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

>Osa09LNT0437500.1

TGGTGAACTCATGTTTTTCTTTTAGAATTAGTATTTACTAATACCATAATGAAGTACATGATTTTCAACATGACTCTAATCTTGCACTACTTACATCTCAGGTGGGTTAATTTCCCACCATGATTGAAATAACTAAACAAAAACCATCTACACAAAGGCAAAGGCAGCAATCTAAAACAAAATGTTTTACAATTAGCCTTTCTCTTCTATACCATGTTCCAATATCTGACATAAGTGGGAGCACCATATAGCTGATTCACTTCACCATCTCTGGAGAACATCAAGTCTTGAGCTTAACCAATTGATGATGTCATTTGCTATATCATCCCTTTCAGGTTCAAAGAGAAGATCATGTAAATATCCATCATACAGTTTTATAGATTTATGTGCTGATGCTGATGATTGGTACAGTCGTTGAGATGCTCCGGGGTCAGTTATTGTGTCAGCTGTGCCATGCAGAACTAAAAAAGGGACAGTTACTCTGCTTAAGTTTCTTTGCAAATATGATGATATCCGAAGAATTTCATTGCCAGTTCTAACTCTAATGGGTCCAGTATACACAAGTGGATCTGCATACTTGATCTTCAAAGCCTCAGGATCACGGGAAACAGGAGGTCCTCTCCTGTGCAAAGCAGCAACTCGGTATTTTGGAGCTAACACAGAGAAGATAGGTGCAACAACCTGGTATAGATAAACGCAAACAAAAAAAATAAAATCTGTAAATAAAAACTCATTCCAACTATATCCTTGATTCCTTGTTGCAGTCACCCAGTTGTTAATAATCACACAAATTACACTCCAGATCAAAAGTCAACAAACCACAGGCAAATCTTCATATGACAGAAAACACGTTGAAATTACTTAATAATATGATGGGAGTCAGACGGTAATTTTTTCATAACAGAAGTGAGATACTCTGTTTGTAGAAATTAACATGGGCTTTAGATATACCGCAGGTTAAACTGTATAGAAGTTGTACAGCCATTAACATAAGATAATAGAATGTTGATATCTCATGTGAACTCATACTCCAGTAAAATCAGAAGATTCCACTGACATTATGAAAATAAGCTTGAGAACATTACTTCATACCTCTCTGCTTACATTTTTTTAATTGGAATATCCAAGTCAAGAATTTCTTCTGTGACAAAAGGAATGTTTCAATCTACTCAAATCAACACTAGTAAACCACCTTACAAACAGTTATATGAGAAATTGACATAACTAAACAAGAAAATAAATAATACAATGACAAACGCCAAACAAAATGAGCTCTAGCAGGATATGAATGTATATCAACATATAGAAATGGTACAGATCTTTGGAATATCAACAATAAATCCTTCTTCTGTTGTTAGATACCAAGGTTAATAGTGTAATTTCACATTGAACACGTGAAGATAGCATCCCAAGTGCAAAAGGAATGCAGGGTATAGAAAACAAAGGCATATATAAAGTAATGTGCTTACTTTGATAATTGGATGAGATGGTTGAACATGAATAGCCGGAGATGTCAAGATCACACCTTCAACATGAACTTCAACACAAGGATCCAGGACTGCCTTCAAAACAATAGCTCCACCTGTGGAGTGGCCAAATAAGAAACATGGCAAACCATAGTTTTCCTCCAGTACAACATCCTCTAGAAATTCTTTCAGGTCACCAACAGCATGATCAAGCGATGAAACATAGCCATGCACCCCATCACTTCCACCATGTCCAATCCAGTCCATTGCATAAACTTTAAGCCCATGATCATTTAACAGCTTTGCAAAATGGTTGTACCTCCCACTATGCTCATTTAGTCCATGTAACAGAACAACGATGCCCTTGACGCGATCGGCGGCGGCGACCGGGGTCCACGACTGCGTGAAGAGAGCGTCCCCCCTGGCCGTCTCGAACACGGCGAACTCCCTCCTGCTGCTCCCCGTCCCCGCCTCCTCCTGCAGCCTCCGGATCGCCATCTCCCGCCTCGCCGCCGCGTCCAGCTCCACCGCCTTGCTCCACCCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT

Coding Potentia
Explanation CPC Score
noncoding -1.069
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa09LNT0437500.1 9 13695714 C A
Osa09LNT0437500.1 9 13696550 G A
Osa09LNT0437500.1 9 13696648 A C
Osa09LNT0437500.1 9 13697906 A G
Osa09LNT0437500.1 9 13698362 A G
Osa09LNT0437500.1 9 13699349 T G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa09LNT0437500.1 osa-miR167e-3p Translation 5.0 17.024 1 21
Osa09LNT0437500.1 osa-miR167i-3p Translation 5.0 17.024 1 21
Osa09LNT0437500.1 osa-miR1857-5p Cleavage 3.0 12.531 1 21
Osa09LNT0437500.1 osa-miR2095-3p Cleavage 4.0 14.619 1 20
Osa09LNT0437500.1 osa-miR2097-5p Cleavage 5.0 14.383 1 22
Osa09LNT0437500.1 osa-miR2871a-3p Cleavage 5.0 14.713 1 21
Osa09LNT0437500.1 osa-miR2871b Cleavage 5.0 14.713 1 21
Osa09LNT0437500.1 osa-miR2877 Cleavage 5.0 14.012 1 24
Osa09LNT0437500.1 osa-miR2931 Cleavage 4.5 15.355 1 20
Osa09LNT0437500.1 osa-miR5340 Cleavage 4.0 9.306 1 23
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa09LNT0437500.1 9 clr9 Resistance or Tolerance Cold tolerance RM285 RM434
Osa09LNT0437500.1 9 qAC9 Physiological trait Eating quality RM4413 RM5122
Osa09LNT0437500.1 9 qLG-9 Physiological trait Germination/dormancy G103 R1751
Osa09LNT0437500.1 9 rdw9 Resistance or Tolerance Drought tolerance R79 R2638
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