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

>Osa10LNT0061400.2

AAAAATTCAAATTATTTTTTAAATTTATTTGAATTTAAGGAGGTTACCGCGGTATTTATATTACCGTACCTCGCGGTAAGCCCGGTAACCGCTCGGTAAGGTAAACCCTGGTACCAGCACAATCCGCAAGCAAAAAAAGAAAAAAAAAGGGGTCTTAGTCCACGGTTCTTCAACAATCCAACCTTAGCTTGTCTTCTGCTCCAATGCCTTCAAATGCAGCATCTGCACAGAAGAATTAGATCTTGTGCATAAAAAGAGAGCAACTCACGGAACAGCGAAAGAAGACTAGTATCTGCACAAGATCTACCGATGTATATATTTTTCATCGAATTCTGGACTCCTTGTGGGATCATGTCCATGGGCACCAGCACTGTCTGGAAGCAATGATAACAATAACAAAAATCTTCGCCCACGGCTCTTCAACAATCCAATCCAGCTTGAGTGCTCAGTGCTCACTCGTTTGCTCCAATGACTGCAGTGTAGAAACTTGTGAAGGGATGACAGCAGGTGATGACATTGCAATCAAAGAGTTTCTTGAACTGCATTGAGTCAACTTGGACCATGTAGAAAGCCATATCCACCACTAAAATAAACGCATTAAGATCCTCAGCATATCCCACAATATCTATTTTCTCTCTCTGCACAGCAGAACTCAGCCCAAGAATGCCATGCAGCTTGACAGTCTTCCGTAGCACCCATTTCGCGGCACCTCCAAGAGTGACCTTCCTCTCCCACATTTGGAATCCGCTGTACGACAGAATGGCAAGGCTGACATTATCATCCTCCCTACGCATGATACAATAGCGGCAATCGCTAGAAAAATTCGTCTCTGGCCAATTGCCATCGGTCACAGCTAGGGTCAACGTTTCGAGATTGAACTCAAGAATGTGATGCCCGGACACAGATAGCAACCAATAGAGGGCATTGCCAACAAGTATGGCAGGTGAACCAAAATGGTAGATGGTGGATACAGGCCCTGTGAAAATGGCATCACCCCATTCGCCGGTCACCAATGAGTAAACGGAGGCAAAGATTCGCCTATCCATCTTGCTGGCGCAGATCAGGACCAAGTTGAAGACCAACTTTAGATGCACTACTGAAATTAGTACAAGGAATGATGTGCAATGGAGCAGTTGGAGAGAAAGCAAAGCTTGCTATGTCTATGCGACGACCTTGTTCAAGTAGTAGCTTTGGATTCTGACCATACAAGGAGATTTTTTTTTTCAGTCAGTGTAATGCACATTTTTAATCTGCCAAGCCAGAAATTGACATCCAAATTCCCTCTCAATGCATCTGCAGTAGCATTTGCTGCGGCAAGTGTCCCTATGAACTGCATCTGCATGGCAATTTTCTTCAGATATTTGTACTAATCGTGGATGGTCCTTAGGGTTCGCACTTCCAAATGCGAGCATTTTGAAGAGGTAGCTCAATTCTTCATCTGAATGGTTGTTAAGAAACATTGGCTTTACAGTTCCAAGTTTCTCTGATTTTCTAAGTCTGCTTATGGTTACCACCTTGCTTCCCTCATTCATTTGTGCCACGGATTTATAGAATTCCTCCCAATTCATCTCATTCACATCTGAAACAAACTCCACAACCATCAAAATGTTCCCTGCCAAGAGAGTATGATTGTGTGCTATTCCCAAAAGATCACCTTCATTCAAATGCAAAATGGAAGAAAACTGTGATTGAACCCTCTCGTCGGCGCATACATGCGCAACCAGAGTTTTCTTCCCAACTCCAAGAGCACCAATGATTGGAAGAACAGCAGGCTGCACACCAGGAGGGTTGTATTCCAATAGGAAATTCAGGAGCCTCTGCTTTTCAGAATGACGGCCAAACATGAAGTTATCTATGTAAAGATAGGTATCATATGGTCTCCTTGACATCCGATCGCATCCACCCAAAAGAACAACAAATTCTGCCATGTGATCAACAGCAGTTTCTAATATTTCCAAAGTTCTGTGCAACTCAAGGTGCCTGGCCTTGTCCTTTCCAGAAGCATCAACAATTTTGCAAAAACGTTTGAGGGGAGGAAATGGGTTGCTAACCTCCTTGATGGGATCCTCCTGAATTAGGGTCCTGCACCTGAACATGTCCAGGACATGGTGGCCTCTGTACATGGCATCAGCAAGTGCCTTCAGCTGCATCAGCATCCCGGAGTTGGTGATGTATCGCCCATCTGCCTCCTCGACAACCATGGAAACTCGTAGGAGAAGCTGCTGCAGTCTTTTCAGCTGCTTCTCCTCTGAGATTTCATGTCTTCTTGAGTACTTGCTCATGAGGTAGGAGATGAACCGGGTGACCAGTTCACCGGTTACTGCTGATACGACATGCTCCATATCCAAACCTTTTTTCACAGCTCTTCAACAATGCAATCCAGCTTATTGAGCTCACTCGTCTGGTCCAATGGCTTCCATTGCTGCAGTGTAGAAACTTGTGAAGGGATGACAGCGGGTGACGACATTGCAATCAAAAAGTTTCTTGGACTGCATTGAGTCAACTCGGAACATGTAGAAATCCGTATCCACCACTAAAATAAACGCATTAGGATCCTCGGAATATCCCACGATATCTGTTTTCTCTCTCTGCACAGCAGAACTCAGCCCAAGAATGTCATGCAGCTTGACAGTCTTCCACAGCACCCATTTCGCGGCACCTCCAAGAGTGACCTTCCTCTCCCACATTTGGAATCCGCGGTACGACAGAATGGCAAGGCCGACATTACCATCCTCCCCACGCATGATACAATAGTGGCAATCGCTAGAAAAATTCATCTGTGGCCAATTGCCATCGATCACAGCTAGGGTCGACGTCTCGAGATTGAACTCAAGAATGTGAGGCCCCCACACAGATAGCAACCAATAGAGTGAGTTGCCAACAAGTATGGCAGGTGAACCAAAATAGTAGATGGTGGATACAGGCCCTGTGAAGATGGCATCACCCCATTCGCCGGTCACCGATGAGTAAATTGAGGCGAAGATTCGCCCATCCATCTTGCTGGCGCCGATCAAGACCACCTTGAAGTGGCAGGACCGGAAGCCGCCGCCGTGCACGTGGCCGTCGTCGCCGGCGGCACAAAGCACCGCGCCGTTCATGACGGATCTCTCCCCACCGTCGAGCTCCTGCGGAACGGCCACGCGGCGGCGATCGCCGGAAACGGGATCCCACACGAGGAACTCGCAGGTGTTGTAGTTGAAGATGAGGACGAGGCCGTGGCGGCAGCCGAGGAGGCTCGCGGCGCGGTAGTCGTCGAGCCGCAGCGCGAAGCGGTCGGGCGGGATGAGATCCGGCGGGTCGAGGACGGATCTGAAGACGGGGTGGTGGAGCTCGTCCTTGAAGACGCCGAGGAGGGGGGGATCCCGGTGGCGGGCGCGGAAGCGGCGGAGGAAGGCGGGGTCGGAGACGAGGCGGCGCCACTGCTTGCAGACGAGGGAGGCGCGGGGGAGGGAGGAGGGATGCGAGGGGAGGCGGAGGAGGATCTCCTGGATGAGGTCGTCGTTGTCCGGCGGAAGCACCGGCGGCGGCGCCGGCGCCGCCGGGGATGTCCGCCGCCGCCGCCGCTGCCGGCGGCAGGTCATTTCGTCGCCAT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.359144
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa10LNT0061400.2 10 2240588 A G
Osa10LNT0061400.2 10 2240261 A G
Osa10LNT0061400.2 10 2240665 C T
Osa10LNT0061400.2 10 2240781 G A
Osa10LNT0061400.2 10 2240785 A G
Osa10LNT0061400.2 10 2240790 G A
Osa10LNT0061400.2 10 2240792 A C
Osa10LNT0061400.2 10 2241395 T C
Osa10LNT0061400.2 10 2241531 A C
Osa10LNT0061400.2 10 2242273 C T
Osa10LNT0061400.2 10 2241009 C A
Osa10LNT0061400.2 10 2243002 A G
Osa10LNT0061400.2 10 2243737 A G
Osa10LNT0061400.2 10 2243801 A C
Osa10LNT0061400.2 10 2243939 A C
Osa10LNT0061400.2 10 2244405 T G
Osa10LNT0061400.2 10 2244637 G A
Osa10LNT0061400.2 10 2244831 A G
Osa10LNT0061400.2 10 2244851 A C
Osa10LNT0061400.2 10 2245028 A G
Osa10LNT0061400.2 10 2245154 G C
Osa10LNT0061400.2 10 2245324 T C
Osa10LNT0061400.2 10 2245327 A C
Osa10LNT0061400.2 10 2245328 A C
Osa10LNT0061400.2 10 2245603 T G
Osa10LNT0061400.2 10 2245859 G C
Osa10LNT0061400.2 10 2241377 A 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
Osa10LNT0061400.2 osa-miR812q Cleavage 4.0 16.31 1 24
Osa10LNT0061400.2 osa-miR5815 Cleavage 5.0 17.785 1 24
Osa10LNT0061400.2 osa-miR396a-3p Translation 4.5 9.22 1 20
Osa10LNT0061400.2 osa-miR396b-3p Translation 4.5 9.22 1 20
Osa10LNT0061400.2 osa-miR168b Cleavage 5.0 22.123 1 21
Osa10LNT0061400.2 osa-miR171c-5p Cleavage 4.5 23.984 1 21
Osa10LNT0061400.2 osa-miR437 Cleavage 4.0 10.4 1 21
Osa10LNT0061400.2 osa-miR439a Cleavage 5.0 19.023 1 21
Osa10LNT0061400.2 osa-miR439b Cleavage 5.0 19.023 1 21
Osa10LNT0061400.2 osa-miR439c Cleavage 5.0 19.023 1 21
Osa10LNT0061400.2 osa-miR439d Cleavage 5.0 19.023 1 21
Osa10LNT0061400.2 osa-miR439e Cleavage 5.0 19.023 1 21
Osa10LNT0061400.2 osa-miR439f Cleavage 5.0 19.023 1 21
Osa10LNT0061400.2 osa-miR439g Cleavage 5.0 19.023 1 21
Osa10LNT0061400.2 osa-miR439h Cleavage 5.0 19.023 1 21
Osa10LNT0061400.2 osa-miR439i Cleavage 5.0 19.023 1 21
Osa10LNT0061400.2 osa-miR396f-3p Cleavage 3.5 23.204 1 24
Osa10LNT0061400.2 osa-miR396f-3p Cleavage 5.0 19.066 1 24
Osa10LNT0061400.2 osa-miR2873a Translation 4.5 19.342 1 24
Osa10LNT0061400.2 osa-miR5492 Cleavage 3.5 10.978 1 21
Osa10LNT0061400.2 osa-miR5492 Cleavage 4.0 15.345 1 21
Osa10LNT0061400.2 osa-miR5509 Cleavage 4.0 10.5 1 21
Osa10LNT0061400.2 osa-miR2929 Translation 4.0 19.657 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa10LNT0061400.2 10 nan Physiological trait Sterility R2309 RG257
Osa10LNT0061400.2 10 nan Physiological trait Sterility C701 C16
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