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1 publications mentioning rco-MIR390b

Open access articles that are associated with the species Ricinus communis and mention the gene name MIR390b. Click the [+] symbols to view sentences that include the gene name, or the word cloud on the right for a summary.

[+] score: 63
Other miRNAs from this paper: rco-MIR156a, rco-MIR156b, rco-MIR156c, rco-MIR156d, rco-MIR156e, rco-MIR156f, rco-MIR156g, rco-MIR156h, rco-MIR159, rco-MIR160a, rco-MIR160b, rco-MIR162, rco-MIR164a, rco-MIR164b, rco-MIR164c, rco-MIR164d, rco-MIR166a, rco-MIR166b, rco-MIR166c, rco-MIR166d, rco-MIR166e, rco-MIR167a, rco-MIR167b, rco-MIR167c, rco-MIR168, rco-MIR169a, rco-MIR169b, rco-MIR169c, rco-MIR171a, rco-MIR171b, rco-MIR171c, rco-MIR171d, rco-MIR171e, rco-MIR171f, rco-MIR171g, rco-MIR172, rco-MIR319a, rco-MIR319b, rco-MIR319c, rco-MIR319d, rco-MIR390a, rco-MIR393, rco-MIR395a, rco-MIR395b, rco-MIR395c, rco-MIR395d, rco-MIR395e, rco-MIR396, rco-MIR398a, rco-MIR398b, rco-MIR399a, rco-MIR399b, rco-MIR399c, rco-MIR399d, rco-MIR399e, rco-MIR399f, rco-MIR408, rco-MIR160c, mes-MIR159a, mes-MIR167a, mes-MIR168a, mes-MIR171a, mes-MIR172a, mes-MIR399a, mes-MIR408, mes-MIR156a, mes-MIR156b, mes-MIR156c, mes-MIR156d, mes-MIR156e, mes-MIR156f, mes-MIR156g, mes-MIR156h, mes-MIR156i, mes-MIR156j, mes-MIR156k, mes-MIR159b, mes-MIR159c, mes-MIR159d, mes-MIR160a, mes-MIR160b, mes-MIR160c, mes-MIR160d, mes-MIR160e, mes-MIR160f, mes-MIR160g, mes-MIR160h, mes-MIR162, mes-MIR164a, mes-MIR164b, mes-MIR164c, mes-MIR164d, mes-MIR166a, mes-MIR166b, mes-MIR166c, mes-MIR166d, mes-MIR166e, mes-MIR166f, mes-MIR166g, mes-MIR166h, mes-MIR166i, mes-MIR166j, mes-MIR167b, mes-MIR167c, mes-MIR167d, mes-MIR167e, mes-MIR167f, mes-MIR167g, mes-MIR167h, mes-MIR169a, mes-MIR169b, mes-MIR169c, mes-MIR169d, mes-MIR169e, mes-MIR169f, mes-MIR169g, mes-MIR169h, mes-MIR169i, mes-MIR169j, mes-MIR169k, mes-MIR169l, mes-MIR169m, mes-MIR169n, mes-MIR169o, mes-MIR169p, mes-MIR169q, mes-MIR169r, mes-MIR169s, mes-MIR169t, mes-MIR169u, mes-MIR169v, mes-MIR169w, mes-MIR169x, mes-MIR169y, mes-MIR169z, mes-MIR169aa, mes-MIR169ab, mes-MIR169ac, mes-MIR171b, mes-MIR171c, mes-MIR171d, mes-MIR171e, mes-MIR171f, mes-MIR171g, mes-MIR171h, mes-MIR171i, mes-MIR171j, mes-MIR171k, mes-MIR172b, mes-MIR172c, mes-MIR172d, mes-MIR172e, mes-MIR172f, mes-MIR319a, mes-MIR319b, mes-MIR319c, mes-MIR319d, mes-MIR319e, mes-MIR319f, mes-MIR319g, mes-MIR319h, mes-MIR390, mes-MIR393a, mes-MIR393b, mes-MIR393c, mes-MIR393d, mes-MIR395a, mes-MIR395b, mes-MIR395c, mes-MIR395d, mes-MIR395e, mes-MIR396a, mes-MIR396b, mes-MIR396c, mes-MIR396d, mes-MIR396e, mes-MIR396f, mes-MIR399b, mes-MIR399c, mes-MIR399d, mes-MIR399e, mes-MIR399f, mes-MIR399g, mes-MIR477h, mes-MIR477i, mes-MIR477a, mes-MIR477b, mes-MIR477c, mes-MIR477d, mes-MIR477e, mes-MIR477f, mes-MIR477g, mes-MIR482, mes-MIR828a, mes-MIR828b, mes-MIR171l, mes-MIR398, mes-MIR399h, mes-MIR477j, mes-MIR477k, mes-MIR2118, mes-MIR3627, mes-MIR169ad
miR167, miR390 and miR393 were also differentially expressed under chilling stress; miR167 was up-regulated under CA while miR393 was up-regulated under CCA in reference to the normal condition. [score:9]
As expected, the three TAS3 loci and the targeting miRNA (i. e., miR390), 3 auxin response factors, and auxin signaling F-box genes were targeted by miR167 and miR393 and two GRAS family transcription factors were targets of miR171. [score:7]
The regions around the two target sites had almost identical sequences, suggesting a strong conservation on and near the miR390 target sites. [score:5]
CS 11(2), 1(6), 0(1) miR390-TAS3c binding site #2 CA + CCA 5(1) CS 5(1) miR167-ARF8 CA + CCA 9(1), 7(1) 001923 m ARF8 auxin response factor 8 miR393-ABF3 NC 10(1), 17(1) 004520 m AFB3 auxin signaling F-box 3 CA + CCA 11(8) CS 11(7) tasiAFR3-ARF3 CA + CCA 11(1) 002399 m ETT/ARF3 Transcriptional factor B3 family protein/auxin-responsive factor AUX/IAA-related CS 11(6) tasiARF1-ARF3 CS 11(1) 002399 m ETT/ARF3 tasiARF1-ARF4 CA + CCA 10(1) 001979 m ARF4 auxin response factor 4 CS 10(1) tasiARF2-NAC2 CS 11(2) 027253 m NAC2 NAC domain containing protein 2 siReport31-CUL4 CA + CCA 18(1) 001768 m CUL4 cullin4 Each target site was detected by ten clones. [score:3]
Moreover, nearly perfect matches around the 10-nt from the 5′-end of miR390 binding sites suggested that both binding sites were cleaved, which were further supported by the phased sequencing reads starting at the position of the cleavage sites of both 5′- and 3′-end target sites (Figure  2B, right panel). [score:3]
Importantly, a substantial number of sequencing reads, arranged in phasing, appeared in the regions defined by the two miR390 target sites (Figure  2A, Additional file 1: Figures S4A, S5A and S6A). [score:3]
As expected, three TAS3 loci and the targeting miRNA, i. e., miR390, were found to be conserved in Cassava and castor bean. [score:3]
Interestingly, the regions between the two pairs of miR390 target sites on TAS3c in the two Euphorbiaceous species had the same length of 190-nt and shared a high sequence identity (Figure  2C). [score:3]
tasiARFs are derived from well-conserved TAS3 genes targeted by miR390 in plants. [score:3]
The yellow colored are the miR390 targets. [score:3]
Among these small RNAs, 5,884 (66.4% of the total of 8,479) were arranged in phase with reference to the putative cleavage site at either the 5′ or 3′ target site of miR390. [score:3]
These shifted siRNAs followed the phasing register set by siRNA D8-, indicating that siRNAs arising from D8- could target and cleave the original transcripts, setting a secondary phasing register different from the register set by miR390. [score:3]
We identified two novel TAS3 loci in both Cassava and castor bean genomes by searching for a pair of miR-390 target sites (Figures  2, Additional file 1: Figures S4, S5 and S6). [score:3]
The two binding sites of miR390 on TAS3c gene have a highly complementary sequence match (Figure  2B, left panel). [score:1]
The two putative cleavage sites of miR390 on TAS3c were cleaved (Table  4), in agreement with the reads from the RNA-seq data (Figure  2B). [score:1]
miR390-triggered siRNAs from TAS3b in castor bean. [score:1]
The registers to which 5′ and 3′ miR390 cleavage sites are aligned are indicated by miR390 5′ and miR390 3′. [score:1]
Figure 2 miR390-triggered siRNAs from TAS3c in Cassava. [score:1]
In Arabidopsis, for example, a TAS3 gene has a pair of miR390 binding sites, which define and produce a single RNA strand that is subsequently turned into a double stranded RNA by RDR6 polymerase. [score:1]
miR390-triggered siRNAs from TAS3b in Cassava. [score:1]
ta-siRNAs triggered by miR390 and Novel TAS3 genes. [score:1]
miR390-triggered siRNAs from TAS3c in castor bean. [score:1]
Similar cleavage sites of miR390 on the TAS3c gene appeared in castor bean (Additional file 1: Figures S6D and S6E). [score:1]
The two arrows marked with miR390 indicate the cleavage sites of miR390 on TAS3c. [score:1]
Eight known miRNA families – miR156, miR160, miR166, miR171, miR319, miR390, miR395, and miR408 – were evolutionally conserved across the 9 species (Table  2). [score:1]
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