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RNA-binding protein squid (Heterogeneous nuclear ribonucleoprotein 40) (HNRNP 40)

 SQD_DROME               Reviewed;         344 AA.
Q08473; Q26273; Q3ZAN7; Q8IH71; Q8INH1; Q8MSY1; Q9VFT5; Q9VFT6;
01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
25-OCT-2004, sequence version 3.
05-DEC-2018, entry version 158.
RecName: Full=RNA-binding protein squid;
AltName: Full=Heterogeneous nuclear ribonucleoprotein 40;
Short=HNRNP 40;
Name=sqd; Synonyms=hrp40; ORFNames=CG16901;
Drosophila melanogaster (Fruit fly).
Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta;
Pterygota; Neoptera; Holometabola; Diptera; Brachycera; Muscomorpha;
Ephydroidea; Drosophilidae; Drosophila; Sophophora.
NCBI_TaxID=7227;
[1]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS B AND C).
STRAIN=Canton-S; TISSUE=Embryo;
PubMed=1730754; DOI=10.1083/jcb.116.2.257;
Matunis E.L., Matunis M.J., Dreyfuss G.;
"Characterization of the major hnRNP proteins from Drosophila
melanogaster.";
J. Cell Biol. 116:257-269(1992).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], ALTERNATIVE SPLICING, FUNCTION,
SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
TISSUE=Ovary;
PubMed=7684991; DOI=10.1101/gad.7.6.948;
Kelley R.L.;
"Initial organization of the Drosophila dorsoventral axis depends on
an RNA-binding protein encoded by the squid gene.";
Genes Dev. 7:948-960(1993).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=Berkeley;
PubMed=10731132; DOI=10.1126/science.287.5461.2185;
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.;
"The genome sequence of Drosophila melanogaster.";
Science 287:2185-2195(2000).
[4]
GENOME REANNOTATION, AND ALTERNATIVE SPLICING.
STRAIN=Berkeley;
PubMed=12537572; DOI=10.1186/gb-2002-3-12-research0083;
Misra S., Crosby M.A., Mungall C.J., Matthews B.B., Campbell K.S.,
Hradecky P., Huang Y., Kaminker J.S., Millburn G.H., Prochnik S.E.,
Smith C.D., Tupy J.L., Whitfield E.J., Bayraktaroglu L., Berman B.P.,
Bettencourt B.R., Celniker S.E., de Grey A.D.N.J., Drysdale R.A.,
Harris N.L., Richter J., Russo S., Schroeder A.J., Shu S.Q.,
Stapleton M., Yamada C., Ashburner M., Gelbart W.M., Rubin G.M.,
Lewis S.E.;
"Annotation of the Drosophila melanogaster euchromatic genome: a
systematic review.";
Genome Biol. 3:RESEARCH0083.1-RESEARCH0083.22(2002).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM A).
STRAIN=Berkeley; TISSUE=Embryo, and Head;
PubMed=12537569; DOI=10.1186/gb-2002-3-12-research0080;
Stapleton M., Carlson J.W., Brokstein P., Yu C., Champe M.,
George R.A., Guarin H., Kronmiller B., Pacleb J.M., Park S., Wan K.H.,
Rubin G.M., Celniker S.E.;
"A Drosophila full-length cDNA resource.";
Genome Biol. 3:RESEARCH0080.1-RESEARCH0080.8(2002).
[6]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM C).
STRAIN=Berkeley; TISSUE=Embryo;
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.
[7]
NUCLEOTIDE SEQUENCE [MRNA] OF 59-102 (ISOFORMS A/B/C).
PubMed=8417324; DOI=10.1128/MCB.13.1.174;
Kim Y.-J., Baker B.S.;
"Isolation of RRM-type RNA-binding protein genes and the analysis of
their relatedness by using a numerical approach.";
Mol. Cell. Biol. 13:174-183(1993).
[8]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-148, AND IDENTIFICATION
BY MASS SPECTROMETRY.
PubMed=17372656; DOI=10.1039/b617545g;
Bodenmiller B., Mueller L.N., Pedrioli P.G.A., Pflieger D.,
Juenger M.A., Eng J.K., Aebersold R., Tao W.A.;
"An integrated chemical, mass spectrometric and computational strategy
for (quantitative) phosphoproteomics: application to Drosophila
melanogaster Kc167 cells.";
Mol. Biosyst. 3:275-286(2007).
-!- FUNCTION: 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.
{ECO:0000269|PubMed:7684991}.
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:7684991}.
Cytoplasm {ECO:0000269|PubMed:7684991}. Note=It is possible that
some isoforms are found only in one of these locations.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=4;
Comment=Additional isoforms seem to exist.;
Name=B; Synonyms=SqdS, HRP40.2;
IsoId=Q08473-1; Sequence=Displayed;
Name=A; Synonyms=SqdA, HRP40.1;
IsoId=Q08473-2; Sequence=VSP_005876;
Name=C; Synonyms=SqdB;
IsoId=Q08473-3; Sequence=VSP_005877;
Name=D;
IsoId=Q08473-4; Sequence=VSP_011797;
Note=No experimental confirmation available.;
-!- DISRUPTION PHENOTYPE: Female are sterile and lay eggs that display
only dorsal structures. {ECO:0000269|PubMed:7684991}.
-----------------------------------------------------------------------
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-----------------------------------------------------------------------
EMBL; X62637; CAA44503.1; -; mRNA.
EMBL; X62638; CAA44504.1; -; mRNA.
EMBL; S61875; AAB26988.1; -; Genomic_DNA.
EMBL; S62100; AAB26989.1; -; Genomic_DNA.
EMBL; S61875; AAB26989.1; JOINED; Genomic_DNA.
EMBL; AE014297; AAF54963.2; -; Genomic_DNA.
EMBL; AE014297; AAF54964.2; -; Genomic_DNA.
EMBL; AE014297; AAN13570.1; -; Genomic_DNA.
EMBL; AE014297; AAS65146.1; -; Genomic_DNA.
EMBL; AY118501; AAM49870.1; -; mRNA.
EMBL; BT001384; AAN71139.1; -; mRNA.
EMBL; BT003283; AAO25040.1; -; mRNA.
EMBL; BT023832; AAZ86753.1; -; mRNA.
EMBL; S51693; AAB24624.1; -; mRNA.
PIR; A47369; A47369.
PIR; B41732; B41732.
PIR; B47369; B47369.
PIR; C48110; C48110.
RefSeq; NP_001247088.1; NM_001260159.2. [Q08473-3]
RefSeq; NP_652209.1; NM_143952.2. [Q08473-3]
RefSeq; NP_731825.1; NM_169528.2. [Q08473-1]
RefSeq; NP_731826.1; NM_169529.3. [Q08473-2]
RefSeq; NP_996203.1; NM_206481.2. [Q08473-4]
UniGene; Dm.7189; -.
ProteinModelPortal; Q08473; -.
SMR; Q08473; -.
BioGrid; 66748; 42.
IntAct; Q08473; 28.
STRING; 7227.FBpp0082320; -.
iPTMnet; Q08473; -.
PaxDb; Q08473; -.
PRIDE; Q08473; -.
EnsemblMetazoa; FBtr0082854; FBpp0082319; FBgn0263396. [Q08473-2]
EnsemblMetazoa; FBtr0082855; FBpp0082320; FBgn0263396. [Q08473-1]
EnsemblMetazoa; FBtr0082856; FBpp0082321; FBgn0263396. [Q08473-3]
EnsemblMetazoa; FBtr0082857; FBpp0089309; FBgn0263396. [Q08473-4]
EnsemblMetazoa; FBtr0309094; FBpp0301102; FBgn0263396. [Q08473-3]
GeneID; 41666; -.
KEGG; dme:Dmel_CG16901; -.
CTD; 41666; -.
FlyBase; FBgn0263396; sqd.
eggNOG; KOG0118; Eukaryota.
eggNOG; COG0724; LUCA.
GeneTree; ENSGT00940000175437; -.
InParanoid; Q08473; -.
KO; K03102; -.
OMA; GPGYTDY; -.
OrthoDB; EOG091G1CPI; -.
PhylomeDB; Q08473; -.
Reactome; R-DME-450408; AUF1 (hnRNP D0) binds and destabilizes mRNA.
Reactome; R-DME-72163; mRNA Splicing - Major Pathway.
Reactome; R-DME-72203; Processing of Capped Intron-Containing Pre-mRNA.
ChiTaRS; sqd; fly.
GenomeRNAi; 41666; -.
PRO; PR:Q08473; -.
Proteomes; UP000000803; Chromosome 3R.
Bgee; FBgn0263396; Expressed in 36 organ(s), highest expression level in material anatomical entity.
ExpressionAtlas; Q08473; baseline and differential.
Genevisible; Q08473; DM.
GO; GO:0071013; C:catalytic step 2 spliceosome; HDA:FlyBase.
GO; GO:0000785; C:chromatin; IDA:FlyBase.
GO; GO:0005737; C:cytoplasm; TAS:FlyBase.
GO; GO:0005654; C:nucleoplasm; IBA:GO_Central.
GO; GO:0005634; C:nucleus; IDA:FlyBase.
GO; GO:0035062; C:omega speckle; IDA:FlyBase.
GO; GO:0005703; C:polytene chromosome puff; IDA:FlyBase.
GO; GO:0071011; C:precatalytic spliceosome; HDA:FlyBase.
GO; GO:1990904; C:ribonucleoprotein complex; IBA:GO_Central.
GO; GO:0003680; F:AT DNA binding; IBA:GO_Central.
GO; GO:0035925; F:mRNA 3'-UTR AU-rich region binding; IBA:GO_Central.
GO; GO:0003730; F:mRNA 3'-UTR binding; TAS:FlyBase.
GO; GO:0003729; F:mRNA binding; ISS:FlyBase.
GO; GO:0003723; F:RNA binding; IBA:GO_Central.
GO; GO:0043565; F:sequence-specific DNA binding; IBA:GO_Central.
GO; GO:1990837; F:sequence-specific double-stranded DNA binding; IBA:GO_Central.
GO; GO:0008069; P:dorsal/ventral axis specification, ovarian follicular epithelium; IMP:FlyBase.
GO; GO:0009953; P:dorsal/ventral pattern formation; IMP:FlyBase.
GO; GO:0007293; P:germarium-derived egg chamber formation; IMP:FlyBase.
GO; GO:0008298; P:intracellular mRNA localization; TAS:FlyBase.
GO; GO:0006406; P:mRNA export from nucleus; NAS:FlyBase.
GO; GO:0000398; P:mRNA splicing, via spliceosome; IC:FlyBase.
GO; GO:0033119; P:negative regulation of RNA splicing; IMP:FlyBase.
GO; GO:0017148; P:negative regulation of translation; TAS:FlyBase.
GO; GO:0000184; P:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; TAS:FlyBase.
GO; GO:0007314; P:oocyte anterior/posterior axis specification; IMP:FlyBase.
GO; GO:0030720; P:oocyte localization involved in germarium-derived egg chamber formation; IMP:FlyBase.
GO; GO:0016325; P:oocyte microtubule cytoskeleton organization; IMP:FlyBase.
GO; GO:0048477; P:oogenesis; IMP:FlyBase.
GO; GO:0007297; P:ovarian follicle cell migration; IMP:FlyBase.
GO; GO:0019094; P:pole plasm mRNA localization; IMP:FlyBase.
GO; GO:0045451; P:pole plasm oskar mRNA localization; IEP:FlyBase.
GO; GO:0000381; P:regulation of alternative mRNA splicing, via spliceosome; HMP:FlyBase.
GO; GO:0006405; P:RNA export from nucleus; TAS:FlyBase.
Gene3D; 3.30.70.330; -; 2.
InterPro; IPR012677; Nucleotide-bd_a/b_plait_sf.
InterPro; IPR035979; RBD_domain_sf.
InterPro; IPR000504; RRM_dom.
Pfam; PF00076; RRM_1; 2.
SMART; SM00360; RRM; 2.
SUPFAM; SSF54928; SSF54928; 2.
PROSITE; PS50102; RRM; 2.
1: Evidence at protein level;
Alternative splicing; Complete proteome; Cytoplasm; Nucleus;
Phosphoprotein; Reference proteome; Repeat; Ribonucleoprotein;
RNA-binding.
CHAIN 1 344 RNA-binding protein squid.
/FTId=PRO_0000081959.
DOMAIN 56 138 RRM 1. {ECO:0000255|PROSITE-
ProRule:PRU00176}.
DOMAIN 136 213 RRM 2. {ECO:0000255|PROSITE-
ProRule:PRU00176}.
COMPBIAS 221 337 Gly-rich.
MOD_RES 148 148 Phosphoserine.
{ECO:0000269|PubMed:17372656}.
VAR_SEQ 1 166 Missing (in isoform D). {ECO:0000305}.
/FTId=VSP_011797.
VAR_SEQ 286 344 DGYGYGGGFEGNGYGGGGGGNMGGGRGGPRGGGGPKGGGGF
NGGKQRGGGGRQQRHQPY -> GKYNKQQSSAQNNYYNNNT
SSNYHQNKNNSNNYQQF (in isoform A).
{ECO:0000303|PubMed:12537569}.
/FTId=VSP_005876.
VAR_SEQ 286 321 Missing (in isoform C).
{ECO:0000303|PubMed:1730754,
ECO:0000303|Ref.6}.
/FTId=VSP_005877.
CONFLICT 84 84 S -> N (in Ref. 7; AAB24624).
{ECO:0000305}.
CONFLICT 169 169 F -> L (in Ref. 2; AAB26988/AAB26989).
{ECO:0000305}.
CONFLICT 305 305 G -> GG (in Ref. 1; CAA44504).
{ECO:0000305}.
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


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