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

>Osa09LNT0435600.1

AAGGGATCTAGAGTCATCTCTATCGGAGCAGCAACGGCACAACTGTGAATTACATAAGTTAGCACAGAGATGAACTAGTGTTACAGCTGAACAGCTCCCAAGTGTATGATTACTAGTAGTAGTACTTAATTAGATCTTGGCAGTGTTTTTCCAGTTCTTTACACTATTAAGAGTGCTTAGCTAATTGTTCCAATAGATCTTACTTATCCAGGCTCCGGCAGCCAAAAGTGCACAAATGACTCCCAAATTGTGATATTACATCCACAAGGCCTCCATATCCAGCAACAGCTGCCATCCCTGAAGAATGTATGGAGACAGAAAATGCTGAGTGAGGAGCACACTTGATTTGTGAAAGAAGAGTCCCATTGATAGAGAAACGAGAGAGCAGAGGTTCAGCACCGACTGCTAAGATTTGGTTTCTGTCAAACAGCAAATCTTGAACAGGAGCATGGCAATCCACATTAAAGATGCACTCATTTGAAAGAAGGCTCCAAACTGATATACCACTAGAAGTACCACAAGCCAGCCAGCTTTCACTTGCATCAATGGCAACACAACTGACCCATGACCCCTCAAAAATCTTGTTTTTCACCGGACGTATAACCTGAGTGCACTTTCCACTTCTGCAATCCCAGATACGGGCTGTGCCATCCTCTGATCCTGTAACTACCTGGCGGTTCGCTTCGCGGACTGCAATGCTGTGCAAATAGTCAGTATGTCCCTTGAAGGTCATTTTACATTTACCACTCTCCACATCCCAGCAATAAGCACATGCATCCCCGGCCGCTGCATAAACAGATCCTTCCTGTTTGTTAATCGCAATGGCGTTGTTTTCAGGTATTGGAGAGCGAGCACCCCAAGGACCCTCATGCTGAGGGTTCACCAAATCAAGTACTGGCTCCAAATGATCCCCTTGCAGAGATAGCGGCACAAGGCAGCTCTGCATCTCGTGCCATCTCCATCCCCGAAGGCGCCCGTCATCCCCGCCGCTGAAGAGCAGCGGCTGCTGCGAATCCGGGTAGAACCTGACGTCGTAGGCCGGGCCACTGTGCGCTTGGACGATGCAGACGGGATCAACCAGAGAGACCGCGGCATCCGGGTGGGTCTGTGGGGTGGGATGGGAGGAGGAGGAGGAGATGCAGGAGGAGAGGGAGAAGGAGGCGAGGGAGCCGTCGCTGGAGGCGGCGGCGAGGAGGACGTCGGGGTCGTCGTCGTGGTGGTCGAAGAAGACGGCGCGGAAGAGGGTGCGGCAGGAGAGGTCCCGCTCCCGCAGGATGCCCCGCCTGTACGCCGCCTCGTCCCACCCCCGCGCGTCCATCCCCGCCAACGCCGCCGCCGCCATCTCGCCTCGCCGCCGCCGCCGCCGCTGCTTCGGAAGCGAGAGCGAGTCGAGGAGTGGGGGG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.652689
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa09LNT0435600.1 9 11909860 C G
Osa09LNT0435600.1 9 11909348 T G
Osa09LNT0435600.1 9 11910706 T G
Osa09LNT0435600.1 9 11910115 C A
Osa09LNT0435600.1 9 11911880 A C
Osa09LNT0435600.1 9 11911094 A G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa09LNT0435600.1 osa-miR156c-3p Translation 4.5 20.071 1 22
Osa09LNT0435600.1 osa-miR156g-3p Translation 4.5 20.071 1 22
Osa09LNT0435600.1 osa-miR156j-3p Translation 4.5 20.071 1 22
Osa09LNT0435600.1 osa-miR166h-5p Cleavage 5.0 14.332 1 21
Osa09LNT0435600.1 osa-miR444d.3 Cleavage 4.0 13.835 1 21
Osa09LNT0435600.1 osa-miR1847.1 Cleavage 4.0 17.983 1 21
Osa09LNT0435600.1 osa-miR2098-3p Translation 5.0 22.67 1 20
Osa09LNT0435600.1 osa-miR2867-5p Cleavage 4.5 20.468 1 22
Osa09LNT0435600.1 osa-miR5082 Cleavage 5.0 23.239 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa09LNT0435600.1 9 clr9 Resistance or Tolerance Cold tolerance RM285 RM434
Osa09LNT0435600.1 9 qPC9 Physiological trait Eating quality RM4413 RM1896
Osa09LNT0435600.1 9 qAC9 Physiological trait Eating quality RM4413 RM5122
Osa09LNT0435600.1 9 qLG-9 Physiological trait Germination/dormancy G103 R1751
Osa09LNT0435600.1 9 nan Resistance or Tolerance Drought tolerance R1164 R79
Osa09LNT0435600.1 9 nan Morphological trait Shoot/Seedling RG553 RZ206
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