SQD_DROME
ID SQD_DROME Reviewed; 344 AA.
AC Q08473; Q26273; Q3ZAN7; Q8IH71; Q8INH1; Q8MSY1; Q9VFT5; Q9VFT6;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 25-OCT-2004, sequence version 3.
DT 03-AUG-2022, entry version 178.
DE RecName: Full=RNA-binding protein squid;
DE AltName: Full=Heterogeneous nuclear ribonucleoprotein 40;
DE Short=HNRNP 40;
GN Name=sqd; Synonyms=hrp40; ORFNames=CG16901;
OS Drosophila melanogaster (Fruit fly).
OC Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota;
OC Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea;
OC Drosophilidae; Drosophila; Sophophora.
OX NCBI_TaxID=7227;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS B AND C).
RC STRAIN=Canton-S; TISSUE=Embryo;
RX PubMed=1730754; DOI=10.1083/jcb.116.2.257;
RA Matunis E.L., Matunis M.J., Dreyfuss G.;
RT "Characterization of the major hnRNP proteins from Drosophila
RT melanogaster.";
RL J. Cell Biol. 116:257-269(1992).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], ALTERNATIVE SPLICING, FUNCTION,
RP SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RC TISSUE=Ovary;
RX PubMed=7684991; DOI=10.1101/gad.7.6.948;
RA Kelley R.L.;
RT "Initial organization of the Drosophila dorsoventral axis depends on an
RT RNA-binding protein encoded by the squid gene.";
RL Genes Dev. 7:948-960(1993).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Berkeley;
RX PubMed=10731132; DOI=10.1126/science.287.5461.2185;
RA Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D.,
RA Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F.,
RA George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N.,
RA Sutton G.G., Wortman J.R., Yandell M.D., Zhang Q., Chen L.X., Brandon R.C.,
RA Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D., Wan K.H., Doyle C.,
RA Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G., Abril J.F., Agbayani A.,
RA An H.-J., Andrews-Pfannkoch C., Baldwin D., Ballew R.M., Basu A.,
RA Baxendale J., Bayraktaroglu L., Beasley E.M., Beeson K.Y., Benos P.V.,
RA Berman B.P., Bhandari D., Bolshakov S., Borkova D., Botchan M.R., Bouck J.,
RA Brokstein P., Brottier P., Burtis K.C., Busam D.A., Butler H., Cadieu E.,
RA Center A., Chandra I., Cherry J.M., Cawley S., Dahlke C., Davenport L.B.,
RA Davies P., de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I.,
RA Dietz S.M., Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C.,
RA Dunn P., Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S.,
RA Fleischmann W., Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M.,
RA Glasser K., Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M.,
RA Harris N.L., Harvey D.A., Heiman T.J., Hernandez J.R., Houck J., Hostin D.,
RA Houston K.A., Howland T.J., Wei M.-H., Ibegwam C., Jalali M., Kalush F.,
RA Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A., Kimmel B.E., Kodira C.D.,
RA Kraft C.L., Kravitz S., Kulp D., Lai Z., Lasko P., Lei Y., Levitsky A.A.,
RA Li J.H., Li Z., Liang Y., Lin X., Liu X., Mattei B., McIntosh T.C.,
RA McLeod M.P., McPherson D., Merkulov G., Milshina N.V., Mobarry C.,
RA Morris J., Moshrefi A., Mount S.M., Moy M., Murphy B., Murphy L.,
RA Muzny D.M., Nelson D.L., Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R.,
RA Pacleb J.M., Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V.,
RA Reese M.G., Reinert K., Remington K., Saunders R.D.C., Scheeler F.,
RA Shen H., Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T.J.,
RA Spier E., Spradling A.C., Stapleton M., Strong R., Sun E., Svirskas R.,
RA Tector C., Turner R., Venter E., Wang A.H., Wang X., Wang Z.-Y.,
RA Wassarman D.A., Weinstock G.M., Weissenbach J., Williams S.M., Woodage T.,
RA Worley K.C., Wu D., Yang S., Yao Q.A., Ye J., Yeh R.-F., Zaveri J.S.,
RA Zhan M., Zhang G., Zhao Q., Zheng L., Zheng X.H., Zhong F.N., Zhong W.,
RA Zhou X., Zhu S.C., Zhu X., Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M.,
RA Venter J.C.;
RT "The genome sequence of Drosophila melanogaster.";
RL Science 287:2185-2195(2000).
RN [4]
RP GENOME REANNOTATION, AND ALTERNATIVE SPLICING.
RC STRAIN=Berkeley;
RX PubMed=12537572; DOI=10.1186/gb-2002-3-12-research0083;
RA Misra S., Crosby M.A., Mungall C.J., Matthews B.B., Campbell K.S.,
RA Hradecky P., Huang Y., Kaminker J.S., Millburn G.H., Prochnik S.E.,
RA Smith C.D., Tupy J.L., Whitfield E.J., Bayraktaroglu L., Berman B.P.,
RA Bettencourt B.R., Celniker S.E., de Grey A.D.N.J., Drysdale R.A.,
RA Harris N.L., Richter J., Russo S., Schroeder A.J., Shu S.Q., Stapleton M.,
RA Yamada C., Ashburner M., Gelbart W.M., Rubin G.M., Lewis S.E.;
RT "Annotation of the Drosophila melanogaster euchromatic genome: a systematic
RT review.";
RL Genome Biol. 3:RESEARCH0083.1-RESEARCH0083.22(2002).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM A).
RC STRAIN=Berkeley; TISSUE=Embryo, and Head;
RX PubMed=12537569; DOI=10.1186/gb-2002-3-12-research0080;
RA Stapleton M., Carlson J.W., Brokstein P., Yu C., Champe M., George R.A.,
RA Guarin H., Kronmiller B., Pacleb J.M., Park S., Wan K.H., Rubin G.M.,
RA Celniker S.E.;
RT "A Drosophila full-length cDNA resource.";
RL Genome Biol. 3:RESEARCH0080.1-RESEARCH0080.8(2002).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM C).
RC STRAIN=Berkeley; TISSUE=Embryo;
RA Stapleton M., Carlson J.W., Frise E., Kapadia B., Park S., Wan K.H., Yu C.,
RA Celniker S.E.;
RL Submitted (NOV-2006) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 59-102 (ISOFORMS A/B/C).
RX PubMed=8417324; DOI=10.1128/mcb.13.1.174-183.1993;
RA Kim Y.-J., Baker B.S.;
RT "Isolation of RRM-type RNA-binding protein genes and the analysis of their
RT relatedness by using a numerical approach.";
RL Mol. Cell. Biol. 13:174-183(1993).
RN [8]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-148, AND IDENTIFICATION BY
RP MASS SPECTROMETRY.
RX PubMed=17372656; DOI=10.1039/b617545g;
RA Bodenmiller B., Mueller L.N., Pedrioli P.G.A., Pflieger D., Juenger M.A.,
RA Eng J.K., Aebersold R., Tao W.A.;
RT "An integrated chemical, mass spectrometric and computational strategy for
RT (quantitative) phosphoproteomics: application to Drosophila melanogaster
RT Kc167 cells.";
RL Mol. Biosyst. 3:275-286(2007).
CC -!- FUNCTION: This protein is a component of ribonucleosomes. Could be
CC needed to organize a concentration gradient of a dorsalizing morphogen
CC (Dm) originating in the germinal vesicle. At least one of the isoforms
CC is essential in somatic tissues. {ECO:0000269|PubMed:7684991}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:7684991}. Cytoplasm
CC {ECO:0000269|PubMed:7684991}. Note=It is possible that some isoforms
CC are found only in one of these locations.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=4;
CC Comment=Additional isoforms seem to exist.;
CC Name=B; Synonyms=SqdS, HRP40.2;
CC IsoId=Q08473-1; Sequence=Displayed;
CC Name=A; Synonyms=SqdA, HRP40.1;
CC IsoId=Q08473-2; Sequence=VSP_005876;
CC Name=C; Synonyms=SqdB;
CC IsoId=Q08473-3; Sequence=VSP_005877;
CC Name=D;
CC IsoId=Q08473-4; Sequence=VSP_011797;
CC -!- DISRUPTION PHENOTYPE: Female are sterile and lay eggs that display only
CC dorsal structures. {ECO:0000269|PubMed:7684991}.
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DR EMBL; X62637; CAA44503.1; -; mRNA.
DR EMBL; X62638; CAA44504.1; -; mRNA.
DR EMBL; S61875; AAB26988.1; -; Genomic_DNA.
DR EMBL; S62100; AAB26989.1; -; Genomic_DNA.
DR EMBL; S61875; AAB26989.1; JOINED; Genomic_DNA.
DR EMBL; AE014297; AAF54963.2; -; Genomic_DNA.
DR EMBL; AE014297; AAF54964.2; -; Genomic_DNA.
DR EMBL; AE014297; AAN13570.1; -; Genomic_DNA.
DR EMBL; AE014297; AAS65146.1; -; Genomic_DNA.
DR EMBL; AY118501; AAM49870.1; -; mRNA.
DR EMBL; BT001384; AAN71139.1; -; mRNA.
DR EMBL; BT003283; AAO25040.1; -; mRNA.
DR EMBL; BT023832; AAZ86753.1; -; mRNA.
DR EMBL; S51693; AAB24624.1; -; mRNA.
DR PIR; A47369; A47369.
DR PIR; B41732; B41732.
DR PIR; B47369; B47369.
DR PIR; C48110; C48110.
DR RefSeq; NP_001247088.1; NM_001260159.2. [Q08473-3]
DR RefSeq; NP_652209.1; NM_143952.2. [Q08473-3]
DR RefSeq; NP_731825.1; NM_169528.2. [Q08473-1]
DR RefSeq; NP_731826.1; NM_169529.3. [Q08473-2]
DR RefSeq; NP_996203.1; NM_206481.2. [Q08473-4]
DR AlphaFoldDB; Q08473; -.
DR SMR; Q08473; -.
DR BioGRID; 66748; 47.
DR IntAct; Q08473; 28.
DR STRING; 7227.FBpp0082320; -.
DR iPTMnet; Q08473; -.
DR PaxDb; Q08473; -.
DR PRIDE; Q08473; -.
DR DNASU; 41666; -.
DR EnsemblMetazoa; FBtr0082854; FBpp0082319; FBgn0263396. [Q08473-2]
DR EnsemblMetazoa; FBtr0082855; FBpp0082320; FBgn0263396. [Q08473-1]
DR EnsemblMetazoa; FBtr0082856; FBpp0082321; FBgn0263396. [Q08473-3]
DR EnsemblMetazoa; FBtr0082857; FBpp0089309; FBgn0263396. [Q08473-4]
DR EnsemblMetazoa; FBtr0309094; FBpp0301102; FBgn0263396. [Q08473-3]
DR GeneID; 41666; -.
DR KEGG; dme:Dmel_CG16901; -.
DR CTD; 41666; -.
DR FlyBase; FBgn0263396; sqd.
DR VEuPathDB; VectorBase:FBgn0263396; -.
DR eggNOG; KOG4205; Eukaryota.
DR GeneTree; ENSGT00940000175437; -.
DR InParanoid; Q08473; -.
DR OMA; RSFNDGF; -.
DR PhylomeDB; Q08473; -.
DR Reactome; R-DME-450408; AUF1 (hnRNP D0) binds and destabilizes mRNA.
DR Reactome; R-DME-72163; mRNA Splicing - Major Pathway.
DR SignaLink; Q08473; -.
DR BioGRID-ORCS; 41666; 1 hit in 3 CRISPR screens.
DR ChiTaRS; sqd; fly.
DR GenomeRNAi; 41666; -.
DR PRO; PR:Q08473; -.
DR Proteomes; UP000000803; Chromosome 3R.
DR Bgee; FBgn0263396; Expressed in wing disc and 29 other tissues.
DR ExpressionAtlas; Q08473; baseline and differential.
DR Genevisible; Q08473; DM.
DR GO; GO:0071013; C:catalytic step 2 spliceosome; HDA:FlyBase.
DR GO; GO:0000785; C:chromatin; IDA:FlyBase.
DR GO; GO:0005737; C:cytoplasm; TAS:FlyBase.
DR GO; GO:0005654; C:nucleoplasm; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IDA:FlyBase.
DR GO; GO:0035062; C:omega speckle; IDA:FlyBase.
DR GO; GO:0005703; C:polytene chromosome puff; IDA:FlyBase.
DR GO; GO:0071011; C:precatalytic spliceosome; HDA:FlyBase.
DR GO; GO:0003730; F:mRNA 3'-UTR binding; TAS:FlyBase.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0008069; P:dorsal/ventral axis specification, ovarian follicular epithelium; IMP:FlyBase.
DR GO; GO:0009953; P:dorsal/ventral pattern formation; IMP:FlyBase.
DR GO; GO:0007293; P:germarium-derived egg chamber formation; IMP:FlyBase.
DR GO; GO:0008298; P:intracellular mRNA localization; TAS:FlyBase.
DR GO; GO:0006406; P:mRNA export from nucleus; NAS:FlyBase.
DR GO; GO:0000398; P:mRNA splicing, via spliceosome; IC:FlyBase.
DR GO; GO:0033119; P:negative regulation of RNA splicing; IMP:FlyBase.
DR GO; GO:0017148; P:negative regulation of translation; TAS:FlyBase.
DR GO; GO:0000184; P:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; TAS:FlyBase.
DR GO; GO:0007314; P:oocyte anterior/posterior axis specification; IMP:FlyBase.
DR GO; GO:0030720; P:oocyte localization involved in germarium-derived egg chamber formation; IMP:FlyBase.
DR GO; GO:0016325; P:oocyte microtubule cytoskeleton organization; IMP:FlyBase.
DR GO; GO:0048477; P:oogenesis; IMP:FlyBase.
DR GO; GO:0007297; P:ovarian follicle cell migration; IMP:FlyBase.
DR GO; GO:0019094; P:pole plasm mRNA localization; IMP:FlyBase.
DR GO; GO:0045451; P:pole plasm oskar mRNA localization; IEP:FlyBase.
DR GO; GO:0000381; P:regulation of alternative mRNA splicing, via spliceosome; HMP:FlyBase.
DR GO; GO:0010468; P:regulation of gene expression; IBA:GO_Central.
DR GO; GO:0006405; P:RNA export from nucleus; TAS:FlyBase.
DR Gene3D; 3.30.70.330; -; 2.
DR InterPro; IPR012677; Nucleotide-bd_a/b_plait_sf.
DR InterPro; IPR035979; RBD_domain_sf.
DR InterPro; IPR000504; RRM_dom.
DR Pfam; PF00076; RRM_1; 2.
DR SMART; SM00360; RRM; 2.
DR SUPFAM; SSF54928; SSF54928; 2.
DR PROSITE; PS50102; RRM; 2.
PE 1: Evidence at protein level;
KW Alternative splicing; Cytoplasm; Nucleus; Phosphoprotein;
KW Reference proteome; Repeat; Ribonucleoprotein; RNA-binding.
FT CHAIN 1..344
FT /note="RNA-binding protein squid"
FT /id="PRO_0000081959"
FT DOMAIN 56..138
FT /note="RRM 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT DOMAIN 136..213
FT /note="RRM 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT REGION 1..55
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 214..238
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 301..344
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..17
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 32..48
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 148
FT /note="Phosphoserine"
FT /evidence="ECO:0000269|PubMed:17372656"
FT VAR_SEQ 1..166
FT /note="Missing (in isoform D)"
FT /evidence="ECO:0000305"
FT /id="VSP_011797"
FT VAR_SEQ 286..344
FT /note="DGYGYGGGFEGNGYGGGGGGNMGGGRGGPRGGGGPKGGGGFNGGKQRGGGGR
FT QQRHQPY -> GKYNKQQSSAQNNYYNNNTSSNYHQNKNNSNNYQQF (in isoform
FT A)"
FT /evidence="ECO:0000303|PubMed:12537569"
FT /id="VSP_005876"
FT VAR_SEQ 286..321
FT /note="Missing (in isoform C)"
FT /evidence="ECO:0000303|PubMed:1730754, ECO:0000303|Ref.6"
FT /id="VSP_005877"
FT CONFLICT 84
FT /note="S -> N (in Ref. 7; AAB24624)"
FT /evidence="ECO:0000305"
FT CONFLICT 169
FT /note="F -> L (in Ref. 2; AAB26988/AAB26989)"
FT /evidence="ECO:0000305"
FT CONFLICT 305
FT /note="G -> GG (in Ref. 1; CAA44504)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 344 AA; 36184 MW; 68E84791A924EED4 CRC64;
MAENKQVDTE INGEDFTKDV TADGPGSENG DAGAAGSTNG SSDNQSAASG QRDDDRKLFV
GGLSWETTEK ELRDHFGKYG EIESINVKTD PQTGRSRGFA FIVFTNTEAI DKVSAADEHI
INSKKVDPKK AKARHGKIFV GGLTTEISDE EIKTYFGQFG NIVEVEMPFD KQKSQRKGFC
FITFDSEQVV TDLLKTPKQK IAGKEVDVKR ATPKPENQMM GGMRGGPRGG MRGGRGGYGG
RGGYNNQWDG QGSYGGYGGG YGGYGAGGYG DYYAGGYYNG YDYGYDGYGY GGGFEGNGYG
GGGGGNMGGG RGGPRGGGGP KGGGGFNGGK QRGGGGRQQR HQPY
