CAF1P_ORYSJ
ID CAF1P_ORYSJ Reviewed; 701 AA.
AC Q5VMQ5; B7EAM6;
DT 03-APR-2007, integrated into UniProtKB/Swiss-Prot.
DT 07-DEC-2004, sequence version 1.
DT 03-AUG-2022, entry version 88.
DE RecName: Full=CRS2-associated factor 1, chloroplastic;
DE AltName: Full=Chloroplastic group IIA intron splicing facilitator CRS2-associated factor 1;
DE Flags: Precursor;
GN OrderedLocusNames=Os01g0495900, LOC_Os01g31110;
GN ORFNames=OJ1126_G08.1, OsJ_01906 {ECO:0000312|EMBL:EEE54638.1},
GN OSJNBa0029L04.25;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12447438; DOI=10.1038/nature01184;
RA Sasaki T., Matsumoto T., Yamamoto K., Sakata K., Baba T., Katayose Y.,
RA Wu J., Niimura Y., Cheng Z., Nagamura Y., Antonio B.A., Kanamori H.,
RA Hosokawa S., Masukawa M., Arikawa K., Chiden Y., Hayashi M., Okamoto M.,
RA Ando T., Aoki H., Arita K., Hamada M., Harada C., Hijishita S., Honda M.,
RA Ichikawa Y., Idonuma A., Iijima M., Ikeda M., Ikeno M., Ito S., Ito T.,
RA Ito Y., Ito Y., Iwabuchi A., Kamiya K., Karasawa W., Katagiri S.,
RA Kikuta A., Kobayashi N., Kono I., Machita K., Maehara T., Mizuno H.,
RA Mizubayashi T., Mukai Y., Nagasaki H., Nakashima M., Nakama Y.,
RA Nakamichi Y., Nakamura M., Namiki N., Negishi M., Ohta I., Ono N., Saji S.,
RA Sakai K., Shibata M., Shimokawa T., Shomura A., Song J., Takazaki Y.,
RA Terasawa K., Tsuji K., Waki K., Yamagata H., Yamane H., Yoshiki S.,
RA Yoshihara R., Yukawa K., Zhong H., Iwama H., Endo T., Ito H., Hahn J.H.,
RA Kim H.-I., Eun M.-Y., Yano M., Jiang J., Gojobori T.;
RT "The genome sequence and structure of rice chromosome 1.";
RL Nature 420:312-316(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
CC -!- FUNCTION: Required for the splicing of group IIB introns in
CC chloroplasts. Forms splicing particles with CRS2. Interacts with RNA
CC and confers intron specificity of the splicing particles (By
CC similarity). {ECO:0000250}.
CC -!- SUBUNIT: Interacts with CRS2 and RNA. Part of large ribonucleo-protein
CC complexes that include group IIB introns, CRS2 and CAF1 (By
CC similarity). {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast stroma {ECO:0000250}.
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DR EMBL; AP004723; BAD68987.1; -; Genomic_DNA.
DR EMBL; AP006236; BAD69270.1; -; Genomic_DNA.
DR EMBL; AP008207; BAF05036.1; -; Genomic_DNA.
DR EMBL; AP014957; BAS72300.1; -; Genomic_DNA.
DR EMBL; CM000138; EEE54638.1; -; Genomic_DNA.
DR EMBL; AK065221; BAG89423.1; -; mRNA.
DR RefSeq; XP_015621913.1; XM_015766427.1.
DR AlphaFoldDB; Q5VMQ5; -.
DR SMR; Q5VMQ5; -.
DR STRING; 4530.OS01T0495900-01; -.
DR PaxDb; Q5VMQ5; -.
DR PRIDE; Q5VMQ5; -.
DR EnsemblPlants; Os01t0495900-01; Os01t0495900-01; Os01g0495900.
DR GeneID; 4324537; -.
DR Gramene; Os01t0495900-01; Os01t0495900-01; Os01g0495900.
DR KEGG; osa:4324537; -.
DR eggNOG; ENOG502QQC4; Eukaryota.
DR HOGENOM; CLU_012688_0_0_1; -.
DR InParanoid; Q5VMQ5; -.
DR OMA; IVPSYME; -.
DR OrthoDB; 408261at2759; -.
DR Proteomes; UP000000763; Chromosome 1.
DR Proteomes; UP000007752; Chromosome 1.
DR Proteomes; UP000059680; Chromosome 1.
DR Genevisible; Q5VMQ5; OS.
DR GO; GO:0009570; C:chloroplast stroma; IEA:UniProtKB-SubCell.
DR GO; GO:0003729; F:mRNA binding; IEA:EnsemblPlants.
DR GO; GO:0000373; P:Group II intron splicing; IEA:EnsemblPlants.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR Gene3D; 3.30.110.60; -; 2.
DR InterPro; IPR044599; CAF1P_plant.
DR InterPro; IPR001890; RNA-binding_CRM.
DR InterPro; IPR035920; YhbY-like_sf.
DR PANTHER; PTHR46247; PTHR46247; 1.
DR Pfam; PF01985; CRS1_YhbY; 2.
DR SMART; SM01103; CRS1_YhbY; 2.
DR SUPFAM; SSF75471; SSF75471; 2.
DR PROSITE; PS51295; CRM; 2.
PE 2: Evidence at transcript level;
KW Chloroplast; mRNA processing; mRNA splicing; Plastid; Reference proteome;
KW Repeat; Ribonucleoprotein; RNA-binding; Transit peptide.
FT TRANSIT 1..77
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 78..701
FT /note="CRS2-associated factor 1, chloroplastic"
FT /id="PRO_0000283616"
FT DOMAIN 183..279
FT /note="CRM 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00626"
FT DOMAIN 301..397
FT /note="CRM 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00626"
FT REGION 581..603
FT /note="CRS2 binding"
FT /evidence="ECO:0000250"
SQ SEQUENCE 701 AA; 77989 MW; 7FD2575CD2FF8B89 CRC64;
MATSHLTSRS LLVQAQYPIS RLPSNLRLSL SHHKQPAAVA KRRRAPAPSH PAFSSVIRGR
PKKVPIPENG EPAAGVRVTE RGLAYHLDGA PFEFQYSYTE TPRARPVALR EAPFLPFGPE
VTPRPWTGRK PLPKSRKELP EFDSFMLPPP GKKGVKPVQS PGPFLAGTEP RYQAASREEV
LGEPLTKEEV DELVKATLKT KRQLNIGRDG LTHNMLENIH SHWKRKRVCK IKCKGVCTVD
MDNVCQQLEE KVGGKVIHHQ GGVIFLFRGR NYNYRTRPIY PLMLWKPAAP VYPRLVKKIP
DGLTPDEAED MRKRGRQLPP ICKLGKNGVY LNLVKQVREA FEACDLVRVD CSGLNKSDCR
KIGAKLKDLV PCTLLSFEFE HILMWRGNDW KSSLPPLEEN DFKVASDQIL NSKEAGSGSA
LTPIELVNNA TSLKKCNLIE GAEKLEDSMK SSFENGMILG SACGNPGVCN SEGIDGTESS
ADAPIEFSPS NSARDLDPSQ TSTLYCQSSL LDKSENGELI EMYPDRCGNS EQSPDVPEAL
TCLMGSSDEI HELETMRRNC KHLNGSDGVN SDSIVPSYME GILLLFKQAI DSGMALVLNE
NEFADANYVY QKSVAFTKTA PRYLVLRHTP RKSHGTQKTE PAKNVRINKH LEEHKVSDHV
KKKEIVMGGS RMQRNDHARE FLSDVVPQGT LRVDELAKLL A
