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

>Osa11LNT0099400.1

TTCGTGCAACAGTATAACATTTCAGCTGCAATATATATCCCGTATAAAGGCAATATATCCTGTATTAAGGATTCCAGTCAATGTAGCCTCATCATACTTACACACCACATGCCGCACTCAAATCTTTAACAAATGAATAGCTAATATAGACAGAACGTGTATGGTTTTCCCTCTGAAATTCCTAGTTGACCAATCTAGCCAAAATGTGGTTCACTGCTCTCCTAATTCTAGCCTCTCTTAACAGTTCCAGTTAGACAGAATCGTGTCTTGCCTGTGGTGACCAAGCTTTCAACACTCAGCATTACACCATCAGATTCATCCTTTCAACTGAAAATGCCATACCACCAGTATGCGGTGGTCAATGAATGATCCAACATGGTGTTCTCATACAATCGCAGTTAGCCAACTCAATTAGACCACTAATTCTTCTATTTGGCTCGTTGAGTCAGTCTGATTAGTGGATTTCACTTCTTCGATATCTTCTTCACCCTCTACACTCTGAAATTGGCTCTCCAGAACCTCATATATGTTGTCCGGAGGGCATTTGTCTGCACGGTTCCTTGGATTCGGTTGGCAGAAGCACTCAGGCCATGAGTTTGTGTAGAAAGATTCTGGATGGACACGCTTGTGGGGGCCACCAAAATATGTGTTGAACATAACCTGCCTGACTCGCTCCTCAAAGCGAGCGGCGCGACCTTCCTCCCTGTCCATGAATATGGGAGCTAGGGCCTTCCTGTTTGGTGTGATTGTTGTCCGGAAACCATAGTATAGGCGGTGGCCCATTAGGTTGTTTGCAAAGTTGCTCGGGCCATCATATGTAGGAATAAAAATGTCTGACAGGAGACAGACCATGTAATCCACTGCAGAACCCGCGAGCCCTCTTGTATTTTCTTCCAGCTTTCCAGGACCAACAGTGCTGTGGTTTTCTAAGCGTGGAAACATAGCCTTAAATGGCTTCATGAATCGTTTCCCACCAAAGAGATCGCCAGAAGCAAGGTAGATTCTTGTTTTATTGTCAAATCCCATGGATCGAAGAATAAGACCTACCTCTTCTGGAGTTAAAGGGCACTTCCCGATGAGCCTTCTTTCCCTATAAATAAGTTCCTTTTCTGCAAAATGTTCCTTGCGGTACTTGATCAGAATTTTCTGTTCTTGAGGTGTGAATATATCAATGCACCCAGCAAATGCAAGCATATCCATCTCAAATCGAAGGTGAATTGACATGAAATGGCCTTCTGTACGGAGCTTATTGACTATCTCACTGCTTGTTTTCATTATGTGAGGCTTGAATCGTAGTGCATGGTAATTCACCCTGCATCTCAATCTCTGGAGCTCTGGATCATCAATGTCTTCTGCCAGGCGGTGTGAAAATGGGGTTAAATATATAGCTCCATACTTCTTCATCTTCTCCAAAGCAACTGTTGTATACCACGTAACTGGTGCATCTCGAGGCGGTCGAATCTGATGGGCTTTCAGCTTCTTGGTCTTTCCATTTGTAGTAATTTCTGGAATGACCATAGCAATTCGAACATCATACTTTAATGTCTTGATGAAGTGGAGCACATCATAAATACCTAAAAAACCACTCTCATCATGCCAGAAAGAATTTGTGTCCAGCTCTGGCAGCACTAGTGTAGCATTCATTATTCGTGCAGCAACAACAGCATTACATATCGCACTACGTTGTTGGTTCAAGCCACCATTGCACCGGACACGTAAGTAACCATTTGACTCAGACTCTATTGGTGGAGGAGGCCAATAGGTGCGCGGTGCAGAAGATGCCCTCCAACCATTTGAATCTGCAGTTCTCCACAACTTATTTACATCAACATCCTGGAGTCCGTAGGAGGAGCGGGCGAGGCCGAGGCCGAGGCCAGCGGAGGAGGAGGAGGAGAAGAGCCAGAGGGTGCCGGCGAGCAGCGCCAGCACCGCGACCCACAGCCTCGCCGGCCCGCGCCGCCGCCGCAGCAGCAACGCCTCGGCGTGGCCGCCCCTGCGCATTGGGGGGGAGTCGCGAGAAGAGGCGATCAGATCTGGGGGAGTGGAGTGGGCTGCGTGCGCGTGCGGGGGTGGGTTGGGTGGGTGAAGGCTGAAGAAGGTGCCAGGTGTTTGCTTGTTTTTGTTTTGTTGAGATCTTTGATGTGTGGTTTTCGTTTCGGTAGATTTTTCTTCCGGTACCATATATATACACGATTTCGTTCACCTAATCCCTTCTATTCCTCTGAATTTTGCTCAATCTCTTACATACCCCTGAATTTTAGTTTGGATCCCTTCCATGCCCTTTCCATATGAAAGGGATCCAAACTAAAATTTAGGTGTATGTAAGGGATTAAGCAACATTTAGGGGTACAGAAGGGATTAGGTGAACTTTCAGGGGTACACAGGGGAATTTTCTCCGTAGTATAATCGTGATTTAGTTATACTGTATTTGGCATAATTTCGGATCCAAAATTGTATGGAGTTGGGTATTTCTAGCTCCACAAATATATAGATCTGGATTTATGATTA

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.837825
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa11LNT0099400.1 11 16866858 C T
Osa11LNT0099400.1 11 16867605 G A
Osa11LNT0099400.1 11 16869269 A T
Osa11LNT0099400.1 11 16869347 G A
Osa11LNT0099400.1 11 16869585 A G
Osa11LNT0099400.1 11 16869602 A G
Osa11LNT0099400.1 11 16869685 T G
Osa11LNT0099400.1 11 16869905 C T
Osa11LNT0099400.1 11 16870115 T C
Osa11LNT0099400.1 11 16870372 C T
Osa11LNT0099400.1 11 16870377 C T
Osa11LNT0099400.1 11 16870541 A T
Osa11LNT0099400.1 11 16870879 T C
Osa11LNT0099400.1 11 16871283 A C
Osa11LNT0099400.1 11 16871313 G A
Osa11LNT0099400.1 11 16871318 A G
Osa11LNT0099400.1 11 16871566 G A
Osa11LNT0099400.1 11 16866862 T C
Osa11LNT0099400.1 11 16866756 G A
Osa11LNT0099400.1 11 16866456 G A
Osa11LNT0099400.1 11 16866783 A G
Osa11LNT0099400.1 11 16866992 T G
Osa11LNT0099400.1 11 16867370 C 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
Osa11LNT0099400.1 osa-miR415 Cleavage 3.5 14.633 1 21
Osa11LNT0099400.1 osa-miR2871a-3p Translation 5.0 16.29 1 21
Osa11LNT0099400.1 osa-miR2871b Translation 5.0 16.29 1 21
Osa11LNT0099400.1 osa-miR5071 Cleavage 4.0 19.356 1 21
Osa11LNT0099400.1 osa-miR5523 Cleavage 5.0 9.088 1 22
Osa11LNT0099400.1 osa-miR5159 Cleavage 5.0 19.474 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa11LNT0099400.1 11 hbd3 Physiological trait Lethality nan nan
Osa11LNT0099400.1 11 Hbd3 Physiological trait Lethality nan nan
Osa11LNT0099400.1 11 elr11-1 Physiological trait Eating quality RM1812 RM209
Osa11LNT0099400.1 11 qDLR11 Resistance or Tolerance Other soil stress tolerance RM2596 RM286
Osa11LNT0099400.1 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