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

>Osa11LNT0089900.1

AGGGATACTAGGCACCTGCTTACCATACGATGTCTCATTGGTTGATCGGTACAGAGGACTGCATGGTCAAATGAGCAAAAATTAAAAAAACATCGAACTGCTACCAGGTAGAAGGTAACTCATTACAAATCCAAAAGTCCGCCCTTTAAGCTACTCGGAGAGAATAAAACACCATGGCATCATCCTTGTGGTCTCAACCTTCTGAATAATCAAAACAGTGGTGCATCAAACATTTTCCTCTTCCTATTCGTCTTCGTCTTCCTCTTCATCTTCTTCTTCGTAAGGGTCTCCAAAAGAGTCTTCATCTTCGTCTTCGTGAGAGTTCTCATCTTCATCTTCCTCCACTTCGTCCTGGTCATTGTCATATCCTTCCAAAATCTCGATTTCCTTACAACTAAAAACTGCACAAAGAAACAAATAAGAAGAGCACAGTAAATTTCAAGAGGTCCAACCTGAAAATTCACTCCAAAATAAAAACTTCAAATCCATTGACAAACTTAGTGTATTGGACCAACCCTTCAAAATACAAATTGACATAAATACTTCATTACTTCTCCAGATCCAAAATCAGATTATGTCCACTACTTCATTCAAAGAAAGGGAAACATAATAAAATGCCGTCACTTGGAGAAGCATTGGTCCTTTATAATATGGTTGCATCCTATGCGGCATAATTGCTGGATTCTCTATAGTATAGCACACAACAAGAAGAAAATTGTATGGTCTAGGGACTATATGGGTACTTATGGCAATTCATAAACAAGATTTTTGGACACAATGGCCAGGAGCTGTGAGCCCAACATAACAAATATAATTTAGTGTCACCGGAGAACATTACCTTAGGCAAACAAAACTACTAAGCAATCTTGCCCAATTATTGGTTACTAGCTGCTATGATATAACCAGGATGGCTAGTGCAGCAAGCTGGCACACTCAGCACCTCTAGTACGGTAAACTGATGGTTACAGAATAACAAAGTTTTCTCACAATAATAGAGTTCAACAACGAGATAAAAAGTATGTGAGGTACTTGCGTACATGGAAAATGGCATGCGAGCTATAAGATGGCAATATCGACTCTCACAAATATACAACTAATGGGAAAGAAAATCAAATCAAATGATTGAAAGATATAATTACATACTACACACATGTTGACATACTTGTTATGTTATGCAAGAAAATTTTAGAAATCTTAATATGCTTTTTTGAATACAACCAGCCAAAAGAGTAGTCTAGATAATGTCTTCCCAACCATACCAAATGCAGTGCATATGCTTTCAATTCCCAATTAATCCATGATCCTAACATCCATTTCCCAATAACTTAGAGTTTCGATACTGCTTACTACATTTCACGCATATGAAGGCAAAGGAAAATTTCAGAATTGTACAAAGAATGAAGAATGTTTAAGTATGTTGAATGTAGACAGATTTCAAAACTTTGAGTACTCTCTTATCAACCGCTTCGCATTTGATTTCAACTATCTCAAGGTGTGTTGATATTACAAGTGATCTATCCATTGAATGGCAGTTTCCTTTGATTTTCATTCTATGTTTAGGTCCCTTGGAATAGATCTGAAGAATGAGATTCTCTAGAACCAGTGCATGTTCAAGAATGCAAGATAGTGCACTAAAATCATCAGGCACACACCAGTATTCATTGAGTAACAAAGTCTTTAACTTGGTAAATGTTGGGCACCATTCCAAATCCCTTTTGAAAATAAACAATCTACGTTCATTTATCAGCACCAACGTCTTAGCTTCTGATAAACCTTCCAAACGCATGCATTTGTGGTCCTTGATATCATAACAAGGTTCAAAGCCCTCACAACAACAATCCCCAAAGTCATAATGACTACACGATTCTTTATAACAGTAGAGGACTCTAACAAATGCGTCAACTAACGATGGCATCCACTCAAGCACTGGAGTCCTGCCATGGAAATCATCCAGCTTCAGAGAAACAAGACTCGGGATAGCGATACGTATCCGAGACGTCTCACTGAAATAGGAATTGGTTATGCTCAAACGTTTTGCAGAGCTAGATGAGATCTTGGCACAGTCAAATTTGCATGACTCAAACACTAGATGCTCCAATGCTGGACAGCTCGAGAAGTTAAGAAAGCTGTCGTTTAGGCCTATGTTCTTAAGCTGTAGCCTCGTCAAGTGTCGGGAGACAAGTGGCATCTCATCTATCAGAAACGGGAAGCGATACCATATATCGACATCGAGCAAGAGGAACCGAACCTTGTGGAGCAAAGCATGCCTGAACCAGTGGTTCACCCGTACTGTGTCATCGAGGCCCTCGTCTCTGTACCAATCGAGCCAACGGAACCTTAGCACGCACGTGTCGAGAGGTGCGCCATCACGGAGTAGCAGCAGACGGTCGAGAAACTCCTTATTGTCCTTCACGCAGCGCAGATAGATATCGTCTTCGCCAATGCGCAGCCCGGTGGCAGACTTCCAGAGGTGGAGCCATCGCCGGGCTAGCAGGCACGTCCGGACAGCCTCCTGCGCCGGTAGGAAGGAGAGCACGTGGTGGAGCACCTCGTCCGGGAGGGTCCCCTATGCGGTCTCCCCCGGTCGAGGGAGGCGATTCCTTGGCCATCTTCTGCGGAGACATTCCGTCGAACAGGTTGCGGGCGTCGCCGCGGCGCCCCCACTGGCGTAGCAAGAACCGCTCGGGCGACACGAGGAGCGCCAAATCCTAGCGTGAACGAGCAGGAGAGAGGGCTGTGCTGTTCGGGTAAGCAGCTCACATCGCCGCCGGAAGCTTTCCCCCGGCCACCGGAGACCAAAGAGAAGAGAGTGGAACGCGCGGCAGCAAGGATACGCACGCCGACGGCGCGACACTCGCTAGCCCGACGAACGGTCAGGTCGCGCGGGGGGTGGGGGAGAGAATTCCGGCGGGGCGAGGCGGATGGAGAAGCAGCGCTGCGATGAGCGGAGGAATCGCCGGATCGGAGTGGAGATGGAGAAGACGAC

Coding Potentia
Explanation CPC Score
noncoding -1.04489
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa11LNT0089900.1 11 5337129 G C
Osa11LNT0089900.1 11 5337308 C A
Osa11LNT0089900.1 11 5337671 T C
Osa11LNT0089900.1 11 5338726 A G
Osa11LNT0089900.1 11 5338793 T G
Osa11LNT0089900.1 11 5339007 A C
Osa11LNT0089900.1 11 5339112 A G
Osa11LNT0089900.1 11 5339303 A G
Osa11LNT0089900.1 11 5339723 T C
Osa11LNT0089900.1 11 5337620 T 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
Osa11LNT0089900.1 osa-miR5542 Cleavage 5.0 11.614 1 21
Osa11LNT0089900.1 osa-miR6251 Translation 4.5 19.275 1 21
Osa11LNT0089900.1 osa-miR395u Cleavage 4.5 18.734 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa11LNT0089900.1 11 nan Morphological trait Seed RM332 RM229
Osa11LNT0089900.1 11 elr11-1 Physiological trait Eating quality RM1812 RM209
Osa11LNT0089900.1 11 qDLR11 Resistance or Tolerance Other soil stress tolerance RM2596 RM286
Osa11LNT0089900.1 11 fer11 Resistance or Tolerance Cold tolerance RM3701 RM552
Osa11LNT0089900.1 11 dc11 Resistance or Tolerance Cold tolerance RM552 RM3137
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