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

>Osa11LNT0084700.1

GAATAAAAAATAAATAAACAAATAAACTTGAACATGACAAATATTTGCAGTTCACAACTTCAAGTAAGGATCTATGGATATATGGCTTCTCTAGCAAACTAACAGAGCCAAAGGTAAGTTCTACCATAGAGGAGCCCAAAAAGGTTTTCACTTGGGCACCTCTTTAAGTAAAAAATGTAATGCCAACATTTGTTTGCCTCAGGACTAAAAATAAGATCTGGCTATGCAAACAAAAGTAAAGTCTAACTAACTTCACATAACCAAGAAGAGTTGAACAACTCCTCAGACCAAAAGGAATAGTTGTACATCACATAAGCCGCAAGCCTATCCTACAAATCTTCCCAATTCATAAGCATTAATCCTGCTTCACGACGCAGGACTCGCCAACTATCAGATCAATCCTCAGGGTATTGTTTAATATACAAAGTTAGCACAAGGTGCTTCCTTTATAGCCCAACAATTGTTGTAGAATCATCATTGCCGTTGGGCAGATGGAGATTGCTGAACCTGCACTGGTGGGAAGAAGCCAGCACCTGGTGGTTGAAAAAATCCTGTCGAGGTCGGCGATTGCTGTGGTGCCTGCGGAGACTGCTGCTGCTGGGGCTGACTCTGGTTCTGAGGTTGTGTAGGCAGAGGCAGAGGTGGAGGCGCGCTTAGTCTTGGAAAACCTGCTGACATAATGTTGGGCAATAGGGGTGGAGGCGGCGCAGAGCCACTCACCATCCCAAAAGGTCCCATTCCAAACATTCCTCCAGTATTTTGAACAAATTGTGGCATAAGTGGTAATGGAGGTGGAGGTGGTGGAAATGAACCGGTTGCTTGGTTTGCTTGTGTTGGTGGCTGTGTGCCTCCAAGAGCAGCTGTTGCTCCAATCTGTGGTTGCACCTGTGGTACTTGCCCAAAGAATGGGGGAGCACCCATGTCACTCACATGAATAGGGTTGTCAAGCCTAGGCTTCTTATTGCTCTCAAAGCCTGGAGGTCCTGCAGAGAGATCTCCAGAAGTCGAACCACTATTCCTTGCTTGTTCAGCAGCAAGGGACGAGAAAATGGAGGAGAGCACCTTCTCAGGAGCTGACAAAGATGCAAGCTTATCTGCCATAGCTGCTGCAGTTTTTTTGGGCTCATCACCAACAGCACTAGATGTGGCAGGAAGTGAGGTTGCTGGATGCAGTGGTTGATAGTGGGGAAATATTGGCATTGCAGCTGAATTCTGCATCATGGCAGCTGTTTGTCCTGGTGGAAGTGTAACCATCAGTGGACTAGAACTAGATCCTGCACCATTGTTCAAGGCACTACCAAGTCGTTGTTTTAGTTGCATGGCATGTTCAGCCTTTGCTCGAGCTACATGCAACTGATTGCGAAGAAGCTCTGACTTTGCTTCCTGTTCGCTGAGGGCTTCTCTTAGTTTATTGATTAGGGTTATTCTAGCCATGTTGACACTTTCAAGTTGCTCAATGCACTGCTTAAGGACTGTTTCCTGCCCTTGAAGGTCAGAAATCAACGATGATCCTTGCTGAATACCTTGGGTACAAGCATCATCTACATCTTTATCCATCCTTTCCAAAACACTAACAGCATTATTGCATTTGTTTAAAGCTGTGTCTTCGTCAAAATGTTGATCAAGCACAGACTGATATGCTGTTACAATCTTTTCTGGCATCCCGCCAATAGTAAGTTTTTTTGTTACTGTACCAGAATCTTTTCGCACAGCTTTGGAAACTGAAGAGGGGTGAGAGCTTGGATTTGAGCTATTGCCATTGTTACCCATTGTATGAGTGCTACCACCAAGAATGTCATCTTTCAGACTTTCAATACGGGTTCCAAAGACCTTCCGTTCATCCCAAATATCTATTAATCTTCCGACTACTTTCTTTCCATCTTCTCCCCCATTGACATAAAAGTCTTTCAATAATCCAGGAAGAACCCTCCAGAATTCATTCACAAACTCCCCTCCCTTGCGTTTACTATTTTGCAGGATATCATTTGACAGGTACAGGAATGATACTTTCTTATCCTTATTTGCACTGTTATACTGCTTCTCCCATGTATCAACAACCTTTCTGGCTCTCTTTCGGTGAAAAATGCACCAATTTGAAAGTGTCTGGATCCTAGTCGCCGTGTTGTTGAGCTTGTTAAGCTTCTCAACAAACGCTTGCTCGCTGAACGAGCCAGAGCCGCCGCCGCCGATAGTTTCCGCCTTTGCCTCCGCCTTGGCGTCCGCCTTGGTGTCCGCCATCACGAAGGCGAAGGCTCCACCACCGAACTCCTCCCCCTCGCGAACAAGCTAATCCCCCGAAGAAACTTGTGCTTCTTGGCCGGCCAAGATCGAACCAATCCCCGGTGGCGAGCTCGTCAGCTTGAATTCGCCGCCGGTGAGCGAGGGAAGGGGGCGGCGAGGCCGGGGCGGGCGGGGGAGGACGAGACGAGAGGGTTTGGTTTTCTTTTTTTTTCCCCTTTCCGTGCTGCGTGT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.994749
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa11LNT0084700.1 11 1383900 T C
Osa11LNT0084700.1 11 1383635 T C
Osa11LNT0084700.1 11 1383747 A G
Osa11LNT0084700.1 11 1384608 A G
Osa11LNT0084700.1 11 1384633 T C
Osa11LNT0084700.1 11 1384960 T C
Osa11LNT0084700.1 11 1386175 A G
Osa11LNT0084700.1 11 1387426 A G
Osa11LNT0084700.1 11 1389204 T C
Osa11LNT0084700.1 11 1389380 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
Osa11LNT0084700.1 osa-miR5541 Cleavage 4.0 15.298 1 21
Osa11LNT0084700.1 osa-miR1437b-5p Cleavage 4.0 17.914 1 21
Osa11LNT0084700.1 osa-miR5079b Cleavage 3.5 15.139 1 22
Osa11LNT0084700.1 osa-miR162a Translation 5.0 22.425 1 21
Osa11LNT0084700.1 osa-miR396e-5p Translation 4.5 20.955 1 21
Osa11LNT0084700.1 osa-miR1423-3p Cleavage 5.0 23.587 1 21
Osa11LNT0084700.1 osa-miR1441 Cleavage 4.0 16.316 1 21
Osa11LNT0084700.1 osa-miR2093-3p Translation 5.0 18.836 1 20
Osa11LNT0084700.1 osa-miR396f-5p Translation 5.0 21.356 1 22
Osa11LNT0084700.1 osa-miR2871a-3p Cleavage 4.5 14.963 1 21
Osa11LNT0084700.1 osa-miR2871b Cleavage 4.5 14.963 1 21
Osa11LNT0084700.1 osa-miR3980a-5p Cleavage 5.0 22.57 1 21
Osa11LNT0084700.1 osa-miR3980b-5p Cleavage 5.0 22.57 1 21
Osa11LNT0084700.1 osa-miR5079a Cleavage 3.5 15.139 1 22
Osa11LNT0084700.1 osa-miR2093-3p Translation 5.0 19.1 1 20
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa11LNT0084700.1 11 qDLR11 Resistance or Tolerance Other soil stress tolerance RM2596 RM286
Osa11LNT0084700.1 11 nan Morphological trait Panicle/flower RM286 RM332
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