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

>Osa10LNT0060200.1

AGTAAAATTAAAAAGGATGACTAAAAATTGTATTTGAAAAGAGTTCCCATTTTTTCTGTTGTTCTAAATTGGCTCCTACGTTGCGCTGCTGCATTTTACACATCATAGCAAGCATTGCAACACTACTAACTCGTAGACTGAACAAATGAATTATGTAACTAGTAATACCTGCATGGCACATATGGCGACTGAAATCAAGATAGAAAGAAACGAGAAGCAAAACGTAGTACATATGGGAAGGAAATCATATGTAGCGTTAGCAGCTGTGATCTTTACAATGGAATGGAAGCTCACGCTTGCTATTGGAGGATTTTAAGGTACATACGTCTTCCTCTTGTTTCTCTTCGTCAGACGAAGCTCGAGTACCATCTTCTTGCTCTGCTACATGTCAGTCGTGACTGAGGGTGGTGAGCTCTCCTTTTCGTCATCTTCCTCTAGCAGATCATCCTCTTTATCTGCCAGATTATTCTCTTGCTCCCGAATATGTCGATCATCCCATCTACGGACTACAAGGGTTGGATTGTTGGGGTGGACCTCGGTTGCACGCCTCAGACCTCGTGCACCAAGAGCGTAACGCTCACACGCTCCAGTGAAGGGAGATGTCCCATGGCCAAGTCGAGATCACCACTGCTACCATTACCGATGGCCATGTCGTTGTCCCATGCTCGGAGGCTGAACTCAAGGTACCTAACCCTCGGCATGGCTCCTCGTGGGAACATGGATGGCACTCTGTCGCGCGTTGGAAGGCGTTGGTGCTGACCACAAATCTCTCCACTACACGCTCCTCTATGCTGCCAGTTCTCCAAGGATTTGTATATCCCCCGGTCGCACTTGATCAACCCACATGTCTATACAGGTGATGAGGAGCAATGGGTTGATCCATGTCGGCAGAGTCGAGAACGAACCGGTAGATCCTTTGGACAGAAATCTGTGGAGAGATACAGGGGGCATCCAGCCTTCCTGCATCAGATTCAGACATCCACCAAATGCGTAGATATTCAGGATCTGCAGCCTGTGCAAACTTCCCAGGCACTCTACTAAAGCTTTGTCCTGCTTCTCACCCACTTCTTCCCATTCGATGGCAAGCACTCTCAGTCTGGTCAGTTGGCGCAGCTCTTTCACAATGTCTACACATTTACTAGTTGAGATACTCGACAACTCTTCTAGCGATGTCATTTCGCCTAGCTTGTCTGGCAGCCTTGTGTCAAAGCTAACACGTAGGCACATCAAACGTCGAAGCTGAACAATAGTGGCAGGCAACTTGTTTATACGAGATCCAACTAAGTCCAGTGTCTGCAAAAACTCTAGTTTGCCAATTTGCACTGAGAGCTCGTGACCAACATATGTGGCGGTATGGCTTTCTGCATATTTACTATTCCATTTTATAATGTATGTGTCTCGTAGTCCTAGGTATCTAAGGTGAAGTCACAACCTTCCAAATCCAATACTCCTATCATTTTAAAGCTTGAAAGGGATGGCATTAAGTTAATTGCAGGACTAAACATAGTGAAGGACCTCACTTGAAGCATAGTCAGGGTACACCAAGGGGTATTGCACTCTGTGGTGCTATGTTGGAGAGATAACCTGCGTACCTTGTTTCGTGAACATGTGATATTCCCAATATCATTGAACACAGTGATGAAGTTTTGTTGGCTTGACATGTGGCATATGAGATCAAGCACCATGTCATGTACACGACAAGCTTTTGCTCTGCCTTCAGCATCGATATCAATGGGTTGGATCATGCTTCTATTTACGAGTTCGTTAAAGTAATTTTCACCTTGCTCAAATAAGCTACCACCATTTTGTGTTTGTTGCACAAAACCTTCTGCTATCCACCTCCATATCAGCCGGTTTCTCCTAATCTCATAATCTTCTGGGAATACACTCAGACACAATAAACAAGACTTCAGATGTGAAGGTAGATCATAATAGCTGAAAGATAATATTTTCTGCATGTCTTCAACATTACGGCCTTCTGTAAGTCCACGTCCAATAGAATTGTGCAAAGTAAACCATTGATCCTTTGTCTGTAACTCCTTATTAGCCAAAAGGCTTGCTATAGTAATTATGGCTAATGGCACACCGCCACATTTTTTCAAAATTTCATTGGATACTTCCTCTAGTTCACAAGGACATCCATTCCCATGAGGAAATATTCTTTTATAGAAGAGTTTCTTGGAGTCATCTTCAGAAAGAGGTTTCATTTTATAGATTATATCATTATTGGCAGAGCAGCATGCTTTAGATACATTGACATTGCGGGTCGTGATGATTAACCTACTGCCAAGATTGTCTTTAGGAAAAGCACACTTGATATAGTCCCATACTCTCTCGTCCCATAAGTCATCGATTATGATAAAGTACCTCTTGTCCTGAAGAAATTCTCTCAATTCGTCAATGAGCTGTATTTCATCCCTTGATGATTCATTGATGTTTGCATATTTTACTTTGTCCAATTGATGAAGCATCTTCTTGAAAATCATTCTTACGTCAGGATTCCTAGAGACAGAAACAAAAGCCGAACAATCAAACTGTGCTTCAATTTTCTCATGCACTGCTCTTGCAAGAGTTGTCTTGCCCGGTCCTCCAAAGCCAACGATGGAGATAATCTTCAGTTGCTGCTTGGATGAATCTTCACCTTCTGTCAATGTCTTGATCAGTTCCTCCCTAGCGTGATCTATACCAACAAGATCTGTTGCGTCGATGTACAATGCTGTCAAGCGTGGATCAATAGTACTAGTAACCATGCCGCTGTTTTGCAGCTCGAGTCCGCTGTACCTTTCACGCAACCCAGCCATCTGCTGCGCGAGGGCTTGGGCTTCCTTGATGGCATCAGCAATCTGATGGAGCTCCTTTGCCTTTCTGAACAATTTGCTTATCTTTTTAATAGGCCTCTTGACTCTGTTCTTGAAGGTACTGGGCCCACTATGGGAGTCATCTTCCACACGTACCATGAATGCATCACCGGCATCCTCCATGTCGTACGAGATCTCTCTCACCTTGGATGCCCAGATCTTGACCTGATCATCTAGCTGGTCTAGGGGCACCTCAGCCACCTTACGGAGTGCAGCATGCATCATCGTGAGCTCTATCTCCAGAGACTTGACCCCTTCCCTCACATGCTTCTCAAGGTTGTATTCATCCTTGAGCAGCTTAGCAAGCTTGGGGAGGAGAGCTCTCATCGCCCCTGCTGTGACCTCCATGCCTCAATTTTGCAGAGAAGGGGAATGCTACTCTGTTGTCGTTTCCTGATGAAACTGGACAGCACCTTCCTGCTCAATTTGATCGTCCAATTCCAAGTCCCAACTCCTCCTCTCAGCTCATCTCACTGCTCGACCCATCGCCCCGACCTGCAC

Coding Potentia
Explanation CPC Score
noncoding -1.0733
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa10LNT0060200.1 10 1541257 A G
Osa10LNT0060200.1 10 1541263 T A
Osa10LNT0060200.1 10 1541341 G T
Osa10LNT0060200.1 10 1541558 G A
Osa10LNT0060200.1 10 1541614 T G
Osa10LNT0060200.1 10 1542079 A C
Osa10LNT0060200.1 10 1542186 C G
Osa10LNT0060200.1 10 1542427 A G
Osa10LNT0060200.1 10 1542689 T C
Osa10LNT0060200.1 10 1542843 G A
Osa10LNT0060200.1 10 1542846 A T
Osa10LNT0060200.1 10 1542962 T C
Osa10LNT0060200.1 10 1543296 A T
Osa10LNT0060200.1 10 1543416 A C
Osa10LNT0060200.1 10 1543590 A G
Osa10LNT0060200.1 10 1545272 A T
Osa10LNT0060200.1 10 1545273 T A
Osa10LNT0060200.1 10 1545337 G A
Osa10LNT0060200.1 10 1545499 C A
Osa10LNT0060200.1 10 1545544 C T
Osa10LNT0060200.1 10 1545570 A G
Osa10LNT0060200.1 10 1545821 C G
Osa10LNT0060200.1 10 1546002 T C
Osa10LNT0060200.1 10 1546008 A G
Osa10LNT0060200.1 10 1546164 G A
Osa10LNT0060200.1 10 1546405 G C
Osa10LNT0060200.1 10 1547917 G C
Osa10LNT0060200.1 10 1543094 C T
Osa10LNT0060200.1 10 1546814 A G
Osa10LNT0060200.1 10 1546889 A G
Osa10LNT0060200.1 10 1547190 T C
Osa10LNT0060200.1 10 1547277 A G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa10LNT0060200.1 DTM_#DNAt_MULE_japo_Os0229 Chr10 - 1543806 1544282 476
Osa10LNT0060200.1 DTM_#DNAt_MULE_japo_Os1617 Chr10 - 1546438 1547546 1108
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa10LNT0060200.1 osa-miR5790 Translation 5.0 16.988 1 24
Osa10LNT0060200.1 osa-miR5837.1 Translation 4.5 12.583 1 21
Osa10LNT0060200.1 osa-miR5837.1 Translation 5.0 20.421 1 21
Osa10LNT0060200.1 osa-miR166g-5p Translation 5.0 15.361 1 21
Osa10LNT0060200.1 osa-miR393b-3p Cleavage 4.5 16.22 1 21
Osa10LNT0060200.1 osa-miR1854-5p Cleavage 5.0 16.364 1 21
Osa10LNT0060200.1 osa-miR1320-3p Cleavage 4.5 12.013 1 21
Osa10LNT0060200.1 osa-miR5152-5p Cleavage 4.5 15.062 1 21
Osa10LNT0060200.1 osa-miR5161 Cleavage 4.0 8.682 1 20
Osa10LNT0060200.1 osa-miR5485 Cleavage 5.0 14.615 1 21
Osa10LNT0060200.1 osa-miR5513 Translation 5.0 22.319 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa10LNT0060200.1 10 hwd1 Physiological trait Lethality nan nan
Osa10LNT0060200.1 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