMR.PF
Phenotype manifest in
Allele
border follicle cell | germline clone
centripetally migrating follicle cell | germline clone
chorion
chorion (with sqd1)
chorion (with sqdK12)
chorion | dorsal
cystocyte | germline clone
dorsal appendage
dorsal appendage (with sqd1)
dorsal appendage (with sqdK12)
dorsal appendage | germline clone
dorsal appendage | maternal effect
egg
egg (with sqd1)
egg (with sqdK12)
egg | germline clone
egg | maternal effect | ventral
egg chamber | germline clone
egg operculum (with sqd1)
egg operculum (with sqdK12)
filzkorper | maternal effect
follicle cell | germline clone
interfollicle cell | germline clone
interommatidial bristle, with Scer\GAL4GMR.PF
microtubule organizing center & oocyte | germ-line clone
nurse cell & nuclear chromosome
nurse cell | germline clone
oocyte
oocyte (with Df(3R)urd)
oocyte (with sqd1)
oocyte (with sqdix50)
oocyte (with sqdix77)
oocyte (with sqdj4B4)
oocyte & microtubule | germ-line clone
oocyte | germline clone
ovariole | germline clone
spermatogonium, with Scer\GAL4ptc-559.1
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (29)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Hsap\HNRNPAB
13 of 15
Yes
Yes
Hsap\HNRNPD
11 of 15
Yes
No
Hsap\HNRNPDL
10 of 15
Yes
No
Hsap\HNRNPA1
3 of 15
No
No
 
Hsap\HNRNPA1L2
3 of 15
No
No
Hsap\HNRNPA2B1
3 of 15
No
No
 
Hsap\HNRNPA3
3 of 15
No
No
Hsap\DAZAP1
2 of 15
No
No
Hsap\HNRNPA0
2 of 15
No
No
Hsap\MSI1
2 of 15
No
No
 
Hsap\MSI2
2 of 15
No
No
 
Hsap\BOLL
1 of 15
No
No
 
Hsap\CIRBP
1 of 15
No
No
Hsap\DAZ1
1 of 15
No
No
Hsap\DAZ2
1 of 15
No
No
Hsap\DAZ3
1 of 15
No
No
Hsap\DAZ4
1 of 15
No
No
Hsap\DAZL
1 of 15
No
No
Hsap\EIF4B
1 of 15
No
No
Hsap\EIF4H
1 of 15
No
No
Hsap\HNRNPC
1 of 15
No
No
 
Hsap\HNRNPCL1
1 of 15
No
No
Hsap\RALY
1 of 15
No
No
Hsap\RALYL
1 of 15
No
No
Hsap\RBM3
1 of 15
Yes
No
Hsap\RBM34
1 of 15
No
No
Hsap\SLIRP
1 of 15
No
No
Hsap\SRSF10
1 of 15
No
No
Hsap\TRNAU1AP
1 of 15
No
No
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (28)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Mmus\Hnrnpab
13 of 15
Yes
Yes
Mmus\Hnrnpd
11 of 15
Yes
No
Mmus\Hnrnpdl
10 of 15
No
Yes
Mmus\Rbm31y
6 of 15
No
Yes
Mmus\Gm21379
3 of 15
No
Yes
Mmus\Hnrnpa1
3 of 15
No
No
Mmus\Hnrnpa3
3 of 15
No
No
Mmus\Dazap1
2 of 15
No
No
Mmus\Hnrnpa0
2 of 15
No
No
Mmus\Hnrnpa2b1
2 of 15
No
No
Mmus\Msi1
2 of 15
No
No
Mmus\Msi2
2 of 15
No
No
Mmus\Boll
1 of 15
No
No
Mmus\Cirbp
1 of 15
No
No
Mmus\Dazl
1 of 15
No
No
Mmus\Eif4b
1 of 15
No
No
Mmus\Eif4h
1 of 15
No
No
Mmus\Gm4916
1 of 15
No
Yes
Mmus\Hnrnpa1l2-ps2
1 of 15
No
Yes
Mmus\Hnrnpc
1 of 15
No
No
Mmus\Raly
1 of 15
No
No
Mmus\Rbm34
1 of 15
No
No
Mmus\Slirp
1 of 15
No
No
Mmus\Srsf10
1 of 15
No
No
Mmus\Srsf12
1 of 15
No
No
Mmus\Tra2b
1 of 15
No
No
Mmus\Trnau1ap
1 of 15
No
No
Mmus\Zcrb1
1 of 15
No
Yes
Rattus norvegicus (Norway rat) (27)
Rnor\Hnrnpd
10 of 13
Yes
Yes
Rnor\Hnrnpdl
8 of 13
No
Yes
Rnor\LOC103689931
8 of 13
No
Yes
Rnor\Hnrnpab
6 of 13
No
Yes
Rnor\Rbm31y
4 of 13
No
Yes
Rnor\Dazap1
2 of 13
No
No
Rnor\Hnrnpa1
2 of 13
No
No
Rnor\Hnrnpa2b1
2 of 13
No
No
Rnor\Hnrnpa3
2 of 13
No
No
Rnor\Hnrnpc
2 of 13
No
No
Rnor\Boll
1 of 13
No
No
Rnor\Cirbp
1 of 13
No
Yes
Rnor\Dazl
1 of 13
No
No
Rnor\Eif4b
1 of 13
No
No
Rnor\Eif4h
1 of 13
No
No
Rnor\LOC679581
1 of 13
No
Yes
Rnor\LOC681410
1 of 13
No
No
Rnor\LOC100911576
1 of 13
No
No
Rnor\Msi1
1 of 13
No
No
Rnor\Msi2
1 of 13
No
No
Rnor\Ralyl
1 of 13
No
No
Rnor\Raly
1 of 13
No
No
Rnor\Rbm3
1 of 13
No
Yes
Rnor\Rbm34
1 of 13
No
No
Rnor\Slirp
1 of 13
No
No
Rnor\Tra2b
1 of 13
No
No
Rnor\Zcrb1
1 of 13
No
Yes
Xenopus tropicalis (Western clawed frog) (19)
Xtro\hnrnpd
9 of 12
Yes
Yes
Xtro\hnrnpdl
8 of 12
No
Yes
Xtro\hnrnpab
7 of 12
No
Yes
Xtro\hnrnpa3
3 of 12
No
No
Xtro\dazap1
2 of 12
No
No
Xtro\hnrnpa1
2 of 12
No
No
Xtro\hnrnpa2b1
2 of 12
No
No
Xtro\cirbp
1 of 12
No
Yes
Xtro\dazl
1 of 12
No
No
Xtro\eif4b
1 of 12
No
No
Xtro\eif4h
1 of 12
No
No
Xtro\hnrnpa0
1 of 12
No
No
Xtro\hnrnpc
1 of 12
No
No
Xtro\msi1
1 of 12
No
No
Xtro\msi2
1 of 12
No
No
Xtro\ralyl
1 of 12
No
No
Xtro\raly
1 of 12
No
No
Xtro\rbm34
1 of 12
No
No
Xtro\trnau1ap
1 of 12
No
No
Danio rerio (Zebrafish) (30)
Drer\hnrnpabb
11 of 15
Yes
Yes
Drer\hnrnpd
11 of 15
Yes
Yes
Drer\hnrpdl
10 of 15
No
Yes
Drer\hnrnpaba
9 of 15
No
Yes
Drer\hnrnpa3
3 of 15
No
No
Drer\dazap1
2 of 15
No
No
Drer\hnrnpa0a
2 of 15
No
No
Drer\hnrnpa0b
2 of 15
No
No
Drer\hnrnpa0l
2 of 15
No
No
Drer\hnrnpa1b
2 of 15
No
No
Drer\msi1
2 of 15
No
No
Drer\msi2a
2 of 15
No
No
Drer\msi2b
2 of 15
No
No
Drer\cirbpa
1 of 15
No
No
Drer\dazl
1 of 15
No
No
Drer\eif4ba
1 of 15
No
No
Drer\eif4h
1 of 15
No
No
Drer\hnrnpa1a
1 of 15
No
No
Drer\hnrnpc
1 of 15
No
No
Drer\LOC100537556
1 of 15
No
No
Drer\ncoa5
1 of 15
No
No
Drer\raly
1 of 15
No
No
Drer\ralyl
1 of 15
No
No
Drer\rbm34
1 of 15
No
No
Drer\srsf10a
1 of 15
No
No
Drer\trnau1apa
1 of 15
No
No
Drer\trnau1apb
1 of 15
No
No
Drer\zcrb1
1 of 15
No
Yes
Drer\zgc:55733
1 of 15
No
No
Drer\zgc:110796
1 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (12)
Cele\sqd-1
7 of 15
Yes
Yes
Cele\H28G03.1
2 of 15
No
No
Cele\hrp-1
2 of 15
No
No
Cele\msi-1
2 of 15
No
No
Cele\daz-1
1 of 15
No
No
Cele\F11A10.7
1 of 15
No
No
Cele\R05D3.8
1 of 15
No
Yes
Cele\R06C1.4
1 of 15
No
No
Cele\R09B3.2
1 of 15
No
No
Cele\T07F10.3
1 of 15
No
No
Cele\ZK616.61
1 of 15
No
Yes
Cele\ztf-4
1 of 15
No
No
Arabidopsis thaliana (thale-cress) (6)
Atha\AT3G13224
2 of 9
Yes
No
Atha\AT5G40490
2 of 9
Yes
No
Atha\AT1G17640
1 of 9
No
Yes
Atha\AT2G33410
1 of 9
No
No
Atha\AT4G14300
1 of 9
No
No
Atha\AT4G36960
1 of 9
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (13)
Scer\HRP1
3 of 15
Yes
No
Scer\CWC2
1 of 15
No
Yes
Scer\MRN1
1 of 15
No
Yes
Scer\MUD1
1 of 15
No
No
Scer\NAB6
1 of 15
No
Yes
Scer\NAM8
1 of 15
No
No
Scer\NGR1
1 of 15
No
No
Scer\NOP6
1 of 15
No
No
Scer\NOP12
1 of 15
No
No
Scer\NOP13
1 of 15
No
No
Scer\NPL3
1 of 15
No
No
Scer\NSR1
1 of 15
No
Yes
Scer\RIM4
1 of 15
No
Yes
Schizosaccharomyces pombe (Fission yeast) (3)
Spom\gar2
2 of 12
Yes
Yes
Spom\SPBC660.15
2 of 12
Yes
No
Spom\rnp24
1 of 12
No
Yes
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG09190EW8 )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Dmel\sqd
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00012433
Drosophila simulans
Dsim\GD20486
Drosophila sechellia
Dsec\GM25920
Drosophila erecta
Dere\GG17035
Drosophila yakuba
Dyak\GE24428
Drosophila ananassae
Dana\GF17370
Drosophila pseudoobscura pseudoobscura
Dpse\GA14206
Drosophila persimilis
Dper\GL23974
Drosophila willistoni
Dwil\GK13337
Drosophila virilis
Dvir\GJ23113
Drosophila mojavensis
Dmoj\GI10695
Drosophila grimshawi
Dgri\GH19060
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG09150DOA )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17007495
Glossina morsitans
Tsetse fly
Gmor\GMOY003874
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_11853
Mayetiola destructor
Hessian fly
Mdes\Mdes000193
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL005515
Anopheles darlingi
American malaria mosquito
Adar\ADAC009371
Anopheles darlingi
American malaria mosquito
Adar\ADAC000515
Anopheles gambiae
Malaria mosquito
Agam\AGAP006668
Anopheles gambiae
Malaria mosquito
Agam\AGAP000399
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ011536
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W0D2X )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Bmor\BGIBMGA013464
Danaus plexippus
Monarch butterfly
Dple\DPOGS210542-PA
Heliconius melpomene
Postman butterfly
Hmel\HMEL006426
Apis florea
Little honeybee
Aflo\2283991348
Apis mellifera
Western honey bee
Amel\GB43300
Bombus impatiens
Common eastern bumble bee
Bimp\BIMP11338
Bombus terrestris
Buff-tailed bumblebee
Bter\15201673
Linepithema humile
Argentine ant
Lhum\LH18367
Linepithema humile
Argentine ant
Lhum\LH22943
Megachile rotundata
Alfalfa leafcutting bee
Mrot\MROTU:0008f1
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG013911
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_11010
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_00411
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_09370
Tribolium castaneum
Red flour beetle
Tcas\TC000928
Pediculus humanus
Human body louse
Phum\PHUM596900
Rhodnius prolixus
Kissing bug
Rpro\RPRC007924
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI003403
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI008564
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI006706
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_10608
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0HEE )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Smar\SMAR006005
Strigamia maritima
European centipede
Smar\SMAR005882
Ixodes scapularis
Black-legged tick
Isca\ISCW007146
Stegodyphus mimosarum
African social velvet spider
Smim\KFM64729.1
Stegodyphus mimosarum
African social velvet spider
Smim\KFM67416.1
Tetranychus urticae
Two-spotted spider mite
Turt\tetur41g00590
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_189289
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G1CPI )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Spur\SPU_022512gn
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Hnrpa
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Dazap
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Msi1
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Hnrpa2B1L
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Unk_9
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Dazap_1
Strongylocentrotus purpuratus
Purple sea urchin
Spur\SPU_007318gn
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000022958
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000017374
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000003877
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000003362
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000013663
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000018579
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000004062
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000016737
Gallus gallus
Domestic chicken
Ggal\DAZAP1
Gallus gallus
Domestic chicken
Ggal\HNRNPA0
Gallus gallus
Domestic chicken
Ggal\HNRNPA2B1
Gallus gallus
Domestic chicken
Ggal\HNRNPAB
Gallus gallus
Domestic chicken
Ggal\HNRNPA3
Gallus gallus
Domestic chicken
Ggal\HNRPDL
Gallus gallus
Domestic chicken
Ggal\MSI2
Gallus gallus
Domestic chicken
Ggal\HNRNPD
Gallus gallus
Domestic chicken
Ggal\MSI2
Gallus gallus
Domestic chicken
Ggal\ENSGALG00000028932
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (23)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
Hrb87F
5 of 10
Hrb98DE
5 of 10
Rbp6
5 of 10
Hrb27C
4 of 10
Rb97D
4 of 10
Rbp4
4 of 10
msi
3 of 10
CG7804
2 of 10
SLIRP2
2 of 10
TBPH
2 of 10
bol
1 of 10
CG4612
1 of 10
CG5213
1 of 10
CG11726
1 of 10
CG12288
1 of 10
CG33278
1 of 10
CG34354
1 of 10
CG42458
1 of 10
eIF4H1
1 of 10
eIF4H2
1 of 10
Secp43
1 of 10
SLIRP1
1 of 10
tra2
1 of 10
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Model Summary Ribbon
    Disease Ontology (DO) Annotations
    Models Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Evidence
    References
    Potential Models Based on Orthology ( 1 )
    Modifiers Based on Experimental Evidence ( 1 )
    Allele
    Disease
    Interaction
    References
    sqdGD8593
    exacerbates  neurodegenerative disease
    modeled by TBPHΔ23, TBPHdsRNA.UAS.cUa
    (Appocher et al., 2017)
    Comments on Models/Modifiers Based on Experimental Evidence ( 0 )
     
    Disease Associations of Human Orthologs (via DIOPT v7.1 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?
    HNRNPAB; heterogeneous nuclear ribonucleoprotein A/B
    13 of 15
    602688
        HNRNPD; heterogeneous nuclear ribonucleoprotein D
        11 of 15
        601324
            HNRNPDL; heterogeneous nuclear ribonucleoprotein D like
            10 of 15
            607137
            HNRNPA1; heterogeneous nuclear ribonucleoprotein A1
            3 of 15
            164017
             
            HNRNPA1L2; heterogeneous nuclear ribonucleoprotein A1 like 2
            3 of 15
                HNRNPA2B1; heterogeneous nuclear ribonucleoprotein A2/B1
                3 of 15
                600124
                 
                HNRNPA3; heterogeneous nuclear ribonucleoprotein A3
                3 of 15
                605372
                    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
                    Show neighbor-neighbor interactions:
                    Select Layout:
                    Legend:
                    Protein
                    RNA
                    Selected Interactor(s)
                    Interactions Browser
                    View in Interactions Browser
                    Please see the Physical Interaction reports below for full details
                    RNA-protein
                    Physical Interaction
                    Assay
                    References
                    sqd - Dscam1
                    anti bait coimmunoprecipitation, nucleotide sequence identification
                    (Olson et al., 2007)
                    sqd - Imp
                    anti bait coimmunoprecipitation, peptide massfingerprinting, western blot, electrophoretic mobility shift assay, autoradiography
                    (Hansen et al., 2015, Clouse et al., 2008, Geng and Macdonald, 2006)
                    sqd - Unr
                    anti bait coimmunoprecipitation, quantitative reverse transcription pcr
                    (Mihailovich et al., 2012)
                    sqd - bcd
                    anti tag coimmunoprecipitation, primer specific pcr
                    (McDermott and Davis, 2013, McDermott et al., 2012)
                    sqd - grk
                    nucleic acid uv cross-linking assay, autoradiography, phage display, anti tag coimmunoprecipitation, primer specific pcr, anti bait coimmunoprecipitation, quantitative reverse transcription pcr, pull down, peptide massfingerprinting
                    (Li et al., 2014, McDermott and Davis, 2013, McDermott et al., 2012, Rom et al., 2007, Norvell et al., 1999)
                    sqd - lncRNA:Hsrω
                    pull down, anti tag western blot, anti bait coimmunoprecipitation, primer specific pcr, southern blot
                    (Onorati et al., 2011, Prasanth et al., 2000)
                    sqd - osk
                    anti tag coimmunoprecipitation, primer specific pcr
                    (McDermott and Davis, 2013, McDermott et al., 2012)
                    sqd - shep
                    coimmunoprecipitation, quantitative reverse transcription pcr
                    (Olesnicky et al., 2018)
                    protein-protein
                    Physical Interaction
                    Assay
                    References
                    sqd - Akt1
                    anti tag coimmunoprecipitation, Identification by mass spectrometry
                    (Vinayagam et al., 2016)
                    sqd - Art1
                    methyltransferase assay, autoradiography
                    (Boulanger et al., 2004)
                    sqd - Dsor1
                    anti tag coimmunoprecipitation, peptide massfingerprinting
                    (Friedman et al., 2011)
                    sqd - Egfr
                    anti tag coimmunoprecipitation, peptide massfingerprinting
                    (Friedman et al., 2011)
                    sqd - Hrb27C
                    anti bait coimmunoprecipitation, molecular weight estimation by autoradiography, peptide massfingerprinting, molecular weight estimation by staining, western blot, two hybrid
                    (Clouse et al., 2008, Goodrich et al., 2004, Amero et al., 1993, Matunis et al., 1992)
                    sqd - Hrb87F
                    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)
                    sqd - Hrb98DE
                    anti bait coimmunoprecipitation, molecular weight estimation by staining, molecular weight estimation by autoradiography
                    (Amero et al., 1993, Matunis et al., 1992)
                    sqd - Hrp39
                    anti bait coimmunoprecipitation, molecular weight estimation by staining
                    (Amero et al., 1993)
                    sqd - Hrp44
                    anti bait coimmunoprecipitation, molecular weight estimation by staining
                    (Amero et al., 1993)
                    sqd - Hrp62
                    anti bait coimmunoprecipitation, molecular weight estimation by staining
                    (Amero et al., 1993)
                    sqd - Hrp70
                    anti bait coimmunoprecipitation, molecular weight estimation by staining
                    (Amero et al., 1993)
                    sqd - Hrp75
                    anti bait coimmunoprecipitation, molecular weight estimation by staining
                    (Amero et al., 1993)
                    sqd - Imp
                    anti bait coimmunoprecipitation, peptide massfingerprinting, western blot, electrophoretic mobility shift assay, autoradiography
                    (Hansen et al., 2015, Clouse et al., 2008, Geng and Macdonald, 2006)
                    sqd - Parp
                    anti tag coimmunoprecipitation, western blot
                    (Ji and Tulin, 2009)
                    sqd - Pdk1
                    anti tag coimmunoprecipitation, Identification by mass spectrometry
                    (Vinayagam et al., 2016)
                    sqd - Pep
                    anti bait coimmunoprecipitation, western blot
                    (Amero et al., 1993)
                    sqd - Pi3K21B
                    anti tag coimmunoprecipitation, Identification by mass spectrometry
                    (Vinayagam et al., 2016)
                    sqd - RasGAP1
                    anti tag coimmunoprecipitation, peptide massfingerprinting
                    (Friedman et al., 2011)
                    sqd - Rbf
                    anti bait coimmunoprecipitation, western blot, anti tag coimmunoprecipitation, multidimensional protein identification technology
                    (Ahlander and Bosco, 2009)
                    sqd - Rheb
                    anti tag coimmunoprecipitation, Identification by mass spectrometry
                    (Vinayagam et al., 2016)
                    sqd - S6k
                    anti tag coimmunoprecipitation, Identification by mass spectrometry
                    (Vinayagam et al., 2016)
                    sqd - S6kII
                    anti tag coimmunoprecipitation, Identification by mass spectrometry
                    (Vinayagam et al., 2016)
                    sqd - Syp
                    anti bait coimmunoprecipitation, western blot
                    (McDermott et al., 2012)
                    sqd - TBPH
                    anti bait coimmunoprecipitation, western blot, far western blotting, Identification by mass spectrometry
                    (Lo Piccolo et al., 2018, Romano et al., 2014)
                    sqd - Thor
                    anti tag coimmunoprecipitation, Identification by mass spectrometry
                    (Vinayagam et al., 2016)
                    sqd - Tnpo
                    pull down, autoradiography
                    (Norvell et al., 1999)
                    sqd - Tsc1
                    anti tag coimmunoprecipitation, Identification by mass spectrometry
                    (Vinayagam et al., 2016)
                    sqd - bru1
                    pull down, autoradiography, anti bait coimmunoprecipitation, western blot
                    (Norvell et al., 1999)
                    sqd - cnk
                    anti tag coimmunoprecipitation, peptide massfingerprinting
                    (Friedman et al., 2011)
                    sqd - cup
                    anti bait coimmunoprecipitation, western blot, peptide massfingerprinting, anti tag coimmunoprecipitation
                    (Clouse et al., 2008)
                    sqd - foxo
                    anti tag coimmunoprecipitation, Identification by mass spectrometry
                    (Vinayagam et al., 2016)
                    sqd - fs(1)K10
                    pull down, autoradiography
                    (Norvell et al., 1999)
                    sqd - gig
                    anti tag coimmunoprecipitation, Identification by mass spectrometry
                    (Vinayagam et al., 2016)
                    sqd - orb2
                    anti tag coimmunoprecipitation, western blot
                    (Khan et al., 2015, Majumdar et al., 2012)
                    sqd - pAbp
                    anti bait coimmunoprecipitation, peptide massfingerprinting, western blot, anti tag coimmunoprecipitation
                    (Clouse et al., 2008)
                    sqd - rictor
                    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
                    sqd
                    enhanceable
                    Hrb27C
                    (Goodrich et al., 2004)
                    sqd
                    suppressible
                    otu
                    (Goodrich et al., 2004)
                    sqd
                    enhanceable
                    Rbf
                    (Ahlander and Bosco, 2009)
                    Starting gene(s)
                    Interaction type
                    Interacting gene(s)
                    Reference
                    Imp
                    enhanceable
                    sqd
                    (Geng and MacDonald, 2007)
                    Rbf
                    enhanceable
                    sqd
                    (Ahlander and Bosco, 2009)
                    Rpp30
                    suppressible
                    sqd
                    (Molla-Herman et al., 2015)
                    TBPH
                    enhanceable
                    sqd
                    (Appocher et al., 2017)
                    External Data
                    Linkouts
                    DroID - A comprehensive database of gene and protein interactions.
                    MIST (protein-protein) - An integrated Molecular Interaction Database
                    Pathways
                    Gene Group - Pathway Membership (FlyBase)
                    External Data
                    Genomic Location and Detailed Mapping Data
                    Chromosome (arm)
                    3R
                    Recombination map
                    3-54
                    Cytogenetic map
                    87F5-87F6
                    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}B52s2249&P{lacW}flflL4179
                    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 (19)
                    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 sequences
                    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.

                    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
                    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(whs)} 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 ( 94 )
                    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.
                    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/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
                    UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
                    Other crossreferences
                    BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
                    Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
                    Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
                    Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
                    GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
                    InterPro - A database of protein families, domains and functional sites
                    KEGG Genes - Molecular building blocks of life in the genomic space.
                    KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
                    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
                    Linkouts
                    ApoDroso - Functional genomic database for photoreceptor development, survival and function
                    DroID - A comprehensive database of gene and protein interactions.
                    Developmental Studies Hybridoma Bank - Monoclonal antibodies for use in research
                    Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
                    KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
                    MIST (protein-protein) - An integrated Molecular Interaction Database
                    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
                    Synonyms and Secondary IDs (27)
                    Reported As
                    Symbol Synonym
                    BcDNA:GM03761
                    CG16901
                    (Appocher et al., 2017, Kolkhof et al., 2017, Meadows, 2017.9.14, Aradska et al., 2015, Brooks et al., 2015, Horan et al., 2015, Hosono et al., 2015, Rosa-Ferreira et al., 2015, Cammarato et al., 2011, Ni et al., 2011.7.19, Ellis and Carney, 2010, Ni et al., 2010.12.1, Blagden et al., 2009, Hansen et al., 2009, Herold et al., 2009, Ni et al., 2008, Puri et al., 2008, Quinones-Coello, 2007, McIntyre et al., 2006, Nybakken et al., 2005, Oliver, 2001.8.16)
                    CG17791
                    (Labourier et al., 2002)
                    CR33328
                    HRP40
                    (Nakamura et al., 1994)
                    Hrb87
                    (Kim and Baker, 1993)
                    Hrb87Fb
                    Hrp40
                    (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
                    (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, 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
                    (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
                    (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
                    Squid
                    (Li et al., 2014, Lowe et al., 2014, Romano et al., 2014, Jokhi et al., 2013, Majumdar et al., 2012, Serbus et al., 2011, Ahlander and Bosco, 2009, Ji and Tulin, 2009, Kalifa et al., 2009, Nie et al., 2009, Boylan et al., 2008, Clouse et al., 2008, Norvell et al., 2008, Meigh et al., 2007, Nurminsky, 2007, Vanzo et al., 2007, Geng and Macdonald, 2006, Jolly and Lakhotia, 2006, Manh et al., 2005, Van De Bor et al., 2005, Lakhotia, 2003, Gim et al., 2001)
                    heterogeneous-nuclear-ribonucleoprotein-87Fb
                    lethal (3) j4B4
                    squid
                    (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
                    References (251)