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

>Osa10LNT0062200.1

AGTTAGTGCGCTTTGCGAATTCACAGGCCCTATCTTGTGGTATGAACTGAGTACGCGATGATTTATGGCGCATATTGGGGGCTTACCAAAAGATAATGCTGTGAATTTGCAAAGCGCTCAAACCCACTGAAGTGTTGTGTAAAGGTAAATATCTGTAAGTGTTCGTGAAGGGAAAGCGGGTAAATATTTCGAATTTATTTCTTTAGAAATGTAGCTGACACATTAGAAAGTTTGAACACACAACATTACATATTAGTTCGAAAGAGCAAAATATAAAATCGTTCCACTCATTAGCCTCATCATCAAAATTTCGTGATGTGCTAGTGTCCTTTTTCTTTCCCTTTCTTCTAGCACTAGCTGGAGGTCTGCGTCTTGACAAAGATAATCTTTCAGGTGAATGTCACTCGCGGACAGACCTATGTGCCACCTTAACACCGCTGAAATCAACATGCCCGTAGTCTTGGGTCAGCTGAGTTATTGGAGGTGGTTCATCAATATGCGACGGTCCTATCTCGTGTAGTGCTGTTGACGACCCCCACCGTAGCTACATGGTTCTCTGTAGGACTGTGTGCTGTCGGCATATCCTATCATTTGGTCGGCAGTGTACATTCATGTTGTTTGTGGTTGCATGATAGGTGATTGACTGAACAACCAATCTCCTTGGCCTAACATGTCCAAAAAGCTTGGTCCTTGTGGTTGTACATTTTCAGTTATGGACATTTGGTAGATCCCCACTGATCGTTCATACCCGTTGGAAACATGAGCATGTTAACTTAAGGTACACCTTGGGGATCGATGTGGCCTCGTTGTTCATTGATGGTCCAAGATTCAACTCTTCAGCGGCGAGATCCAACAGAAACACCTCTGCTGCCTGGCCCTGGCTGCGCCACAAGCCCACAACCAGGAGCTCCAACCGGCGGAGAAGACGCCGACAACATCGAGGTCGCTGCTTCTTGCTTCGCCGCATCCTCTCTCGATCTCTCTCTCACCGACAGCTTCTCTTGCTTTCCTCCCATTCATGCAGGAGAAATTGGAAGATGAGGATTTATGTTTTTGAACTGTAGCTTGGGCTCGTTTGTGGCTGAAGGGAGGACACGCCTTGGGCTGGCTTGTGCACAAATCTTGAAGAAAAATCCCATGGCCACAAATCCAGCTGACAAAAGCGCAAAAAAAAAAAAAACAGCAGGCAGCTGTCTAACAAATCCCTAATTTTGTAATCTGCTCCCGGTAATAAACCCTTTACTAAACTAGCGGTGAAGATGCAGCTCTAGATCCAATCCGTCCATCTGGGCTTTCCCCTTCTTCCTACCATGATCACAGCCGTCCATCCCCCTCGCCCTCGTGCCTTCGCGACCCTGCTCTCCTCGGTGACCGTGTAGGCTTGCCGCCGGCACCATCAGTGACTCGACCAGAGGCTTCTCGTTCCCGCGCTTGCCACCGGAGCCCAGCCGGAGCGTCACATCAACCGTGGCACTCGCCGGCTCACCCGTCGTCGGCGAGGACGATGGCGACGGCGACAACAAGCTGCTCTTTGGAAAGAGGGATCCCGGCGGCCACCTGTGACCAATCTGCGACGGCGGCAGCGGCAAGAAGCTGAGTCGCACAGGTGTAAGACGCCAGAAGAGCACCGCAAGTTGCACGGTTAGAGCAACCACCGGAAGCGGTGGCGGTGGCGACAACGACGACTGCGGCGGCGGTGGCAGCAGCTGCCTCGCGGACGTGATCCTCGTGGCGGCGGCAGTGATCCTCGTGGCCGGCCATGGCTTGCTGCGACGGGAACCTCTTGCCGCACACCCTGCACGCGAACGACGACGACCTTCCCTTGGGCGGATCGCGAGCACCACCACCAGCTGGCTTCGTCGCCGTCTTCTCCTTCTTCCCCGCCACCGGCGACGTCGAGCTCGCGCTGGAGGAGCGCGGCCTCATCGGAGACATGGCTGCCGGCCGCGATGGATCGATGAAAATGGGT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.934477
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa10LNT0062200.1 10 3966550 T C
Osa10LNT0062200.1 10 3966906 A G
Osa10LNT0062200.1 10 3961551 T C
Osa10LNT0062200.1 10 3961572 A G
Osa10LNT0062200.1 10 3961673 T C
Osa10LNT0062200.1 10 3961875 T C
Osa10LNT0062200.1 10 3961924 A G
Osa10LNT0062200.1 10 3965738 A G
Osa10LNT0062200.1 10 3965869 T C
Osa10LNT0062200.1 10 3966046 C T
Osa10LNT0062200.1 10 3966128 A G
Osa10LNT0062200.1 10 3966444 T C
Osa10LNT0062200.1 10 3966564 A T
Osa10LNT0062200.1 10 3966574 G A
Osa10LNT0062200.1 10 3966594 A G
Osa10LNT0062200.1 10 3966630 C T
Osa10LNT0062200.1 10 3966651 A G
Osa10LNT0062200.1 10 3966666 C T
Osa10LNT0062200.1 10 3966714 T A
Osa10LNT0062200.1 10 3966785 G A
Osa10LNT0062200.1 10 3966876 A C
Osa10LNT0062200.1 10 3966890 G A
Osa10LNT0062200.1 10 3967099 A G
Osa10LNT0062200.1 10 3967168 A G
Osa10LNT0062200.1 10 3967194 T C
Osa10LNT0062200.1 10 3967197 T C
Osa10LNT0062200.1 10 3967241 A C
Osa10LNT0062200.1 10 3967311 G A
Osa10LNT0062200.1 10 3967464 T C
Osa10LNT0062200.1 10 3967499 T 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
Osa10LNT0062200.1 osa-miR5813 Cleavage 4.5 23.568 1 22
Osa10LNT0062200.1 osa-miR169r-3p Translation 4.5 24.193 1 21
Osa10LNT0062200.1 osa-miR1853-3p Cleavage 5.0 13.326 1 22
Osa10LNT0062200.1 osa-miR1863c Cleavage 5.0 22.879 1 24
Osa10LNT0062200.1 osa-miR2926 Translation 3.5 19.764 1 20
Osa10LNT0062200.1 osa-miR5076 Translation 4.5 17.51 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa10LNT0062200.1 10 nan Resistance or Tolerance Other stress resistance R1933 R1629
Osa10LNT0062200.1 10 nan Resistance or Tolerance Other stress resistance R1933 R1629
Osa10LNT0062200.1 10 nan Physiological trait Sterility C701 C16
Osa10LNT0062200.1 10 nan Physiological trait Sterility R2309 RG257
pre-miRNA
Transcript ID Pre-miRNA Identity(%) Alignment Length Pre-miRNA start Pre-miRNA end E-value Bitscore
Osa10LNT0062200.1 osa-MIR1428a 89.916 119 2 120 3.95e-38 154
Osa10LNT0062200.1 osa-MIR1428d 91.87 123 2 124 1.13e-43 172
Osa10LNT0062200.1 osa-MIR1428e 88.288 111 1 109 5.98e-31 130
Osa10LNT0062200.1 osa-MIR1428f 91.589 107 2 108 1.63e-36 148
Osa10LNT0062200.1 osa-MIR1428g 100.0 109 1 109 1.24e-52 202
GWAS
Transcript ID Chromosome Locus Trait Value Plus Minus