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

>Osa09LNT0434400.2

TCACACCCAACACAACGCATTTAAAAAGTCCAATCCTGTTAGTTCTTGGAGGTAATATGCTCTTCAGTTCAGTCTTGACTAATCCCCCTCTTTTCCTCCCAAATTACTGCACAAAATTTGGCCATCAAGCAGCCCCACGAACAGCCCCTAACTAGGTTCGGAATTTGCCAAAGAGGGTTGAAATGTACCATCACCGGGGGGGGGGGGGGGTTACTGTACTCATCAATGAGTTCTGAACCAAGCAAAAAGTTTAGCCCCTAACTAGGTTCGGAGTTCCTGTTAGTTCAGCATTAGCGCATACGGCAAGAGGCAAGAGGCAGATGTGTATTTGACAGTTTGACACAAGCCATCAGGAGTGCTTTGGCCGCCGGGACAATCTTCTCAGGTTCACCCTCTCCTGGGTTCCATCATGGTCGTATTCGACAAGGAAGACACATCTGCACCCCCTTATATCATGTTGTTTCCGCTGGATTTCCAGAACATGCGCATCGAAATGCAATGCTTCATCATTGCTCTCCTTGAAACAGAGGACAAGGTCTCCTTCCCTGATGAGTTTGCATTCTGATGATTCCAACGGGATGGATTGCAGGCGGATAGCCTTCCGGACATTGATCCATTCATCCTCTTCAGCCCCAAATCCTTGAAATCTCACTCGGACTTCCTAGAACAATAATGAAGAAATAGAGTTTTCAAAAATAGATCTTTAATTTGTACGGTGCGAACAATTATAAAATGCAATAACGAGATTCATGTGATCAGACCTAAGAAGAAAACGAATATGTTATCATTGAAGACTCTCCAAAATCCATGTGGTTCAAACTTAAGATCAAGCTGAAGCGCATGGAAACGTTATTATTAAAGAGTCTAAAATTTTTAGTAGTATAAAGAAAGGTCCGGAATTTTGAATCAAAGACTTCTTGGGAGAAAGGCAGCATACAATTAGTAACATAGGGGTCTGAGACATTCTAAAATTCAGGGCAGTGCACAAATACTTCTGAGGAAAAAAAAAAAGAACACATGACATATGCTAGCAAGCCGATAAATAAACTATCAGCTGAAGAGACATAAATGCAAACATATCCTACAACATCAATTATTCTACTTACAAATTCACCAGAACTTAACTTCCTGTATGCTAAGAAAGTGGCGATATCATACCAAGCAAAATCCTTTGAAGACCTAGCCTCGAACTGCATGTCTTCAATTTCAGGAAGCTTATCTATGTTGTCTATAGGTAAATCCGGCGAAACCTCGCCTATATCATTTGAAATGCTTGTATCAACAGCTAAAGCATTTTCTTCAGATGATGGAGGCTTTTCTTCAGAAACCGGTGCACTTGCTTGGGAGGCTAAAGCCTTTTCTTCAGAGCCAGTAGGCAAACAAGGAGGTATAACAGTTGATGCAGGGAACTTTTGACGGAACCATTCTTGAACCTGCACAGCCTGTAGTGCTTTACTTCCAACTCGGCCTGGAGAACAATTAAATTCTTCTGCGAGCTTCCGGCAGAAAATTTCATCCAAGACTTGTTCCTTTTTATGTGTAACCAACTTCTCCATCCTTGCAATCTCGGATGGCGCGAAGCGAACGCTCGATCGCCGCTCCATTTCTCGCCGCCGGCGAGGTCTCCGCCGCCGGAAGAACGGGGAAGACGCCCTCCTCCCAACTTGCAG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.841647
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa09LNT0434400.2 9 10873221 G A
Osa09LNT0434400.2 9 10873741 A C
Osa09LNT0434400.2 9 10873780 A G
Osa09LNT0434400.2 9 10873968 A G
Osa09LNT0434400.2 9 10873979 A G
Osa09LNT0434400.2 9 10874089 T C
Osa09LNT0434400.2 9 10874348 A G
Osa09LNT0434400.2 9 10875155 G C
Osa09LNT0434400.2 9 10875355 A C
Osa09LNT0434400.2 9 10875684 A G
Osa09LNT0434400.2 9 10875997 A G
Osa09LNT0434400.2 9 10876117 A G
Osa09LNT0434400.2 9 10876720 A C
Osa09LNT0434400.2 9 10876761 A T
Osa09LNT0434400.2 9 10876786 G A
Osa09LNT0434400.2 9 10876790 C G
Osa09LNT0434400.2 9 10877100 A G
Osa09LNT0434400.2 9 10877332 A T
Osa09LNT0434400.2 9 10873188 A G
Osa09LNT0434400.2 9 10877731 A C
Osa09LNT0434400.2 9 10876889 A C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa09LNT0434400.2 osa-miR812v Translation 5.0 5.84 1 24
Osa09LNT0434400.2 osa-miR159a.1 Translation 5.0 22.856 1 21
Osa09LNT0434400.2 osa-miR159b Translation 5.0 22.856 1 21
Osa09LNT0434400.2 osa-miR159c Translation 5.0 22.856 1 21
Osa09LNT0434400.2 osa-miR159d Translation 5.0 22.856 1 21
Osa09LNT0434400.2 osa-miR159e Translation 5.0 22.856 1 21
Osa09LNT0434400.2 osa-miR319a-3p.2-3p Translation 4.5 21.794 1 20
Osa09LNT0434400.2 osa-miR319b Translation 4.5 21.794 1 20
Osa09LNT0434400.2 osa-miR5489 Translation 4.5 15.803 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa09LNT0434400.2 9 apd9 Others Others CDO590 G103
Osa09LNT0434400.2 9 nan Morphological trait Root C711 G103
Osa09LNT0434400.2 9 nan Resistance or Tolerance Drought tolerance R1164 R79
Osa09LNT0434400.2 9 nan Morphological trait Shoot/Seedling RG553 RZ206
Osa09LNT0434400.2 9 qAC9 Physiological trait Eating quality RM4413 RM5122
Osa09LNT0434400.2 9 qPC9 Physiological trait Eating quality RM4413 RM1896
Osa09LNT0434400.2 9 clr9 Resistance or Tolerance Cold tolerance RM285 RM434
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