ABOUT THIS RECORDspecies: Arabidopsis thaliana
miRNA family: MIR398
source: miRBase, original name: ath-MIR398b (MI0001018)
Taxonomy by NCBI:
Arabidopsis thaliana Arabidopsis Brassicaceae Brassicales malvids rosids core eudicotyledons eudicotyledons Magnoliophyta Spermatophyta Euphyllophyta Tracheophyta Embryophyta Streptophytina Streptophyta Viridiplantae Eukaryota cellular organisms
SEQUENCE & STRUCTURE| miRNA TGTGTTCTCAGGTCACCCCTG miRNA* GGGTTGATATGAGAACACACG mismatches: 2 bulges: 0 |
pre-miRNA
TGGATCTCGACAGGGTTGATATGAGAACACACGAGTAATCAACGGCTGTAATGACGCTACGTCATTGTTACAGCTCTCGTTTTCATGTGTTCTCAGGTCA
CCCCTGCTGAGCTCTT
dot-bracket secondary structure
.(((.((((.(((((.((((.((((((((((.(((.(((....(((((((((((((...))))))...)))))))...)))))).)))))))))).))))
.))))).)))).))).
SIMILARITIES
MORE
miRNEST target predictions: none
non-miRNEST targets
HuntMi prediction: true miRNA
additional data
download this record
evidence: 5'RACE, Northern, PCR, cloned
deep sequencing data evidence
references
[1] Rajagopalan R, Vaucheret H, Trejo J, Bartel DP, Genes Dev. 20:3407-3425(2006)., "A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana"
[2] Sunkar R, Zhu JK, Plant Cell. 16:2001-2019(2004)., "Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis"
[3] Lu C, Kulkarni K, Souret FF, MuthuValliappan R, Tej SS, Poethig RS, Henderson IR, Jacobsen SE, Wang W, Green PJ, Meyers BC, Genome Res. 16:1276-1288(2006)., "MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant"
[4] Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC, Plant Physiol. 138:2145-2154(2005)., "Expression of Arabidopsis MIRNA genes"
[5] Jones-Rhoades MW, Bartel DP, Mol Cell. 14:787-799(2004)., "Computational identification of plant microRNAs and their targets, including a stress-induced miRNA"
TGGATCTCGACAGGGTTGATATGAGAACACACGAGTAATCAACGGCTGTAATGACGCTACGTCATTGTTACAGCTCTCGTTTTCATGTGTTCTCAGGTCA
CCCCTGCTGAGCTCTT
dot-bracket secondary structure
.(((.((((.(((((.((((.((((((((((.(((.(((....(((((((((((((...))))))...)))))))...)))))).)))))))))).))))
.))))).)))).))).
SIMILARITIES| miRBase ath-MIR398c: 2e-49 PMRD ath-miR398b: 2e-61 microPC miR398: 1e-16 | UniProt no hits RFAM MIR398: 3e-60 |
Identical with: ath-miR398b from PMRD (MNEST047013) |
MOREmiRNEST target predictions: none
non-miRNEST targets
HuntMi prediction: true miRNA
additional data
download this record
evidence: 5'RACE, Northern, PCR, cloned
deep sequencing data evidence
references
[1] Rajagopalan R, Vaucheret H, Trejo J, Bartel DP, Genes Dev. 20:3407-3425(2006)., "A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana"
[2] Sunkar R, Zhu JK, Plant Cell. 16:2001-2019(2004)., "Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis"
[3] Lu C, Kulkarni K, Souret FF, MuthuValliappan R, Tej SS, Poethig RS, Henderson IR, Jacobsen SE, Wang W, Green PJ, Meyers BC, Genome Res. 16:1276-1288(2006)., "MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant"
[4] Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC, Plant Physiol. 138:2145-2154(2005)., "Expression of Arabidopsis MIRNA genes"
[5] Jones-Rhoades MW, Bartel DP, Mol Cell. 14:787-799(2004)., "Computational identification of plant microRNAs and their targets, including a stress-induced miRNA"
