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

>Osa08LNT0402200.2

ATAGAATATATCGGTTTACAACCAGATGCGAATTGCTCAAAATTGCATAGCATGGACTAGTCCAAGACAACAGTTTACCAACAAGACCACATATTCTGCATTTCAGAAGAAAACCGTTGAAATTTATCCTCAAGAATACAGAACATGCGAATGCCACTCATCTACACAAGGGTGAAAAAATCATTGACTATTTGCTACAAAAATTCAGAATCTCGTATCCTCTATTTACAAAGGAGACTCCAACTATTACGTTGCACCAGTGGCAACTGCATGCCCTAACCATCTAAAAAAACTGCACGCCCTAGTCAATGTACTCATGTTGTCAATTGTAACTCTTGCTTGAGTACAAGTTTGTACCCAGTGTTGCTATGACCAAAATTGCCTACAATACACAGTTGATAACAAACCAAATCTGAGAACATGCCAAAGGCTCCTGCCAACGATGAGATTAAGAAATTTGAGCCAAAAAAACATTGAGCAATGGAACCTATCTGGAAAATGTAGGGCCTGTTTGGTAGGCCATGGCTCTAAAATCTGAATTGAAGTGGAAGTTCAAAGGAGATGACAGCTAAGTGAGTTTTACTAAAATAATTAACTTCTAAAGTTAAATATTAGCGTAGTCCTTATATCCAGCGGAAACAATCGCAAGCAATATGCAGAACACCAGAAATTCTGTCTGCATATTGTGATTGAAGAGGTTGGCAAAGATTATACACAAACGATTATAGCTATGAAAAACCCATCATAGGACATGGGGTATTTGAAAAGAAAATGAAGCTTTGGTTCTGAAACAGAACAGTTAGAAAAAGGAACTATCCCCCCACACTAACAATGGAAGGAAACAGCCATCACTGCAGAAAGGACATAATCATGAGAAGGAATCAGTCATCACTCCTGAAAGGACACAATATAGAACTAATCGACTGGGAATATTTGAGCATGCCAAACAAGGCGACCAAATTCTTGTGATTGAAGAATTTGGCAAAGAGCATATACACATGATCAATGGTAAGAAAAATCCACCATAGGGACATACTGCATTTGAAAAGAAAGGAAGCTTTGGCTCTGCAGCAGAGTAGTTAGAAAGAAGAGTTCTTCCCCTGTGGTAACAACTGAATGAATCAGCTATCACTGCTGAAAGGACACAATCATAAGTTAAACCACGATGAGATTGAACTAACCATTTGAGAATCATTTGAGATTAACCGGGTATATTTGAACATGCCAAATAAGATGGACAAGGCAACACAAATAGGTCAAGGTTGAGAACCTAAGGAACATAGAATGCTAGGTTCACCCTGGGAACACACTTGGATAAGCATGAGATTCATCGAAACTTGTGTGGACGGGTATTTGATGCTCTTTCCTGGACCCAAGGAAATTATGGGATGGCACGAGAAGTTGAAAGGAACAGATTGAAGTGTCCAGCTATATTGAAAACTATAACAGGAACCTTAAGTAGACATAATGAAAGCTTTGATCAAATTCTCTGCCGATTGCTTCTGTTCAGTGGTGCCAGATATGCGAGCAACATGGCCATGACGAGACGATTTTGATTCAATAATTTCAATGTGAGCTCCAGAAATCTTTATAATGTTGTCCAGGTTTGTGCCATGTTTCCCCATTACTTTTGACAGGCCACTAGCAGGAATAGTCATTTCCATATGTGGAGGACGTTTGAGATCAGGGTTCATGGGAAGTTCTGTTCCAACATACCCTCCATATCCCTTTGATGCATATGACGAGACTGCTGAATAGCCATCATCTATAGCCTGCAAGGAGCTGTACCCATACAAACTGCTATGCGGATATACTTCCAAACCACGTTCTATGTCACCCCTATGATCATAGCCCAGGGGAGTGATCTGTTGTCTGTAAGGTAATAATGCAGGCAAAGGATAACTGCTTGCATACAAAGGATCAGTAGTGGCAACAGTTAGCTTCCCATCTTTCTCAGAATTTTGCCTGTCCACACTGTCCCTCAAAACATCATCCCTGAGTCTTAAAACTATCTGTACAAGAGCATCACGCAGATTTTCCACTTCTCCAAACACCTCGACAAGCTCATCACTGGAAGATGCCTTCCGTGGTTTTTCACCCTTTGATATGTAGATAGCTGCCTTAGTCTTACTCCGCATGTCATTGACAATCGAACCGCCCTTGCCAATAAGACAGCCTATTACCTTACCTGGAACAAGAAGGCGAAGATTCATTTTACCTTCATTGTCATCATTGATCTTCGATTGCAGAAGCAGAACAGCTTCCACTGCTGCAGACTTAGCATCATCGGTGGCCTCATTGGATGTAATGGTGATTATACTTTCCTCTCGGTCATTTTTTGAGTCATCAACATCTATCCTTGCACCACTCTCTTTCCTTATACTCTTTATGGTCACCCCACCTTTACCAATAACCAACCCAATCTTGCCAGCAGGGCATAAAACACGCAATACTAGCTCCCCAGAACATTTCGGTGTATTATAAGCAGGAATTACAGGAAGCACAGATTGGTAAATGGGCAGTCGACTATGAGCATCAGCCGATACTGTAAGTTCAGGAACATGAGGTGTTGACCCTAAGATTGATAGACTTGGATGTCCAGAAGATATGGCAGCATCAGAGGGTGAGTAGAAGTTACTAGATGGGTAAACAGGAAGCTCAGAAGGAACTATAATGCTTGGAGGAAGGTCTGAAACAGAAGTTTCAAGAGGAATGGTCTCTTTTGATGGGCACTTGTAAATGATGGTTGATACTGCAAATAGTGCCTTTCTGACAGCTCTAGCATCACCGGTTATCTGAACAAAATTATCAAAGCTCATAGCACATGAATGTGTAACTTCATTTGGATCTTTTGGGCTCACTTTAATAAATGCTTTCGAAGTTGACCGAAGCCTCTTGATGACAGCACCAGACTTTCCTATGACACTTGCAGATTGACTAGCTGGTACAAGGATATTTGCTTCTTCATCATCAGAGTCCCTAGTGATGGACAGAGCATCAACAATTGCATCATGTACCTTGAGTAATGCATCTTGTGCTGTGCAAACAGGCTCCCTGTCATCGTCGTCATTAACATCTAGGTTTCTATGCTTGACAAAACAATATACCAAAATAACCCTCTTGTCTGCACCAGGGTGAGGGTCGACAACCTTGACTTTAGCACTCGTCTGTTGTCGGATAGAGTTTATCACCTTGCCGTTCTTGCCAATTACATTACCTATTACTCTGTCCGGACAGAGTATGCGGTAAACAACCAATTCATCATTACCAGAGTTTTCCTGGGCACGTGGCACTGGCCTCCTCTTTTGGTCCCTCCTTTCTTCTCTGTCATGGTCCCTGTGTTGCTGAGGGCGTTTGCCAGTATGCCTCATTTCGTTAACGAAACCGCCGCCACGCATCGACGGCGGGGGTGGGGGTGGGGGTGGGGGGAGGAAGGGGAGGGGCACTTCGGCGGCGAGACGGGATCGAGGAGGAGCGGAAACCCTAGGGAGGAAGAGGATCGAGTCGAGGGGAAGCTCTGCTCTGCTCTGCTCGGGTCGTCTCTCTCCGTCTCCGTCTCCGGTCTCAGCCTTCAAC

Coding Potentia
Explanation CPC Score
noncoding -1.15808
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa08LNT0402200.2 8 5811644 T C
Osa08LNT0402200.2 8 5811722 G A
Osa08LNT0402200.2 8 5813580 T C
Osa08LNT0402200.2 8 5811574 T A
Osa08LNT0402200.2 8 5812284 C A
Osa08LNT0402200.2 8 5810114 C T
Osa08LNT0402200.2 8 5811083 G A
Osa08LNT0402200.2 8 5811281 A G
Osa08LNT0402200.2 8 5812467 T C
Osa08LNT0402200.2 8 5813770 A G
Osa08LNT0402200.2 8 5813919 A G
Osa08LNT0402200.2 8 5814207 C T
Osa08LNT0402200.2 8 5814209 T C
Osa08LNT0402200.2 8 5814787 A T
Osa08LNT0402200.2 8 5815641 A 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
Osa08LNT0402200.2 osa-miR812q Cleavage 4.0 19.481 1 24
Osa08LNT0402200.2 osa-miR5820 Translation 4.5 14.915 1 21
Osa08LNT0402200.2 osa-miR1440b Cleavage 4.5 13.591 1 21
Osa08LNT0402200.2 osa-miR6255 Cleavage 3.5 16.326 1 22
Osa08LNT0402200.2 osa-miR395b Cleavage 4.5 9.467 1 21
Osa08LNT0402200.2 osa-miR395d Cleavage 4.5 9.467 1 21
Osa08LNT0402200.2 osa-miR395e Cleavage 4.5 9.467 1 21
Osa08LNT0402200.2 osa-miR395g Cleavage 4.5 9.467 1 21
Osa08LNT0402200.2 osa-miR395h Cleavage 4.5 9.467 1 21
Osa08LNT0402200.2 osa-miR395i Cleavage 4.5 9.467 1 21
Osa08LNT0402200.2 osa-miR395j Cleavage 4.5 9.467 1 21
Osa08LNT0402200.2 osa-miR395k Cleavage 4.5 9.467 1 21
Osa08LNT0402200.2 osa-miR395l Cleavage 4.5 9.467 1 21
Osa08LNT0402200.2 osa-miR395s Cleavage 4.5 9.467 1 21
Osa08LNT0402200.2 osa-miR398b Cleavage 4.5 14.688 1 21
Osa08LNT0402200.2 osa-miR167d-3p Cleavage 4.0 14.405 1 22
Osa08LNT0402200.2 osa-miR426 Translation 4.0 14.031 1 21
Osa08LNT0402200.2 osa-miR395m Cleavage 4.5 9.467 1 21
Osa08LNT0402200.2 osa-miR395n Cleavage 4.5 9.467 1 21
Osa08LNT0402200.2 osa-miR395p Cleavage 4.5 9.467 1 21
Osa08LNT0402200.2 osa-miR395q Cleavage 4.5 9.467 1 21
Osa08LNT0402200.2 osa-miR395r Cleavage 4.5 9.467 1 21
Osa08LNT0402200.2 osa-miR1432-3p Cleavage 4.5 11.244 1 21
Osa08LNT0402200.2 osa-miR169r-3p Translation 4.0 16.34 1 21
Osa08LNT0402200.2 osa-miR1846a-5p Cleavage 4.0 19.099 1 21
Osa08LNT0402200.2 osa-miR1846b-5p Cleavage 4.0 19.099 1 21
Osa08LNT0402200.2 osa-miR1846c-5p Cleavage 4.0 19.099 1 21
Osa08LNT0402200.2 osa-miR1846e Cleavage 5.0 19.122 1 20
Osa08LNT0402200.2 osa-miR2099-5p Cleavage 3.5 17.466 1 22
Osa08LNT0402200.2 osa-miR2867-5p Cleavage 4.5 16.094 1 22
Osa08LNT0402200.2 osa-miR395y Cleavage 4.5 9.467 1 21
Osa08LNT0402200.2 osa-miR5150-3p Translation 4.0 11.166 1 24
Osa08LNT0402200.2 osa-miR5503 Cleavage 4.0 18.756 1 22
Osa08LNT0402200.2 osa-miR164d Translation 5.0 16.339 1 21
Osa08LNT0402200.2 osa-miR7693-5p Cleavage 1.5 19.737 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa08LNT0402200.2 8 qDSR 8 Resistance or Tolerance Other soil stress tolerance RM3572 RM404
Osa08LNT0402200.2 8 hd8 Physiological trait Flowering RZ562 RG978
Osa08LNT0402200.2 8 dth8 Physiological trait Flowering RG333 RZ66
Osa08LNT0402200.2 8 qALRR-8 Resistance or Tolerance Other soil stress tolerance RG978 C1121
Osa08LNT0402200.2 8 nfb8 Morphological trait Panicle/flower RG108 RZ562
Osa08LNT0402200.2 8 nfb8 Morphological trait Seed RG108 RZ562
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