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Protein

RNA-binding protein squid

Gene

sqd

Organism
Drosophila melanogaster (Fruit fly)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.1 Publication

GO - Molecular functioni

  • mRNA 3'-UTR binding Source: FlyBase
  • mRNA binding Source: FlyBase
  • nucleotide binding Source: InterPro

GO - Biological processi

  • dorsal/ventral axis specification, ovarian follicular epithelium Source: FlyBase
  • dorsal/ventral pattern formation Source: FlyBase
  • germarium-derived egg chamber formation Source: FlyBase
  • intracellular mRNA localization Source: FlyBase
  • mRNA export from nucleus Source: FlyBase
  • mRNA splicing, via spliceosome Source: FlyBase
  • negative regulation of RNA splicing Source: FlyBase
  • negative regulation of translation Source: FlyBase
  • nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Source: FlyBase
  • oocyte anterior/posterior axis specification Source: FlyBase
  • oocyte localization involved in germarium-derived egg chamber formation Source: FlyBase
  • oocyte microtubule cytoskeleton organization Source: FlyBase
  • oogenesis Source: FlyBase
  • ovarian follicle cell migration Source: FlyBase
  • pole plasm mRNA localization Source: FlyBase
  • pole plasm oskar mRNA localization Source: FlyBase
  • regulation of alternative mRNA splicing, via spliceosome Source: FlyBase
  • RNA export from nucleus Source: FlyBase
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

ReactomeiR-DME-450408. AUF1 (hnRNP D0) binds and destabilizes mRNA.
R-DME-72163. mRNA Splicing - Major Pathway.
R-DME-72203. Processing of Capped Intron-Containing Pre-mRNA.

Names & Taxonomyi

Protein namesi
Recommended name:
RNA-binding protein squid
Alternative name(s):
Heterogeneous nuclear ribonucleoprotein 40
Short name:
HNRNP 40
Gene namesi
Name:sqd
Synonyms:hrp40
ORF Names:CG16901
OrganismiDrosophila melanogaster (Fruit fly)
Taxonomic identifieri7227 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaArthropodaHexapodaInsectaPterygotaNeopteraEndopterygotaDipteraBrachyceraMuscomorphaEphydroideaDrosophilidaeDrosophilaSophophora
Proteomesi
  • UP000000803 Componenti: Chromosome 3R

Organism-specific databases

FlyBaseiFBgn0263396. sqd.

Subcellular locationi

  • Nucleus 1 Publication
  • Cytoplasm 1 Publication

  • Note: It is possible that some isoforms are found only in one of these locations.

GO - Cellular componenti

  • catalytic step 2 spliceosome Source: FlyBase
  • chromatin Source: FlyBase
  • cytoplasm Source: FlyBase
  • nucleus Source: FlyBase
  • omega speckle Source: FlyBase
  • polytene chromosome puff Source: FlyBase
  • precatalytic spliceosome Source: FlyBase
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Disruption phenotypei

Female are sterile and lay eggs that display only dorsal structures.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000819591 – 344RNA-binding protein squidAdd BLAST344

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei148Phosphoserine1 Publication1

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ08473.
PRIDEiQ08473.

PTM databases

iPTMnetiQ08473.

Expressioni

Gene expression databases

BgeeiFBgn0263396.
ExpressionAtlasiQ08473. baseline.
GenevisibleiQ08473. DM.

Interactioni

Protein-protein interaction databases

BioGridi66748. 12 interactors.
IntActiQ08473. 28 interactors.
MINTiMINT-847475.
STRINGi7227.FBpp0082320.

Structurei

3D structure databases

ProteinModelPortaliQ08473.
SMRiQ08473.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini56 – 138RRM 1PROSITE-ProRule annotationAdd BLAST83
Domaini136 – 213RRM 2PROSITE-ProRule annotationAdd BLAST78

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi221 – 337Gly-richAdd BLAST117

Sequence similaritiesi

Contains 2 RRM (RNA recognition motif) domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0118. Eukaryota.
COG0724. LUCA.
GeneTreeiENSGT00760000118873.
InParanoidiQ08473.
KOiK03102.
OMAiGRQQRHQ.
OrthoDBiEOG091G1CPI.
PhylomeDBiQ08473.

Family and domain databases

Gene3Di3.30.70.330. 2 hits.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF00076. RRM_1. 2 hits.
[Graphical view]
SMARTiSM00360. RRM. 2 hits.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 2 hits.
PROSITEiPS50102. RRM. 2 hits.
[Graphical view]

Sequences (4)i

Sequence statusi: Complete.

This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket

Note: Additional isoforms seem to exist.
Isoform B (identifier: Q08473-1) [UniParc]FASTAAdd to basket
Also known as: SqdS, HRP40.2

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MAENKQVDTE INGEDFTKDV TADGPGSENG DAGAAGSTNG SSDNQSAASG
60 70 80 90 100
QRDDDRKLFV GGLSWETTEK ELRDHFGKYG EIESINVKTD PQTGRSRGFA
110 120 130 140 150
FIVFTNTEAI DKVSAADEHI INSKKVDPKK AKARHGKIFV GGLTTEISDE
160 170 180 190 200
EIKTYFGQFG NIVEVEMPFD KQKSQRKGFC FITFDSEQVV TDLLKTPKQK
210 220 230 240 250
IAGKEVDVKR ATPKPENQMM GGMRGGPRGG MRGGRGGYGG RGGYNNQWDG
260 270 280 290 300
QGSYGGYGGG YGGYGAGGYG DYYAGGYYNG YDYGYDGYGY GGGFEGNGYG
310 320 330 340
GGGGGNMGGG RGGPRGGGGP KGGGGFNGGK QRGGGGRQQR HQPY
Length:344
Mass (Da):36,184
Last modified:October 25, 2004 - v3
Checksum:i68E84791A924EED4
GO
Isoform A (identifier: Q08473-2) [UniParc]FASTAAdd to basket
Also known as: SqdA, HRP40.1

The sequence of this isoform differs from the canonical sequence as follows:
     286-344: DGYGYGGGFE...GGRQQRHQPY → GKYNKQQSSA...KNNSNNYQQF

Show »
Length:321
Mass (Da):35,003
Checksum:iF422FA6506608157
GO
Isoform C (identifier: Q08473-3) [UniParc]FASTAAdd to basket
Also known as: SqdB

The sequence of this isoform differs from the canonical sequence as follows:
     286-321: Missing.

Show »
Length:308
Mass (Da):33,054
Checksum:iE6DF06142EBE59BF
GO
Isoform D (identifier: Q08473-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-166: Missing.

Note: No experimental confirmation available.
Show »
Length:178
Mass (Da):18,266
Checksum:i4F59033895438B1D
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti84S → N in AAB24624 (PubMed:8417324).Curated1
Sequence conflicti169F → L in AAB26988 (PubMed:7684991).Curated1
Sequence conflicti169F → L in AAB26989 (PubMed:7684991).Curated1
Sequence conflicti305G → GG in CAA44504 (PubMed:1730754).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0117971 – 166Missing in isoform D. CuratedAdd BLAST166
Alternative sequenceiVSP_005876286 – 344DGYGY…RHQPY → GKYNKQQSSAQNNYYNNNTS SNYHQNKNNSNNYQQF in isoform A. 1 PublicationAdd BLAST59
Alternative sequenceiVSP_005877286 – 321Missing in isoform C. 2 PublicationsAdd BLAST36

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X62637 mRNA. Translation: CAA44503.1.
X62638 mRNA. Translation: CAA44504.1.
S61875 Genomic DNA. Translation: AAB26988.1.
S62100, S61875 Genomic DNA. Translation: AAB26989.1.
AE014297 Genomic DNA. Translation: AAF54963.2.
AE014297 Genomic DNA. Translation: AAF54964.2.
AE014297 Genomic DNA. Translation: AAN13570.1.
AE014297 Genomic DNA. Translation: AAS65146.1.
AY118501 mRNA. Translation: AAM49870.1.
BT001384 mRNA. Translation: AAN71139.1.
BT003283 mRNA. Translation: AAO25040.1.
BT023832 mRNA. Translation: AAZ86753.1.
S51693 mRNA. Translation: AAB24624.1.
PIRiA47369.
B41732.
B47369.
C48110.
RefSeqiNP_001247088.1. NM_001260159.2. [Q08473-3]
NP_652209.1. NM_143952.2. [Q08473-3]
NP_731825.1. NM_169528.2. [Q08473-1]
NP_731826.1. NM_169529.3. [Q08473-2]
NP_996203.1. NM_206481.2. [Q08473-4]
UniGeneiDm.7189.

Genome annotation databases

EnsemblMetazoaiFBtr0082855; FBpp0082320; FBgn0263396. [Q08473-1]
GeneIDi41666.
KEGGidme:Dmel_CG16901.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X62637 mRNA. Translation: CAA44503.1.
X62638 mRNA. Translation: CAA44504.1.
S61875 Genomic DNA. Translation: AAB26988.1.
S62100, S61875 Genomic DNA. Translation: AAB26989.1.
AE014297 Genomic DNA. Translation: AAF54963.2.
AE014297 Genomic DNA. Translation: AAF54964.2.
AE014297 Genomic DNA. Translation: AAN13570.1.
AE014297 Genomic DNA. Translation: AAS65146.1.
AY118501 mRNA. Translation: AAM49870.1.
BT001384 mRNA. Translation: AAN71139.1.
BT003283 mRNA. Translation: AAO25040.1.
BT023832 mRNA. Translation: AAZ86753.1.
S51693 mRNA. Translation: AAB24624.1.
PIRiA47369.
B41732.
B47369.
C48110.
RefSeqiNP_001247088.1. NM_001260159.2. [Q08473-3]
NP_652209.1. NM_143952.2. [Q08473-3]
NP_731825.1. NM_169528.2. [Q08473-1]
NP_731826.1. NM_169529.3. [Q08473-2]
NP_996203.1. NM_206481.2. [Q08473-4]
UniGeneiDm.7189.

3D structure databases

ProteinModelPortaliQ08473.
SMRiQ08473.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi66748. 12 interactors.
IntActiQ08473. 28 interactors.
MINTiMINT-847475.
STRINGi7227.FBpp0082320.

PTM databases

iPTMnetiQ08473.

Proteomic databases

PaxDbiQ08473.
PRIDEiQ08473.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblMetazoaiFBtr0082855; FBpp0082320; FBgn0263396. [Q08473-1]
GeneIDi41666.
KEGGidme:Dmel_CG16901.

Organism-specific databases

CTDi41666.
FlyBaseiFBgn0263396. sqd.

Phylogenomic databases

eggNOGiKOG0118. Eukaryota.
COG0724. LUCA.
GeneTreeiENSGT00760000118873.
InParanoidiQ08473.
KOiK03102.
OMAiGRQQRHQ.
OrthoDBiEOG091G1CPI.
PhylomeDBiQ08473.

Enzyme and pathway databases

ReactomeiR-DME-450408. AUF1 (hnRNP D0) binds and destabilizes mRNA.
R-DME-72163. mRNA Splicing - Major Pathway.
R-DME-72203. Processing of Capped Intron-Containing Pre-mRNA.

Miscellaneous databases

ChiTaRSisqd. fly.
GenomeRNAii41666.
PROiQ08473.

Gene expression databases

BgeeiFBgn0263396.
ExpressionAtlasiQ08473. baseline.
GenevisibleiQ08473. DM.

Family and domain databases

Gene3Di3.30.70.330. 2 hits.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF00076. RRM_1. 2 hits.
[Graphical view]
SMARTiSM00360. RRM. 2 hits.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 2 hits.
PROSITEiPS50102. RRM. 2 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSQD_DROME
AccessioniPrimary (citable) accession number: Q08473
Secondary accession number(s): Q26273
, Q3ZAN7, Q8IH71, Q8INH1, Q8MSY1, Q9VFT5, Q9VFT6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: October 25, 2004
Last modified: November 30, 2016
This is version 142 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programDrosophila annotation project

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Drosophila
    Drosophila: entries, gene names and cross-references to FlyBase
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.