RNPC3_DANRE
ID RNPC3_DANRE Reviewed; 505 AA.
AC F1Q8J0; Q29RB3;
DT 31-JAN-2018, integrated into UniProtKB/Swiss-Prot.
DT 03-MAY-2011, sequence version 1.
DT 03-AUG-2022, entry version 71.
DE RecName: Full=RNA-binding region-containing protein 3 {ECO:0000303|PubMed:24516132};
DE AltName: Full=RNA-binding protein 40 {ECO:0000250|UniProtKB:Q96LT9};
GN Name=rnpc3 {ECO:0000303|PubMed:24516132,
GN ECO:0000312|ZFIN:ZDB-GENE-060312-35};
OS Danio rerio (Zebrafish) (Brachydanio rerio).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC Danionidae; Danioninae; Danio.
OX NCBI_TaxID=7955 {ECO:0000312|Proteomes:UP000000437};
RN [1] {ECO:0000312|Proteomes:UP000000437}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen {ECO:0000312|Proteomes:UP000000437};
RX PubMed=23594743; DOI=10.1038/nature12111;
RA Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA Clee C., Oliver K., Clark R., Riddle C., Elliot D., Threadgold G.,
RA Harden G., Ware D., Begum S., Mortimore B., Kerry G., Heath P.,
RA Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S.,
RA Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N.,
RA Lloyd C., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J.,
RA Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J.,
RA Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
RA McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
RA Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
RA Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A.,
RA Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P.,
RA Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J.,
RA Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E.,
RA Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C.,
RA Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C.,
RA Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M.,
RA Oberlander M., Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G.,
RA Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F.,
RA Schuster S.C., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M.,
RA Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M.,
RA de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C.,
RA Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.;
RT "The zebrafish reference genome sequence and its relationship to the human
RT genome.";
RL Nature 496:498-503(2013).
RN [2] {ECO:0000312|EMBL:AAI14289.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (MAR-2006) to the EMBL/GenBank/DDBJ databases.
RN [3] {ECO:0000305}
RP FUNCTION, DEVELOPMENTAL STAGE, AND DISRUPTION PHENOTYPE.
RX PubMed=24516132; DOI=10.1073/pnas.1305536111;
RA Markmiller S., Cloonan N., Lardelli R.M., Doggett K., Keightley M.C.,
RA Boglev Y., Trotter A.J., Ng A.Y., Wilkins S.J., Verkade H., Ober E.A.,
RA Field H.A., Grimmond S.M., Lieschke G.J., Stainier D.Y., Heath J.K.;
RT "Minor class splicing shapes the zebrafish transcriptome during
RT development.";
RL Proc. Natl. Acad. Sci. U.S.A. 111:3062-3067(2014).
CC -!- FUNCTION: Participates in pre-mRNA U12-dependent splicing, performed by
CC the minor spliceosome which removes U12-type introns. U12-type introns
CC comprise less than 1% of all non-coding sequences.
CC {ECO:0000269|PubMed:24516132}.
CC -!- SUBUNIT: Component of the U11/U12 snRNPs that are part of the U12-type
CC spliceosome. {ECO:0000305|PubMed:24516132}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305|PubMed:24516132}.
CC -!- DEVELOPMENTAL STAGE: Widely expressed until 24 hours post-fertilization
CC (hpf), probably due to inheritance of maternal transcripts. Expression
CC becomes restricted to lens, pharyngeal region, liver/pancreas anlage
CC and intestine at 48-72 hpf. Strongly expressed in pancreas and
CC intestine at 96-120 hpf. {ECO:0000269|PubMed:24516132}.
CC -!- DISRUPTION PHENOTYPE: Larval lethal with complete lethality by 10 days
CC post-fertilization. Development of multiple organs is affected. Head,
CC eye, lens, pancreas and liver are smaller than normal, and the swim
CC bladder fails to inflate. The intestinal epithelium also remains thin
CC and unfolded. U12-type introns are retained in mRNAs, whereas excision
CC of U2-type introns is not affected. Assembly of both U12- and U11-
CC containing snRNP complexes may be abnormal. Gene expression levels are
CC broadly impacted; effects are not limited to U12-type intron-containing
CC genes. {ECO:0000269|PubMed:24516132}.
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DR EMBL; CT961047; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC114288; AAI14289.1; -; mRNA.
DR RefSeq; NP_001035019.1; NM_001039930.1.
DR RefSeq; XP_005162876.1; XM_005162819.3.
DR RefSeq; XP_005162877.1; XM_005162820.2.
DR RefSeq; XP_005162878.1; XM_005162821.3.
DR AlphaFoldDB; F1Q8J0; -.
DR SMR; F1Q8J0; -.
DR STRING; 7955.ENSDARP00000106976; -.
DR PaxDb; F1Q8J0; -.
DR Ensembl; ENSDART00000017427; ENSDARP00000019728; ENSDARG00000011247.
DR Ensembl; ENSDART00000183580; ENSDARP00000155505; ENSDARG00000011247.
DR Ensembl; ENSDART00000185020; ENSDARP00000155778; ENSDARG00000011247.
DR GeneID; 565672; -.
DR KEGG; dre:565672; -.
DR CTD; 55599; -.
DR ZFIN; ZDB-GENE-060312-35; rnpc3.
DR eggNOG; KOG4206; Eukaryota.
DR GeneTree; ENSGT00530000063786; -.
DR HOGENOM; CLU_039888_2_1_1; -.
DR InParanoid; F1Q8J0; -.
DR OMA; RPINTKK; -.
DR OrthoDB; 1080666at2759; -.
DR PhylomeDB; F1Q8J0; -.
DR TreeFam; TF324298; -.
DR Reactome; R-DRE-72165; mRNA Splicing - Minor Pathway.
DR PRO; PR:F1Q8J0; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 24.
DR Bgee; ENSDARG00000011247; Expressed in pharyngeal gill and 37 other tissues.
DR ExpressionAtlas; F1Q8J0; baseline.
DR GO; GO:0005689; C:U12-type spliceosomal complex; IBA:GO_Central.
DR GO; GO:0097157; F:pre-mRNA intronic binding; IBA:GO_Central.
DR GO; GO:0030626; F:U12 snRNA binding; IBA:GO_Central.
DR GO; GO:0048565; P:digestive tract development; IMP:ZFIN.
DR GO; GO:0001889; P:liver development; IMP:ZFIN.
DR GO; GO:0000398; P:mRNA splicing, via spliceosome; IMP:ZFIN.
DR GO; GO:0031016; P:pancreas development; IMP:ZFIN.
DR CDD; cd12238; RRM1_RBM40_like; 1.
DR Gene3D; 3.30.70.330; -; 2.
DR InterPro; IPR012677; Nucleotide-bd_a/b_plait_sf.
DR InterPro; IPR035979; RBD_domain_sf.
DR InterPro; IPR034147; RBM40_RRM1.
DR InterPro; IPR045164; RBM41/RNPC3.
DR InterPro; IPR000504; RRM_dom.
DR PANTHER; PTHR16105; PTHR16105; 1.
DR Pfam; PF00076; RRM_1; 2.
DR SMART; SM00360; RRM; 2.
DR SUPFAM; SSF54928; SSF54928; 2.
DR PROSITE; PS50102; RRM; 2.
PE 2: Evidence at transcript level;
KW mRNA processing; mRNA splicing; Nucleus; Reference proteome; Repeat;
KW RNA-binding; Spliceosome.
FT CHAIN 1..505
FT /note="RNA-binding region-containing protein 3"
FT /id="PRO_0000442796"
FT DOMAIN 15..90
FT /note="RRM 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT DOMAIN 405..488
FT /note="RRM 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT REGION 96..123
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 193..236
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 354..374
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 486..505
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 193..215
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 96
FT /note="I -> V (in Ref. 2; AAI14289)"
FT /evidence="ECO:0000305"
FT CONFLICT 231
FT /note="E -> G (in Ref. 2; AAI14289)"
FT /evidence="ECO:0000305"
FT CONFLICT 258
FT /note="T -> I (in Ref. 2; AAI14289)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 505 AA; 56943 MW; 47DCE302AE06E006 CRC64;
MAETDEADVQ TKKSKTLIIR HLPRELSRDE KEDLLKYFGA SSVRVLSEKG PLKHMAFATF
SSETSASKAL NRLHQLRILG RTLVVEFAKD QDSASILKDP PVSDRTAAAV AEKEKKEKQQ
PSVPLMDTSI APSLGLKFQT NPTLKYLYPP PSSGILTNIT HTLLSVPKFY VQVLHLMNKM
NLPSPFRPVT APPPMFEMPS GPLPPPFPPE NPPLPEHDES GSEEESEYES EDEEERERMI
RLMGLVNQPC KRPLRTKTSS KRKKPKLKDL LFIPKPDSHG PSGPVLQPAD VFEQPHALGQ
KKIEFHISSE VSAILEGPGQ NQKLPFADAT EDTPDMEVSA QETTEGFGKI YPSAQVPRQE
EEQEEDEDIP SEFISRRELE RGRLSRDEIK KLSVFKKYEP GEPTCRLYVK NVAKHVEEKD
LKFIYGRYID ISSEEERNMF DIVLMKEGRM KGQAFIGLPS ERSAQKALKE TNGYVLKDKP
LVVQFARSAK PKQESADPKK GGRKH
