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

>Osa11LNT0092600.2

TTTAGGATTGGGTCAAAGTTTGCTGTTTGCATGATTAAGTTCCACTGATGTACAGTACAATTTCACTATTTTCTTTGATTAAAAATGAACAATGTGTCTGATCAAAACAAAGTACCTTAATGAACTTTCTCATTGTTCACAAGGATTTCTCTCCAAGTTCTTAGAAACCAGCCTATTTGCAGCATGAGTACAGTTACAAGCTCAGACTACATACGAGAACTACATCAAAGTTTTTCTACGTACAGTATTACATCCACTTTGTTGATTCCCATCACATGTTCTATGTTACCAACTTACCATCTGCTTTCCTCATTTGCTTCCCATCCATTTTTACTCCAAATATCTGAAAAATGAGTGATGTACATGGACAACATTCTACACCAAAGAAGAAGCATCCTTATGAGCTGAAAGCTCTTGAGATTGCATATATGAAGTCCAATAAACCAGTCCCCTTGAGAAGGCCTTTCCCAGTTAAAAGTTCAAAGTCTATTAACAAGAGAAAGCCAATTATAGCGGCTTTCCCATTAATTAGTTCATTCTTATTAGTGAAACCAAAACCTCCGACATCCTCATCAATCACCATTCTCACCTCTTCGATATTGACATCGGATGCAGTAAATCCAGGTTGTGCTTTCCCACTGAATATAATCTCTGCGGATCCACCGGAGGTAACAGCCCCCTTGATACTGATGTATATATTCTCCCCATCGATTTTCACAGGGTACACGAATAGTTTTCTCAATGCAGGTGTAAGAGCCCTTAAAACAGGGTTGTTGGGATACCATTCCTTTATTTCACCAGTACGAAGATCAAATGTACTATCTGTTGTTGGGCAAACAATGCAGCCGTCCTGGGTGAGCTTGGCGTTGAGGAGGCCCTCGGTGTAGGCGCCCTCGGCGGGGGATCGATTCTCGACGGCGTACACCTGCTCCTTGTACCACAGCAGCAGGATCTCCTCCCCGTCCTGCACGATCACCCGCCGCTCCCCACGCGGCAGCGCCGCCAGCGGCACCACCGGCACCCAGTTCCCATCCCCGCTCGCCTCCCCCGCCGCCGCCGACGGCTCCGCCCCCGACACCTCCGCCGCGCGGCAACCGACGACCCTCTGGTGGTGCCGCAGGGTGGCTGTGGCTGTGGCGCGCGGGGGCGGCGAGGCGGACGCGGCGACGCGGCGGCGGTGGAGGAAGGAGGAGGCGGCTGCGGCTGCGGCGGTGGTGGTGATGGACGCCATGTGGAGAGGATGCGGAGATGGCGCGTGGTGGGGTTAGGGTTTGAGGGGGAGGAGGAGGAGGGGGAGGGGGTGGTGGAGTGGAGTGGCGCGGCCATGGCCACAGGATGGGGATAAAAGGGGAGGAGGATTTGTATTTTGTGGGGAAGAGAAGAGGACACATTTATACGCTGCTGTCCACGCGAAAACGCGCGCTCCCTCCCACGTTCAAATTCAACGCGGGAGGCGACGTGGCGAGACGAGAAGCTGGCCATGGATTCTCCTCTCTGCTCTGCAGCACTCGTGTGGAGATGATTTTCTGCTGGAATTTCCTCAGCCGCGAGAGATGTCTGCGATCCTCTCTGTGGGTGGGTGGCCGCTGAGGTGTTTTGCCTTGGAGCCGGAGGCCGTGGGCACAAGGTGTTTGAGGAAATGCCTGAGAGGGATGGATGGTATGGATGAATGAATGGCATCGCCATCTCAGCCATTCAGCCGAGCCCCACCCATCCTGGTGCCTCTGCAATGGCCGTGAAGGAATAAATTAGTCAGATTTTAGACGTGTTTGTCCCTTCGGCTGCAGCTTGGCAAAACAGGACAGGTTTGGCGTGTCCATTGACCATTGTTCAGGTGTTCTGTGCACGTCGCAGTGTTGGAGATGGAGGTGTGATGCCGGATTGCCAAT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.570544
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa11LNT0092600.2 11 7639526 A G
Osa11LNT0092600.2 11 7641651 A G
Osa11LNT0092600.2 11 7641658 C A
Osa11LNT0092600.2 11 7641745 C T
Osa11LNT0092600.2 11 7641813 T C
Osa11LNT0092600.2 11 7641869 A T
Osa11LNT0092600.2 11 7641902 G A
Osa11LNT0092600.2 11 7641973 T C
Osa11LNT0092600.2 11 7642314 G A
Osa11LNT0092600.2 11 7643001 T C
Osa11LNT0092600.2 11 7643507 C T
Osa11LNT0092600.2 11 7643512 G T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa11LNT0092600.2 osa-miR812t Cleavage 4.5 18.189 1 24
Osa11LNT0092600.2 osa-miR812u Cleavage 4.5 18.189 1 24
Osa11LNT0092600.2 osa-miR5143b Cleavage 4.5 8.263 1 24
Osa11LNT0092600.2 osa-miR5143b Cleavage 4.0 20.358 1 24
Osa11LNT0092600.2 osa-miR5822 Cleavage 5.0 17.618 1 21
Osa11LNT0092600.2 osa-miR408-3p Cleavage 5.0 10.606 1 21
Osa11LNT0092600.2 osa-miR419 Translation 5.0 6.263 1 21
Osa11LNT0092600.2 osa-miR529a Cleavage 5.0 3.175 1 20
Osa11LNT0092600.2 osa-miR2104 Cleavage 4.0 15.275 1 22
Osa11LNT0092600.2 osa-miR812n-3p Cleavage 4.5 18.189 1 24
Osa11LNT0092600.2 osa-miR5143a Cleavage 4.5 8.263 1 24
Osa11LNT0092600.2 osa-miR5143a Cleavage 4.0 20.358 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa11LNT0092600.2 11 Tid1 Morphological trait Dwarf nan nan
Osa11LNT0092600.2 11 elr11-1 Physiological trait Eating quality RM1812 RM209
Osa11LNT0092600.2 11 qDLR11 Resistance or Tolerance Other soil stress tolerance RM2596 RM286
Osa11LNT0092600.2 11 fer11 Resistance or Tolerance Cold tolerance RM3701 RM552
Osa11LNT0092600.2 11 nan Morphological trait Seed RM332 RM229
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