2024-05-03 08:45:35, GGRNA.v2 : RefSeq release 222 (Jan, 2024)
LOCUS NM_001422728 4791 bp mRNA linear PLN 22-JUN-2023 DEFINITION Oryza sativa Japonica Group endoribonuclease Dicer homolog 2b-like (LOC4346696), mRNA. ACCESSION NM_001422728 XM_015756031 VERSION NM_001422728.1 KEYWORDS RefSeq. SOURCE Oryza sativa Japonica Group (Japanese rice) ORGANISM Oryza sativa Japonica Group Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa. REFERENCE 1 (bases 1 to 4791) AUTHORS Kikuchi S, Satoh K, Nagata T, Kawagashira N, Doi K, Kishimoto N, Yazaki J, Ishikawa M, Yamada H, Ooka H, Hotta I, Kojima K, Namiki T, Ohneda E, Yahagi W, Suzuki K, Li CJ, Ohtsuki K, Shishiki T, Otomo Y, Murakami K, Iida Y, Sugano S, Fujimura T, Suzuki Y, Tsunoda Y, Kurosaki T, Kodama T, Masuda H, Kobayashi M, Xie Q, Lu M, Narikawa R, Sugiyama A, Mizuno K, Yokomizo S, Niikura J, Ikeda R, Ishibiki J, Kawamata M, Yoshimura A, Miura J, Kusumegi T, Oka M, Ryu R, Ueda M, Matsubara K, Kawai J, Carninci P, Adachi J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Hayatsu N, Imotani K, Ishii Y, Itoh M, Kagawa I, Kondo S, Konno H, Miyazaki A, Osato N, Ota Y, Saito R, Sasaki D, Sato K, Shibata K, Shinagawa A, Shiraki T, Yoshino M, Hayashizaki Y and Yasunishi A. CONSRTM Rice Full-Length cDNA Consortium; National Institute of Agrobiological Sciences Rice Full-Length cDNA Project Team; Foundation of Advancement of International Science Genome Sequencing & Analysis Group; RIKEN TITLE Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice JOURNAL Science 301 (5631), 376-379 (2003) PUBMED 12869764 REMARK Erratum:[Science. 2003 Sep;301(5641):1849] COMMENT VALIDATED REFSEQ: This record has undergone validation or preliminary review. The reference sequence was derived from AP014965.1. On Jun 22, 2023 this sequence version replaced XM_015756031.2. ##Evidence-Data-START## RNAseq introns :: mixed sample support SAMD00008650, SAMD00020310 [ECO:0006172] ##Evidence-Data-END## PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP 1-386 AP014965.1 8660840-8661225 c 387-816 AP014965.1 8660296-8660725 c 817-904 AP014965.1 8659932-8660019 c 905-966 AP014965.1 8659790-8659851 c 967-1107 AP014965.1 8659529-8659669 c 1108-1233 AP014965.1 8658345-8658470 c 1234-1366 AP014965.1 8658137-8658269 c 1367-1457 AP014965.1 8657707-8657797 c 1458-1650 AP014965.1 8655959-8656151 c 1651-1811 AP014965.1 8655685-8655845 c 1812-2170 AP014965.1 8654703-8655061 c 2171-2439 AP014965.1 8653920-8654188 c 2440-2858 AP014965.1 8653407-8653825 c 2859-2962 AP014965.1 8653204-8653307 c 2963-3159 AP014965.1 8652038-8652234 c 3160-3369 AP014965.1 8651042-8651251 c 3370-3783 AP014965.1 8649740-8650153 c 3784-4053 AP014965.1 8647924-8648193 c 4054-4791 AP014965.1 8646683-8647420 c FEATURES Location/Qualifiers source 1..4791 /organism="Oryza sativa Japonica Group" /mol_type="mRNA" /db_xref="taxon:39947" /chromosome="9" /map="9" gene 1..4791 /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /note="endoribonuclease Dicer homolog 2b-like" /db_xref="GeneID:4346696" exon 1..386 /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /inference="alignment:Splign:2.1.0" misc_feature 70..72 /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /note="upstream in-frame stop codon" CDS 280..4413 /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /EC_number="3.1.26.-" /note="Os09g0315050; CAF protein-like; OSJNBb0079G12.35-1; OSJNBa0057D11.8-1; Dicer-like protein 2b; LOC_Os09g14610" /codon_start=1 /product="endoribonuclease Dicer homolog 2b" /protein_id="NP_001409657.1" /db_xref="GeneID:4346696" /translation="
MGGPLTAAGGRGDGGAKAVEPLRPPPPPDPKTMARWYQLEALERAVRGNTLAFLETGSGKTLIAVMLLRAYAHRVRRPDSRRFAVFLVPTVVLVGQQARVVEQHTDLVVKQFCGEMGVDFWDAATWRSQLEDGEVLVMTPQILLDNLRHSFFRLQDIALLIFDECHHARGNTPYACIFKEFYHPQLNSSASDPLPRIFGMSASLIYSKDLNQHNYSKQISEIENLMNSKVYTVDSESALSEYIPFASTKIVHFDDSNISSELHANILSCLNRLTKKHIEALDRKLHGSSLENAKQRISKLHRTFVYCLYNLGVWLAAKAAEVQSYEENSLSFWGETLDKNVEGFIRNYSEEVHRELSCFLKNGHIGEKFPADSQDGILTPKVHCLIRTLLQYRHMQDLRCIVFVQRVITSIVLEPLLSSIHQMSGWNVKHMAGSRPGLLSQSRKNHTEIVESFRKGKVHIIIATQILEEGLDVPSCNLVIRFDPSATVCSFIQSRGRARMENSDYLLLVGRGDVEAHTNAKKFLASGQIMREESLRLGSISCQPLENTLCEDTYYRVESTPAFDIDKASGTCTLHLPKSSPVQTVNVEGEGSILKETVCLKACQELHAIGALTDSLLPELDVPCDEEPDIVVENKIEQPSYFPEEFVDNWRSFSRLGIYYCYKISLEGCPKTASPTDILLALKCDLGSDFTSSSFKLPGGQDNASVTMKYVGIIHLNQEQVIIARRFQTTILSFLIGDDHLEVSNGIKYFHEMQVPIGVVYLLLPLVSGRIDWCSMKFSSSPIYEANNKHMTHCHSCRDIDLLQTKDGPFCRCILKNSIVCTPHNNIFYVISGFLDLDANSRLPQHDGTVVTYKDYFKTRHGLTLTFENQPLLAGSKHVKVRNFLHNYYYKKEKEPGDRYSVELPPELCRIIMSPVSANNLHIFSYVPSIMFRIQCMLLSVKLKVQLGPTVQQFDVPVLKILEALTTKKCQEEFSQESLETLGDSFLKYVTTRHLFSEYRLQHEGILTKMKKNLISNAALCQLACSSNLVGYIHAEEFNPRDWIIPCLDYDERGNKKISFLAPNGMYSQRKMSIKSKRIADSVEALIGAYLSTAGEKAAFLLMKSLGMNIEFHTEIPVERKISMKAEEFIDVRSLEGMLGYKFNDSLLLLEALTHGSYQTSGPTSCYQRLEFLGDAILDHLFTEYYYSKYPDCTPELLTDLRSASVNNNCYAHAAVKSGLNKHILHSSSELHRKMSYYLGQSFTGPSYGWEAGIGLPKVLGDVIESIAGAIYLDSKCDKEVVWRSMKRLLEPLATPETIEPDPVKGLQEFCDRRSFKITYEKNHVDGVSSVIARVKAGETTYSATKSGPCKLAKKLASKAVLKDLIAGHKDTEAAAV"
misc_feature 280..369 /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /note="propagated from UniProtKB/Swiss-Prot (Q69LX2.2); Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite" misc_feature 379..984 /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /note="DEXH-box helicase domain of endoribonuclease Dicer; Region: DEXHc_dicer; cd18034" /db_xref="CDD:350792" misc_feature order(379..384,391..393,442..465,580..582,769..771, 883..885) /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /note="ATP binding site [chemical binding]; other site" /db_xref="CDD:350792" misc_feature order(544..549,616..621,694..696,700..705,712..714, 787..795) /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /note="nucleic acid binding site [nucleotide binding]; other site" /db_xref="CDD:350792" misc_feature 766..777 /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /note="propagated from UniProtKB/Swiss-Prot (Q69LX2.2); Region: DECH box. /evidence=ECO:0000250" misc_feature 1408..1806 /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /note="C-terminal helicase domain of the DEAD-like helicases; Region: DEAD-like_helicase_C; cl38915" /db_xref="CDD:365791" misc_feature 1768..1770 /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /note="ATP binding site [chemical binding]; other site" /db_xref="CDD:350171" misc_feature 1921..2133 /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /note="Dicer dimerization domain; Region: Dicer_dimer; pfam03368" /db_xref="CDD:427264" misc_feature 2635..3024 /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /note="PAZ domain, CAF_like subfamily. CAF (for carpel factory) is a plant homolog of Dicer. CAF has been implicated in flower morphogenesis and in early Arabidopsis development and might function through posttranscriptional regulation of specific mRNA...; Region: PAZ_CAF_like; cd02844" /db_xref="CDD:239210" misc_feature order(2764..2766,2836..2838,2848..2850,2902..2904, 2983..2985,2989..2991) /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /note="nucleic acid-binding interface [nucleotide binding]; other site" /db_xref="CDD:239210" misc_feature 3160..3624 /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /note="Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional...; Region: RIBOc; cd00593" /db_xref="CDD:238333" misc_feature order(3208..3213,3220..3225,3232..3234,3241..3246, 3253..3258,3262..3270,3298..3300,3550..3552,3577..3579) /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /note="dimerization interface [polypeptide binding]; other site" /db_xref="CDD:238333" misc_feature order(3208..3210,3217..3219,3229..3231,3520..3522, 3529..3531) /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /note="active site" /db_xref="CDD:238333" misc_feature order(3217..3219,3520..3522,3529..3531) /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /note="metal binding site [ion binding]; metal-binding site" /db_xref="CDD:238333" misc_feature 3721..4173 /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /note="Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional...; Region: RIBOc; cd00593" /db_xref="CDD:238333" misc_feature order(3781..3786,3793..3798,3805..3807,3814..3819, 3826..3831,3835..3843,3871..3873,4093..4095,4126..4128) /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /note="dimerization interface [polypeptide binding]; other site" /db_xref="CDD:238333" misc_feature order(3781..3783,3790..3792,3802..3804,4063..4065, 4072..4074) /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /note="active site" /db_xref="CDD:238333" misc_feature order(3790..3792,4063..4065,4072..4074) /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /note="metal binding site [ion binding]; metal-binding site" /db_xref="CDD:238333" misc_feature 4051..4053 /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /note="Important for activity. /evidence=ECO:0000250; propagated from UniProtKB/Swiss-Prot (Q69LX2.2); other site" misc_feature 4186..4383 /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /note="double-stranded RNA binding motif (DSRM) superfamily; Region: DSRM_SF; cl00054" /db_xref="CDD:444671" misc_feature order(4201..4206,4210..4212,4270..4272,4327..4332, 4339..4341) /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /note="RNA binding site [nucleotide binding]; other site" /db_xref="CDD:380679" exon 387..816 /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /inference="alignment:Splign:2.1.0" exon 817..904 /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /inference="alignment:Splign:2.1.0" exon 905..966 /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /inference="alignment:Splign:2.1.0" exon 967..1107 /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /inference="alignment:Splign:2.1.0" exon 1108..1233 /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /inference="alignment:Splign:2.1.0" exon 1234..1366 /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /inference="alignment:Splign:2.1.0" exon 1367..1457 /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /inference="alignment:Splign:2.1.0" exon 1458..1650 /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /inference="alignment:Splign:2.1.0" exon 1651..1811 /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /inference="alignment:Splign:2.1.0" exon 1812..2170 /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /inference="alignment:Splign:2.1.0" exon 2171..2439 /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /inference="alignment:Splign:2.1.0" exon 2440..2858 /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /inference="alignment:Splign:2.1.0" exon 2859..2962 /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /inference="alignment:Splign:2.1.0" exon 2963..3159 /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /inference="alignment:Splign:2.1.0" exon 3160..3369 /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /inference="alignment:Splign:2.1.0" exon 3370..3783 /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /inference="alignment:Splign:2.1.0" exon 3784..4053 /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /inference="alignment:Splign:2.1.0" exon 4054..4791 /gene="LOC4346696" /gene_synonym="DCL2B; OsDCL2b" /inference="alignment:Splign:2.1.0" ORIGIN
gcgaatccttcgccccgaagcctcccactaccaattggtcccatccctcctcctcccgcttcccccccataagatcatttatctctcgtcattgttcgagcccaacacgcgcgcgcgcgactcgtaggaattcggttcggattcgtgcgtgcaccgaaggaggcggaggcggaggcggcccaagcgtcggcgccacctcactctcccacccccatcccgccgcctcccccgattcctcccccaaacccctcctcctcctccgccgccgctgccgtcgccatgggtggccccctcaccgccgccggaggtcgaggagatgggggcgccaaggcggtggaaccgctccggcctccgccgccgcccgacccgaagacaatggccagatggtaccagctggaggcgctggagcgggcggtgcgggggaacaccctggcgttcctggagaccgggagcgggaagacgctcatcgcggtgatgctgctccgggcgtacgcgcaccgcgtgcggaggccggactcgcgccgcttcgccgtcttcctcgtccccaccgtcgtcctcgtgggccagcaggcgcgcgtcgtcgagcagcacaccgacctcgtcgtcaagcagttctgcggcgagatgggggtcgacttctgggacgccgccacctggcgatcccaactggaggacggcgaggtgctcgtcatgacgccgcagatcctgctcgacaacctccgccacagcttcttccgcctccaggacatcgcgctgctcatcttcgacgagtgtcaccacgccaggggcaatacaccgtacgcctgcattttcaaggaattttatcacccccagttgaattctagtgcgtcagaccctctgccaaggatatttgggatgtctgcttcgctcatttattcaaaagatttgaatcagcacaattattcaaagcaaatttctgagattgagaatctcatgaattccaaggtgtacactgttgatagtgaatcagctttgtcggagtacataccatttgcttctacaaaaatagtgcactttgacgattccaacatttcatctgagctgcatgccaatattctcagttgtttgaatagattgacaaaaaagcatatagaagctctggacagaaaactacatggttcatctctggaaaacgctaagcaaaggatatcaaaattgcatcgtacatttgtatattgtttatataatctaggagtatggctggcagcaaaggctgctgaggtacaatcatacgaggaaaacagcctatccttctggggtgaaacattggataaaaatgttgagggcttcattagaaactacagcgaagaagtacatagagaactttcatgtttcttgaagaatggtcatattggtgaaaaatttccagctgattcgcaagatgggatattgacacccaaagttcattgccttattcgaactcttctgcagtacaggcatatgcaagacttaagatgcattgtgtttgttcagagagttatcacaagcatagtattagagcccctactttcatctattcatcaaatgtctgggtggaatgttaagcacatggcaggaagccgtcctggtttgctatctcagagcaggaaaaatcatacagaaattgttgaatcttttcgaaaaggaaaggtacatataattattgccacacaaattttggaggagggtttagatgtgccaagttgtaacttggtaattcgctttgatccatcagcaacagtatgcagctttatacagtcccgtggtcgagctaggatggaaaactctgactatcttttacttgtcggaaggggggatgtggaagctcatactaatgcaaagaagtttctcgcaagtgggcaaataatgcgggaggaatctctgagattgggatcaatttcttgtcaaccacttgagaacaccttgtgcgaggatacctattaccgtgtcgagtcaactccagcgttcgatatagacaaggcatctggcacatgcactctgcatcttcctaagagcagtcctgtgcagacagttaatgtagaaggagaaggttctattctcaaggagacagtttgtcttaaggcctgccaagaactacatgccattggtgcactcacagattctcttttaccagaattagatgttccatgtgatgaagaacctgacatcgttgttgagaacaaaattgagcagccttcttactttccagaagaatttgtggataattggcgctccttttctcgtcttggcatatattattgctataagatctcattggaaggatgtcccaaaacagcttctccaactgacatactgttagctttgaagtgtgatttgggatctgactttacttctagctcatttaaattgccaggtgggcaagacaatgctagtgttaccatgaaatatgttggcatcatccatctcaatcaagaacaggtaattattgctagaagatttcagacaactattctttcgtttcttattggtgatgaccatttggaggttagcaatggtattaaatacttccatgagatgcaagtgcctattggagtagtctatctacttctgcctttagtttctggcagaattgattggtgcagtatgaagttctcatcctcaccaatatatgaagctaacaacaaacatatgacacattgccattcttgtagagatattgatttactgcagacaaaagatggtcctttctgcaggtgcatccttaaaaattccattgtgtgtacccctcataataacatcttttatgttattagtgggtttcttgacttagatgcaaattcccgtttgcctcaacatgatgggactgttgttacctacaaagattattttaagactaggcatggtcttactttgacttttgaaaatcagccgctcttggctggcagtaaacatgtgaaagtgcggaacttcctccacaactactactataaaaaagaaaaagaacctggtgatagatatagtgttgagttgccacctgaactctgcagaattatcatgtcaccagtgtccgccaataatttgcacatcttctcatatgttccttccataatgttccgcatccagtgcatgcttctttctgtgaaattaaaggtccaattaggcccaacagtgcagcagtttgacgtaccggttttgaagatcctggaagcattaacaacaaagaaatgccaagaagaattttcacaggaatcattagaaacacttggggattctttcctcaaatatgttacaactcggcacctttttagtgaatacaggcttcaacatgaaggcatattaacaaaaatgaagaaaaacttgatctccaatgcagctctgtgccagctggcctgcagcagtaatcttgtgggttacattcatgctgaggagtttaatccaagagattggatcatcccttgcttggactatgatgagcgtggtaacaaaaaaatttcctttctggcacccaatggtatgtacagccaaaggaaaatgtctattaaaagtaagaggattgcggattcagttgaggccttaattggggcttacctcagtactgctggggaaaaggcagcatttcttttgatgaaatcattagggatgaatatagaatttcacactgaaattccagttgaaaggaaaatttcaatgaaagctgaagagttcattgatgtgaggagcttagagggaatgcttggttacaagttcaatgattctttattattgctcgaagcattgacacatggctcatatcagacttctggccctacttcatgctatcagaggctcgagtttcttggagatgctattttggatcatcttttcactgaatattactacagcaaataccctgactgtactccagaattgttgacagatcttagatctgcctctgtgaacaacaattgttacgcgcatgcagctgttaaatcaggattaaacaagcatatccttcactcatcatcagaactgcataggaagatgagctactaccttgggcagtcatttacaggtccatcttatggctgggaagcgggcattggtctaccaaaggttctcggggatgtgattgaatcaatagctggtgcaatttatctcgacagcaagtgtgacaaggaggttgtttggagaagcatgaagcggctattggaacctcttgccacccccgaaaccatcgagcctgacccggtgaaagggctgcaagaattttgtgatcgtagatcattcaaaataacctacgaaaaaaaccatgttgatggagtctcatcggtcattgctcgggtgaaggctggagagactacatactccgcaacaaaatcaggtccctgcaagttggcgaaaaagttggcatcaaaggctgtgcttaaagatctgattgctggtcacaaagatacagaggctgctgcagtatagtgatgcttaactatttaagcgtgcaacagtagctaacaattgatatagatagttgcgcacaatagaaaagttttggttggattcatacatgtaatttggaaatgctcctttttgtgtgctcgcaaacgatgcgtgtgaacggcctcatgaattctggtaggttttcatgcttcaaacttacaagtatcgcaattttgtaaattacaaatacgggcatagcacacctgcccatgccatgcagtagtttttttttcctcgaaatagtagcattagttgtatattactcatagcatcagattgtacagaaagcatgccagcaaaaacgaaaaaatgtacagacagcattttgttcgcatcaagggaaaacttgttttaaga
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@meso_cacase at
DBCLS
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If you use GGRNA in your work, please cite:
Naito Y, Bono H. (2012)
GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts.
Nucleic Acids Res., 40, W592-W596.
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