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

>Osa09LNT0426600.1

TTCTCTCACTTTATCCCAAATTTTGCACAGAACAAAATTTAGAGCTCTGCTAGATTGCTACAAGGTGCAGACCACTTCAACATTGGTAACACTTGATTAATTACAACAGCTGGAGTATTGCAATGATACAAAACACCAAATGAGAAAAGAGCATTAATTTTACATAAGCCAATTTGTTGTACAAATCATCTTCATCATGTATTGCCTTTCCACCAACTGAATCATGCATTCTTCACTTCGTGGATTACTGCATTGGTATCCTACATCATTTGTGTCATTGATCTGAGCAATGGTCAATGAAATCACCATGGAAAGTTGTTTCCATTTCATTTCTTTATAATGAGTTTCCTATGAAAACATGGTCACAGACTTATTGTGCTGAAAACAACTTTTCTCCCTTCCTCACGTTATTGCCTTTTGCTCTTGCAATCTGTATTTCTTTTAGTCTCAAACAATGGAACTCACAAATGGATCATCTTTTATTTCAAAAAATTCATAGAACTATAGCTTGTTATGACAGGCCGTCCTAGTAAACTAATAGTAGTTCAACTTGTAACTGCGCATATATCTCACACTGAAGTTAGGATCCAAATTATAGCTAGCAGAGCAGAAGAATGTTGGGCTAGCTGTTTATGGGCAATCAGCTAGCAGAGCAGAAGAATGTTGGGCTAGCTGTTTATGGGCAATCAACACAATATGCCGTATACATGTTAACTCTCATATGTTCCCTTCTGACACGAAATGCATGAAGTTGAACTGATCAGTTGAATGCCATTGATTCTGACAACCGTATCATTAGAAGAAATATCTACCTAGTAGCTACACAAGAATGTATGCGCATATATATAATGTAACAGGAATTCTAGTGATAGGAAGTATATAGCAAAACATGAATGTCAGTTCATCAAATTGCATAGGTGAGATTCAGTAATGCCTCCCAAGCCAGATGACAGGTACTTTTGCTAAGTTACGGTTGATGGGCTGAGGTATATAGAAAGACAAATATATTCTGCTTACCCAGATCGCCATAGCCCATGGCCTTGCTTAGAGCTTGATAATGTCATGGCACTTGGAATTAGCAAGATCATCAAGTGGAGCTCGTTCCTGTAGAGACATTGGTAGTTGAGACTTGAGAATAACCTATAAAGAGTATGGATGGACACATAAATGTATAAATATATATTCTGTAAATGATAATAGTATGGTTCAGCATTTTCGTAAAAAAAATAGTATGGTTCTGCAACTTGAAACAATGCATATAATGGTATTCGAGCAATGACAAACCCCTGAATTCGTCAGTCCGCTTACAATTCCAGCAACATGACAATCTGCAAGGCTAGAAAAAAGGGGATCCATTATTATTTAAAACAACCCATGACAACAAAGTGCTTTACCTTTGCCATACAAAGTGCATAATTTTGTGGCTTAATCAAGTTGAGGCACTAAATAAAACAGAAGCCCGCCCCAGTCCTCAACGCACAAAAACAATGTGAATGTTAGATCGGAGCAAACAAAACTCAAAGTAAAGCAAGCATGAAGCAATGGCTGAACCAACATGGAAGGAAGAATATATATGTGGTCTGAGAGTACCAAATAACATAATCAATGGGTCACTTGCAGTTTGGCCGACCTGGCTTCAACAAAAAAAGGAAAATCATGGTACAGGCCAATGCTCAAGGAAGAAGATTAGGGATTAGGGACTTGATGAGGGACCAAGGCGGAGCTCCGGCAGAGATCCGGCAGAGATCCGGCGAGGATGCGGCGGAGCGGCGGCAGCGGGGAGGAGGAGGCGCGAGCGAAGAGGCCGGCCGCGTCGATGGGGAGGAAGAAGGACCCGGCGGCGGCGGCTCCGGAGTGGCCGCGGAGGAGCGGTGGCGGCGGCGGCTCCGGCGTGGCCGCGGAGGAGCGGGGAGGATCTCCTGCCAGGACGCGGGGAGGAGGAGGAGCGAGCGAGGAGGAGTCGAGGAGCGACGTCTTCGCGGCAGCGGGTGGATGAGGACGGAGGAGCGATGTCTTCGGCGAATCGGCG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.944176
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa09LNT0426600.1 9 1240040 C T
Osa09LNT0426600.1 9 1240403 T 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
Osa09LNT0426600.1 osa-miR156f-3p Cleavage 4.5 24.216 1 22
Osa09LNT0426600.1 osa-miR156h-3p Cleavage 4.5 24.216 1 22
Osa09LNT0426600.1 osa-miR156j-3p Cleavage 2.5 24.216 1 22
Osa09LNT0426600.1 osa-miR171a Cleavage 4.5 20.646 1 21
Osa09LNT0426600.1 osa-miR156l-3p Cleavage 4.5 24.216 1 22
Osa09LNT0426600.1 osa-miR319a-3p.2-3p Cleavage 4.5 9.217 1 20
Osa09LNT0426600.1 osa-miR319b Cleavage 4.5 9.217 1 20
Osa09LNT0426600.1 osa-miR171b Cleavage 5.0 20.646 1 21
Osa09LNT0426600.1 osa-miR171c-3p Cleavage 5.0 20.646 1 21
Osa09LNT0426600.1 osa-miR171d-3p Cleavage 5.0 20.646 1 21
Osa09LNT0426600.1 osa-miR171e-3p Cleavage 5.0 20.646 1 21
Osa09LNT0426600.1 osa-miR171f-3p Cleavage 5.0 20.646 1 21
Osa09LNT0426600.1 osa-miR416 Cleavage 4.5 13.632 1 21
Osa09LNT0426600.1 osa-miR444f Cleavage 5.0 10.615 1 21
Osa09LNT0426600.1 osa-miR1872 Cleavage 4.5 18.46 1 24
Osa09LNT0426600.1 osa-miR5151 Translation 4.5 19.491 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa09LNT0426600.1 9 qPC9 Physiological trait Eating quality RM4413 RM1896
Osa09LNT0426600.1 9 qAC9 Physiological trait Eating quality RM4413 RM5122
Osa09LNT0426600.1 9 nan Morphological trait Root C711 G103
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