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RiceLncPedia: a curated knowledgebase of rice Long non-coding RNAs
Summary
Sequence
Coding Potentia
Genome Browser
Expression
Variation
Sequence

>Osa09LNT0436800.1

TTTCAGACTGTAGATAAGTGTCATTTATTACCGTGCGAAATGGTCTCTTTGTTACACTAGTACAAACACCACTGTTACAATAATACAAATGTTACTGTCAGGCAATAGTTTTTCAACGTTTTACAAAAACATGTGCCGAATACAACAGAATAGGAGATAGTTAATTCTTTTCAGGGGCGACTATGAACTAGACAGGCTTCCCATTCAACTTTGGGAAAGGATCTTGTTTGCTGAGGACAAGAACTTTGCTCTTATGAGCAAAGTATCCTTTAATGAGATTCTTGTATATTAGGCACGCCATGATGCACTCCACCTCATCCACGTCCATGTCAATTTCAAGCCATTTCAAAGCTTTTACAACGACTTCTAGCTTAATTTGATGTGCCTTGGCTGGCTCCTTCTGCCTCTGAATGATATGGATTTTCTTAACTAATCTCTGATAGACTTGAAGTTCAAGCTTCTCCAATACAAGGTAGACACCAGATTTTAAGAATTGGTCTTCATGCCTTTCGAGTGCTTGCCTAAGAAGCCTGAGATCTCCTCTCTTAAGTGAGGTCACAACATCTGCATACTCAAGCAGATTGTACCTCTCCAGTAGTGTTATTCTTGGCAAAACACCTATTGAAAGCTTTACTGGGATAAGAAACTTCAAAATTCTCCTCAAATTTGACTCATACTGAGGATTACAGTGCACCAAAGCATAAGTTAGCTTCTGATCTGCAACAAGAAAGTTCTCATTAAACACCTCTAATCTGCCGGTATAATACATATAAGTGACCTTATCTTTCACTGGAAAATCTTCAAAATCAAAATTCCTGGCAGTTTCAATACTTCTTATGACACTGCGACAAAGGTGAACTGTTCCAAGTCTGAAGTAAATTTTAAATAGCTGGCAGGTAACATAGAGTGCTCCAATGCGTTTAGGCCCTTTAACCGCGAGTGCACCGAAAACCTTCATCAGGAAGGACCCAGCAGACTGCAGCTTGTCAGGGTTCTTCCCACTCGTTGCAAGCTCCCTATCTGCCTTCTCAGCCAGCAGCCTGATCTCAAGCGCCACCGTGTGCATCGCCTCCATCGCCCACGGCGTCTCCCAGTTCCGGAACTCCTGCAAGAACGCGCTGCAACCAAAACCACATCAATCTTCCAGGAATGCGAAAAAGAAAAAGGATAAAAAAAACATGAATAAATCAGGGGTAAGGTAGTGAGGAGAGAAGGATGGGGAACGAACTTGGCGGCCTTCTCGAAGGAGGAGTAGGCGTCGGCGAAGCGGCGGAGGGAGTGGGAGTGGATGGCGCGGAGGAGCGGGGGGAGGAGGTCGGAGAGGTGCGGGTAGCGGTCGGCGGCGAGGCGCGGGAAGTCCGGGAAGGCGGAGAGCGCGTCGGAGAGCGGGGCGGGGGCCTGCGCGGAGGAGACGGCGAGGAGGGAGGCGAGCGCGGCGCCGTCCGACGAGGAGACGGAGTCCGCCACGCGGGAGAGGTAGTCGGCGATGCGGCGGTGCGCCTCTCCCATGCTCAGGTACGCCGCCATCTCCGGCGCGGCGGCTGCGGCGCCGCCGGGGGGTAGGGTTCGTGGTTTCGGCGGCGGCGGCGGCGGCGATGGCGTCGGAGTCGGACCCGAAGAAGGGCGGTTTCTGATTTCTGAAGGGTGGTGACGATCGCCGATCCTGGCCGTCGGATGGGAAATCGATGCTTGGGGGTAGTT

Coding Potentia
Explanation CPC Score
noncoding -1.04915
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa09LNT0436800.1 9 13175522 C T
Osa09LNT0436800.1 9 13175637 G A
Osa09LNT0436800.1 9 13175756 A G
Osa09LNT0436800.1 9 13176182 T C
Osa09LNT0436800.1 9 13176369 G A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa09LNT0436800.1 osa-miR166a-5p Cleavage 5.0 18.844 1 21
Osa09LNT0436800.1 osa-miR166e-5p Cleavage 5.0 18.844 1 21
Osa09LNT0436800.1 osa-miR1872 Cleavage 5.0 11.041 1 24
Osa09LNT0436800.1 osa-miR2927 Translation 4.5 16.834 1 23
Osa09LNT0436800.1 osa-miR5078 Translation 4.5 15.815 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa09LNT0436800.1 9 clr9 Resistance or Tolerance Cold tolerance RM285 RM434
Osa09LNT0436800.1 9 qAC9 Physiological trait Eating quality RM4413 RM5122
Osa09LNT0436800.1 9 qLG-9 Physiological trait Germination/dormancy G103 R1751
Osa09LNT0436800.1 9 rdw9 Resistance or Tolerance Drought tolerance R79 R2638
pre-miRNA
Transcript ID Pre-miRNA Identity(%) Alignment Length Pre-miRNA start Pre-miRNA end E-value Bitscore
GWAS
Transcript ID Chromosome Locus Trait Value Plus Minus