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

>Osa02LNT0142900.1

AGCAAAATGAGGATATGATTATCAGTTCGATTCAAACCAAAAGCTGCAACAGCCTATGCGGTTATCTGATTGTACATTTCCTTCTCTTTGCGTAGAATTACATAGCCCCAAAATGGCGAGAAAGCATCAGCCTCTATGTACACCACCAGGTAAAACCTATTTACTCGCCCCAGCCAAGCCAAACAAACCCAGGAAAGGAAAGGCCCTACCTATTAGTACAAAAATATCCAAAAGGGAGAAATAATACAGGGATTACAAAATTTCTCCGCTAGCTCGAGAAATAGTCCCCCTAGCTGCTTTAGCTGTTATTTGCACCCAGCTAATTGGGGGCAGAACAGTTAGCCGTCGGGATTTTGCACATCCTGGAAGCTGTCAACTCTCGTGCAAAGCACTTGGATTGGAATGATCAACTGTTGAATGTTGCTCTTCCAAGAAACTGTGTACTCGCGTGCGGAACTTCTGGGCTAGTTCAGCGAGATCGTTCGCCATCTGGATGTTGATCTCACCAAGGTGTCTCAATGGGTATTTGCTCCTTTGCGGCAACTGATTTGCGACATCAATTGTCAAGGTTGCACAGAGCTTGCTGCTTGTGAGCACTTCCAGTGTTGGCTTTGAAAAATTAGCATGCGAAGCTAGTCGGTTTAGAAGGATTAGAACCTCTCTCATTAGCAAATACCTTTCTTTCAATAGCTCATGTTCTCCATTTGAAAGGGCTGTGTCATATTCCATCTGTGACGCAAGGACTTCCATGATCAACTCCAAGAAATTGGCACCACGGACAGTAACTGGACCTAGAAGCACTTCATACCCCAATTTGCCACTTGAAGCTATATATGCTAACAGAGTGACAACTACCCGACAAAGCTTGATCCCCAGAGAACTTGTTGCCCTACAACTCAAGCATTCAGATAGGTCCTTAAAAATTGAGCTTATAGCTTCTTGTGATCTATCATTTTCACATCTTATAGCTTCAATCTGCTCAGGGCTATCTTTACCTCCATTGCATAGCAACTTCAATGTCGTTGGCAATTCAATAGCAAGAAAAGTAGATCCACAGAATGCTTCTTAACAAGCAATCCATTTTCCTTCTGCAACAGTTGATGCAATTTTTCCATTACAGAAGTAAATCCGAATTTTTCCCGCTCCACTTTGGGATCACTTGTCCTTGCAATGATAATCATTATAGATAATGCATCAACACGAATATTCTCCTCCGAATGCCTGTCCGCAATTTGTAGCATTGCAGTGAAGAGTGAAGTCCAGACTGTAAAAGGAAGCTGTGTGTTTTCAGTGTGAAGCCCATCATGGCTTCTTGATAGACTCGATGCATCAGGTGTATTCAGCGAAGTGGAGCTACCTTTGTGACTGTTCCGCTCCATGTGAACAGTATTGTTAACACATGGCTCAATAGAAACATTATTCCTGATGTTACACTCTGATTAGACATCGTTCTGTTATTCAGCAAGTGCTGCAAGACACTATGTAACATCCGCAGGGCTCTACTAACAACAGCATCATTACCAACAGCAGCCAAATTTAGCAATGCTTCGAGAAGAGTTTGTATAGGTATTGTATCACTGCTCGTCTTTATGATGATATCATATACTTGGGAAATAGCATTTCTGACCGATGAGCTCGCTTCAGAAGAGGCTTCACACTTGTCTAGCGATCCCGTAGACTGGACAAGTGTCAAAATTTCTTCTGAGCAAGAAACCAGGATCTTTGATATCAGACTCCTCCCCATCAAACTGTTAGTTGGCATGCCCCACACTGCACACAGATTGCTAGAGATACGGTCAACCAATACTTTCTTGTGCTCAAGATATTCGTTATTCCCTGGAAGATCTGTCTGAACCCCTACAGTCTTGATTTCCTTGTGTTTGCTGCCTTTTGATTCAAAGCGAACACTTTCCTCCAAGACCTCAGATGCATATGTTTGATTCCTTTGGTTCAAACAGAGACCGTCTTGAGGGGAACTGAGCTCCTTGTTTCTACCATTTAATGTCTCTGCTCTTCTCGTGGATGCCAAGCAAGAATCCCCAGTATGCAAAGCCCCATTTGCAGGGGCATGAACAGACTGATCAATATCCATAGCCATACTGCCGGCATATTTGTTAGCAGAACCCACATTTGCCCTTCTCAAACTTTGAATCTCTGCTTCTTTAGCCTTGATTTCAAGGTCTTTCCTTGTCCTGTCTTTCTTCAGCTCACTGCATTCGTTTTTCACGTCGTTCATTTGCTTCGAGACACGATTCAGCTCCCTCTTGAGCCTCTCGACCTCCCTCCGATCAGCCGCCTCCCTGGCATCCCTCTCCCTCCGCGCGCCCCCGCCCCCGCCCCCTCTGAAGCGATCAGCACCGGCGATGCCCGACGACACCGCGACGATCTCGCGGCTGCTCACCTCCGCCGCCGGGCGCTGCGAGAGCTCGCGCGGAGGGGAGAAGTCACGGAGCCCGACGTCGAATCCCTGCGGATGCTGGGAGAGCTCGCGGGGAGGCAAGAAGTGAACAGGGGCGGCGGAGAAGACATGGGGCCCGGGGGTGATGTAGGAGAGCGGAAGCGCGGCGGCGGCGGCGGAGGAGGAAGGGTACGATGAGGTGGAGGGCGGCGGGAGGTAGGAGATGAGGTCGGGAGGAGGAGGAGGGGGAGGGGGAGTGGGGTTAGGGTTGCGGGAGGCGACGGCCTCGTCCTGGGCGCGGAAGAGCTCGGCGAGGAACTTGTCGTCGTCCCACTCGTCGTCGAGGCCGTCCATCCCCCTCGCGGCGCACCGCGCCTCACCGGCGGCGGCGGCGGCGGCGGCGCGAGGTGAGAGAGAGAAAGAGGGGAAGTGGGAGAGGGTG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.988534
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0142900.1 2 1462446 T G
Osa02LNT0142900.1 2 1462208 T C
Osa02LNT0142900.1 2 1462577 C T
Osa02LNT0142900.1 2 1462702 A G
Osa02LNT0142900.1 2 1462856 T C
Osa02LNT0142900.1 2 1463885 T G
Osa02LNT0142900.1 2 1464369 T C
Osa02LNT0142900.1 2 1464674 G A
Osa02LNT0142900.1 2 1465714 G A
Osa02LNT0142900.1 2 1466168 C T
Osa02LNT0142900.1 2 1466547 T C
Osa02LNT0142900.1 2 1466548 T C
Osa02LNT0142900.1 2 1466495 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
Osa02LNT0142900.1 osa-miR166c-5p Cleavage 4.5 17.268 1 20
Osa02LNT0142900.1 osa-miR398b Translation 5.0 19.528 1 21
Osa02LNT0142900.1 osa-miR2097-5p Cleavage 4.5 15.471 1 22
Osa02LNT0142900.1 osa-miR2099-5p Cleavage 5.0 12.669 1 22
Osa02LNT0142900.1 osa-miR2103 Cleavage 5.0 23.66 1 22
Osa02LNT0142900.1 osa-miR5075 Cleavage 3.5 17.346 1 21
Osa02LNT0142900.1 osa-miR5075 Cleavage 3.5 21.714 1 21
Osa02LNT0142900.1 osa-miR5147 Translation 4.5 17.292 1 21
Osa02LNT0142900.1 osa-miR5147 Cleavage 5.0 10.841 1 21
Osa02LNT0142900.1 osa-miR5145 Cleavage 2.5 16.847 1 24
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