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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
  • intracellular ribonucleoprotein complex 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)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 344344RNA-binding protein squidPRO_0000081959Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei148 – 1481Phosphoserine1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ08473.

PTM databases

iPTMnetiQ08473.

Expressioni

Gene expression databases

BgeeiQ08473.
GenevisibleiQ08473. DM.

Interactioni

Protein-protein interaction databases

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

Structurei

3D structure databases

ProteinModelPortaliQ08473.
SMRiQ08473. Positions 57-214.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini56 – 13883RRM 1PROSITE-ProRule annotationAdd
BLAST
Domaini136 – 21378RRM 2PROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi221 – 337117Gly-richAdd
BLAST

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.
OrthoDBiEOG715Q6V.
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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti84 – 841S → N in AAB24624 (PubMed:8417324).Curated
Sequence conflicti169 – 1691F → L in AAB26988 (PubMed:7684991).Curated
Sequence conflicti169 – 1691F → L in AAB26989 (PubMed:7684991).Curated
Sequence conflicti305 – 3051G → GG in CAA44504 (PubMed:1730754).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 166166Missing in isoform D. CuratedVSP_011797Add
BLAST
Alternative sequencei286 – 34459DGYGY…RHQPY → GKYNKQQSSAQNNYYNNNTS SNYHQNKNNSNNYQQF in isoform A. 1 PublicationVSP_005876Add
BLAST
Alternative sequencei286 – 32136Missing in isoform C. 2 PublicationsVSP_005877Add
BLAST

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. Positions 57-214.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

PTM databases

iPTMnetiQ08473.

Proteomic databases

PaxDbiQ08473.

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.
OrthoDBiEOG715Q6V.
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.
NextBioi824926.
PROiQ08473.

Gene expression databases

BgeeiQ08473.
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...

Publicationsi

« Hide 'large scale' publications
  1. "Characterization of the major hnRNP proteins from Drosophila melanogaster."
    Matunis E.L., Matunis M.J., Dreyfuss G.
    J. Cell Biol. 116:257-269(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS B AND C).
    Strain: Canton-S.
    Tissue: Embryo.
  2. "Initial organization of the Drosophila dorsoventral axis depends on an RNA-binding protein encoded by the squid gene."
    Kelley R.L.
    Genes Dev. 7:948-960(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], ALTERNATIVE SPLICING, FUNCTION, SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE.
    Tissue: Ovary.
  3. "The genome sequence of Drosophila melanogaster."
    Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D., Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F., George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N., Sutton G.G., Wortman J.R., Yandell M.D.
    , Zhang Q., Chen L.X., Brandon R.C., Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D., Wan K.H., Doyle C., Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G., Abril J.F., Agbayani A., An H.-J., Andrews-Pfannkoch C., Baldwin D., Ballew R.M., Basu A., Baxendale J., Bayraktaroglu L., Beasley E.M., Beeson K.Y., Benos P.V., Berman B.P., Bhandari D., Bolshakov S., Borkova D., Botchan M.R., Bouck J., Brokstein P., Brottier P., Burtis K.C., Busam D.A., Butler H., Cadieu E., Center A., Chandra I., Cherry J.M., Cawley S., Dahlke C., Davenport L.B., Davies P., de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I., Dietz S.M., Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C., Dunn P., Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S., Fleischmann W., Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M., Glasser K., Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M., Harris N.L., Harvey D.A., Heiman T.J., Hernandez J.R., Houck J., Hostin D., Houston K.A., Howland T.J., Wei M.-H., Ibegwam C., Jalali M., Kalush F., Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A., Kimmel B.E., Kodira C.D., Kraft C.L., Kravitz S., Kulp D., Lai Z., Lasko P., Lei Y., Levitsky A.A., Li J.H., Li Z., Liang Y., Lin X., Liu X., Mattei B., McIntosh T.C., McLeod M.P., McPherson D., Merkulov G., Milshina N.V., Mobarry C., Morris J., Moshrefi A., Mount S.M., Moy M., Murphy B., Murphy L., Muzny D.M., Nelson D.L., Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R., Pacleb J.M., Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V., Reese M.G., Reinert K., Remington K., Saunders R.D.C., Scheeler F., Shen H., Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T.J., Spier E., Spradling A.C., Stapleton M., Strong R., Sun E., Svirskas R., Tector C., Turner R., Venter E., Wang A.H., Wang X., Wang Z.-Y., Wassarman D.A., Weinstock G.M., Weissenbach J., Williams S.M., Woodage T., Worley K.C., Wu D., Yang S., Yao Q.A., Ye J., Yeh R.-F., Zaveri J.S., Zhan M., Zhang G., Zhao Q., Zheng L., Zheng X.H., Zhong F.N., Zhong W., Zhou X., Zhu S.C., Zhu X., Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M., Venter J.C.
    Science 287:2185-2195(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Berkeley.
  4. Cited for: GENOME REANNOTATION, ALTERNATIVE SPLICING.
    Strain: Berkeley.
  5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM A).
    Strain: Berkeley.
    Tissue: Embryo and Head.
  6. Stapleton M., Carlson J.W., Frise E., Kapadia B., Park S., Wan K.H., Yu C., Celniker S.E.
    Submitted (NOV-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM C).
    Strain: Berkeley.
    Tissue: Embryo.
  7. "Isolation of RRM-type RNA-binding protein genes and the analysis of their relatedness by using a numerical approach."
    Kim Y.-J., Baker B.S.
    Mol. Cell. Biol. 13:174-183(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 59-102 (ISOFORMS A/B/C).
  8. "An integrated chemical, mass spectrometric and computational strategy for (quantitative) phosphoproteomics: application to Drosophila melanogaster Kc167 cells."
    Bodenmiller B., Mueller L.N., Pedrioli P.G.A., Pflieger D., Juenger M.A., Eng J.K., Aebersold R., Tao W.A.
    Mol. Biosyst. 3:275-286(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-148, IDENTIFICATION BY MASS SPECTROMETRY.

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: May 11, 2016
This is version 136 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.