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

>Osa06LNT0351600.4

CAGATGAAACTTCTCTACTTCAAATGGTCATGCAACTGACATGCTCATTTCACACTTTTACACTGTGGGCACAGTAATGAGAGCGGTCCACTGTTCCAACACCACAGCGAAAAAACGTTCTCATGTCAATTGTCAATACAGTTTCAACTCAAAAGCCTACCCAGATCTTAGAAACAATGCACCAGGCTACTAGAACTACTACCCCAAAGACCAGGGGTGGTCACACGCTAAAATTATAGTACATGCCTTCAGATTTACATAATCAAACGTGGAAAATGATAAGGTACAAAATGGCAATTACAAGGATTGCCTGATAGGCTTAGTTGAGCAGTAAGTGATGTTTTCAACCAATGTGTGTACAGTTGGCGCCAAGAGTCAGAATCAGGGGTGCATTTCCTGTCCTTCGTGTCATCCGTGTTCCTAGCGGATATTTCCGTGTTAAGATGTGTATTCACAGTTGTTAAGATGACTTGGTTCTCTTGTGTTGAGCCTGGCCTTGGAGGCACAGCCTGAATCGCTGGGTTAGGCTCTCCCCCATCTCTTGCCTCTCCTGTTTGAGCCTCTTCCATAGAGATCGATTCTTCCTCTCCTTTGGTATAGCGAGCGGTTTCCTTCGTATCCGTCTCAGTGGTGTTGCCAAGGCCCGTAGCGTCATGCTCTTATGCTTATGACTAGGAATTTCAGGGCGCTCGCCTAGGGATGATCCATCACTCGCTGCCCCCAAGGAAGAACATCTTCCCCAGCTCTCTCGGTTTGAACTTGTGTATGAGCAGCACTCCTCATTTTGCCTGTGAGATTTATCCTCTAAATGAGACTCAGCAGTGTGAGTGTCCATCTCAGTGAGGTTATGATTTTCATCCAAAAGAAAATCCAAGTCATTATCTGTTTTAATAGACAACTGATTGACCCTCTCTGTCAGCAATTCAACCACTGATTTTGTAGTCACACCATTTGTGAAGTTAGCTGCAGCTGCCGATGAACTGCCTGCATCAGGACCAGCAGCCCTTAGACCATTGATGATTTCATACAGTAAGCTCTCATTTGTTCCAGCTCCAACCTTAAAAGCACCAAGGTTGTAGTACTTATCTAACTTATTTGAGCATACTGAAGGAAACTGAGGTGGGTGTAGAACATTATAGAAGAATATTGAAACAGAATCATAATAAAATTGAGGCCTGGGGGAATTGTGATCGCCATCAAATTTGATTAAGTTTTTGTCCCCCGCATATGCCTGATGAATACGGTCCGTGTGATGGGGCTGAATAAACATGTCATTTGATGCATGTCCAAATAATGCAGGAATAAATGTCTTGGGGGCAAACTGAACAACATCAAGATCCATTATATCAAACTTAGCTCTTCTTTGAATTACACGGCGCATGTACTGCACAGCCATCTTAACCGTGAACTTAGGAACTCGGATTTTGTAAACATCTACAAGCTCCATCATTAAGTCATATAGGTTAGAGAAAGCACTGTCCAAAACCAGACCGGCAATTGAGGGGTCTTCTGCTCCATACAGTAGGCTTGTAACAGCACCCATTGATCGCCCCCAAAGGCCTATGCAAGAAACTTCCTTATTGTTTCGCAAAAAGGACACCGCGCATTTGAGATCCTGTTTCTCATGCCAACCAAGGCTGACATACTCTCCACCTGATAGCCCTGACCCTGCAAAGTCAAGTGTAAAGAGGGTGATATTTGAAGGGAGAAGTATGACAGCTGCTTCATTTGCATCCGCTCTGCATCCACTATTTCCATGGCAGTAGATCACACAAGGAAGGGCAGTATTGTCTGGGATGACAGCAGGAACATAGTGGCTGCATTTTAAGGTCTGGTCTCTTCCGTTCGTAAGTTGCCTCCAAATCTATTCGTTTGTACTTTCTTCCCGCAAGAGTAAACTCCGGTTCCCACAGATACTGATCTGGATTGTACTCTGCACGCGGCGGACGGATGACAAAATTTACGAACTGCTCGATCATCGCGCCGCCGGAAGCTCCCCGACGAAGACGCAGCCGCGTAGGATGCTCGCGGCGCTCATGTACCAGGCGCAGCCACAAAGCCCCAACCTCCTCCTATCCCCCTCAGCTTCCCCC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.396596
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0351600.4 6 24277492 C G
Osa06LNT0351600.4 6 24277626 A G
Osa06LNT0351600.4 6 24279562 A T
Osa06LNT0351600.4 6 24279939 G T
Osa06LNT0351600.4 6 24280019 A G
Osa06LNT0351600.4 6 24281395 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
Osa06LNT0351600.4 osa-miR5541 Translation 5.0 11.976 1 21
Osa06LNT0351600.4 osa-miR6252 Cleavage 5.0 17.07 1 23
Osa06LNT0351600.4 osa-miR528-5p Translation 4.5 14.083 1 21
Osa06LNT0351600.4 osa-miR444b.1 Cleavage 4.0 20.716 1 21
Osa06LNT0351600.4 osa-miR444c.1 Cleavage 4.0 20.716 1 21
Osa06LNT0351600.4 osa-miR812k Translation 4.0 17.629 1 24
Osa06LNT0351600.4 osa-miR812l Translation 4.0 17.629 1 24
Osa06LNT0351600.4 osa-miR812m Translation 4.0 17.629 1 24
Osa06LNT0351600.4 osa-miR812n-5p Cleavage 4.0 18.333 1 24
Osa06LNT0351600.4 osa-miR812n-5p Translation 5.0 20.109 1 24
Osa06LNT0351600.4 osa-miR812o-5p Cleavage 4.5 9.339 1 21
Osa06LNT0351600.4 osa-miR5502 Cleavage 5.0 21.0 1 22
Osa06LNT0351600.4 osa-miR169i-3p Cleavage 5.0 21.035 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0351600.4 6 ph6 Morphological trait Dwarf RZ667 RG653
Osa06LNT0351600.4 6 qLDLJ-6-1,2,3 Physiological trait Source activity RM217 RM3
Osa06LNT0351600.4 6 prt6.1 Resistance or Tolerance Drought tolerance R2549 RG716
Osa06LNT0351600.4 6 gw6 Morphological trait Panicle/flower RG424 R2549
Osa06LNT0351600.4 6 qGL-6 Morphological trait Seed R674 R2549
Osa06LNT0351600.4 6 RPLD4 Physiological trait Eating quality RG424 RG172
Osa06LNT0351600.4 6 nan Physiological trait Eating quality RM253 RM162
Osa06LNT0351600.4 6 amy6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0351600.4 6 asv6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0351600.4 6 qDLR6-2 Resistance or Tolerance Other soil stress tolerance RM1340 RM5957
Osa06LNT0351600.4 6 tgw6.1 Physiological trait Source activity RG264 RM3
Osa06LNT0351600.4 6 nan Morphological trait Root RM4447 RM5509
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