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

>Osa02LNT0139300.2

ACAATGACGAGAATTGCCTCCCTATTTACATTTGAACTGCATTGCGCATACGCAACGAGTGCATATTTACATAGAAATGTATATTCGCATGAGCACAGGCGCATGTACCCACACGTCAAAAGGTCGATAAAAGATGAACAAGCAGGTACTGCAAAAGACAACCGTGGAAGTAGTAGTACGTGATTGGTACCGCAAAATGAGTGAACATCCTACGAAATAACATCTTCCGATCGACCTTGTAAACAAGAAAGAAAGAAAGTAGAGAGGCAGCTCAGGACACCTCCACGACCAAAAGAGAAGAAAGAAGCTACTACTGGGCTCGTCCACGGGCACGGGGTGGGTGGTCTGTCAACAGTCGAATAAGCTTGTCGGATCTCCCCATTGCATCTCTTGACGATTTCACTTTTTCTTCCTTTCTGGTATCCACAAATATATCAGGACCTGTGAATTCTTTGAGCATCATAGCTGACACAGGCTGCAATCTCCTTCTAGTGTTCTTTCTATTGCAAGGCTTAGAAGCAGAGAGATCCTCTATTTTATCTGTCAGTTTTTCAGCCTGATTGTCCTTGGTTGGAGATATTGGAGCTTTCCTTGGGGAAGATTTTCCATTTAGCGTACATGGATACATGCCTCCATGATCATCCACTACATGTGGAGGTTGAGCACAGCCATATTCCACAATGGTTATTTCTACTGTTGGCTTGCATCTTTCTGACTGAGGATCCTGCTGAAGAGCACCCATCCCTTGCAACTGACTGGAGCTAACATGTAATGAGCCAGAGTTCACTTCTTGGGAACAACTTGGAGTACTATGATGTTTCACCCCTCTTGTGTGAACATTCTGTTGAATCCCCTCCGTTGTTATATTGTGTATCTCTTCCCTTTCTTCTTCACTTTGCTCTATGGGAGATTTCTTGCTAGCACCAATAAATTGTGGAGACAGGTTTGCGCTTTCATTCTGTAGGCATGTATCTGTAAAGCTTTGATCAGATGGATGATCCAAACTACTGGATGAATGTGTGACACCACCACCATCAGAGCAACTTTCAGACCTATCCAACTTCTTATCAAGCACCTGTACCACTATCCCAATGTTTTCTTTTTCCACATCATGCTCAGGAATAAAAGCATCGGAACTACTTGCTTTCTCTGGCTTACAATCTCCGGAGCACAATTCTTCTTCCGCTATCAGCTTAATAATAGAAGTATCACAAACATCAGATCCCCCTGTCCCTGTTATAGAAAAATGGATTCTCAGGCCTATGAGAACCATCTGATGATATTGTCCTGAACATGTACACCATGGAAATGTAACCTGTCTTGTCATCATAATCTGAAGACCTTTCAGGGCCATGACCTGTAGATTCTTCTGAGACCTCTTCTACTGCTAAAGATTTGTTTAGAGCAGAGTCAATAGATACAAGATCAGTTTGACTTGATAGAGAAACAAAACTTTGAGCCACTTGACCAGAAGACACATCATTGTTTTGCTCAACAAAGGTATCTTCAACAGCTGGAAATTTCTTGCATGAACAACTTAGAACCTTCAACTTCTTCTCCAGCTCCATAATTTTGATGTCTTTAGATCTAAGCAATTCTCTTGTGCTCTCAACAGCATTCTCAGACTCCAAAAGTTTTTGTTTATACTGCTTTAAAACAGTCCATAAAGCCCTGGCAAAGTTTGTCATTATTTCTTCATTTCTCGAAACTCTTCGCAATTCTGAATTAAGAAGCTTGTACTGTGACTCATCTTTTTCAGAAATTGTAACACCATCATCCTTATCAATGTCATCCTTTCCTGCGACCTTATGAATCTTCCTCTTTTTCGTGTTCTCTTGGCAAATCAGGGAAGCACTGCTTCTCTTTTGGGAAACCAATCCAGAAGAGTCCTCAAGGTTGGTATACTTTATTTTCATGTACGGAGATGCTTGTCTTAGCAAAAAAGATGTATCCAAATAATCATCATCTCCTGGTTTCACATTCAAAATCAGAGTCATTTTCTTCCTTCCTTCCAGGTAGTCTCTCAAGTACCTTGTCAACATTGAGTTCTTGAAGTGCTTCTCCAAGGGTTTCTTCTTGTTTTTCTGATGCTCTAACAAAGACCTCAAACAGAGACCAAAAACCATGGATGTATTGTTGATGAAATTACTCTCTAGCAATCGTGTACCTTGATTTCCAGTTCTCCTTTCCCGCTCTGCCCCCGCAAGGTCTGCTATGGTCAGGACAGCATTATTAAGCGAATTCTCACTTTCTGCATCAGAGCTTTTATGAACAGCACGTATAGTGATAATGCACTGCGATCGACTTGACTTGCTGTTAGCATTTGTTGCAGCTGTGGTACGCTTCAGCATCCCAGAAAAAAGTAAGGCCTCAGCATCCGCAAAATTTTCAACGGATACCTCTTTAAGACCTTTAATTGTTGACTGCTGGAGAACAAGGTCGGTCGCATCAGACAGTAGGTCAAGAATCCGCTCTCCTTTTCCCTCAGAAAGTATCTCGAACATTGAGAAGCAAAATGATCTGTAGTTATGAGAAGAGATATGATATGGAATTTAAAAG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.984794
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0139300.2 2 98060 C T
Osa02LNT0139300.2 2 98718 G A
Osa02LNT0139300.2 2 99881 C A
Osa02LNT0139300.2 2 101329 A G
Osa02LNT0139300.2 2 101529 G A
Osa02LNT0139300.2 2 101663 A G
Osa02LNT0139300.2 2 102007 G T
Osa02LNT0139300.2 2 102902 A T
Osa02LNT0139300.2 2 103273 T A
Osa02LNT0139300.2 2 104337 C T
Osa02LNT0139300.2 2 105848 A G
Osa02LNT0139300.2 2 106690 A G
Osa02LNT0139300.2 2 106756 T C
Osa02LNT0139300.2 2 98588 T C
Osa02LNT0139300.2 2 98523 G C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa02LNT0139300.2 osa-miR169p Cleavage 4.0 20.895 1 22
Osa02LNT0139300.2 osa-miR172a Translation 5.0 10.344 1 21
Osa02LNT0139300.2 osa-miR172d-3p Translation 5.0 10.344 1 21
Osa02LNT0139300.2 osa-miR169r-5p Cleavage 4.5 20.895 1 21
Osa02LNT0139300.2 osa-miR1858a Translation 4.0 11.685 1 21
Osa02LNT0139300.2 osa-miR1858b Translation 4.0 11.685 1 21
Osa02LNT0139300.2 osa-miR2106 Translation 4.5 22.346 1 21
Osa02LNT0139300.2 osa-miR3981-3p Translation 4.5 14.612 1 21
Osa02LNT0139300.2 osa-miR5148a Translation 4.0 17.307 1 24
Osa02LNT0139300.2 osa-miR5148b Translation 4.0 17.307 1 24
Osa02LNT0139300.2 osa-miR5148c Translation 4.0 17.307 1 24
Osa02LNT0139300.2 osa-miR5339 Cleavage 5.0 18.111 1 21
Osa02LNT0139300.2 osa-miR5499 Cleavage 5.0 17.847 1 21
Osa02LNT0139300.2 osa-miR5513 Cleavage 5.0 20.895 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
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