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

>Osa10LNT0059300.1

ACTTCAATATTGGAATTCCATACGAAATAACTGTAGTTCATGTGCTCGAATTACAAAACCTTTCTGAACAGAGTACTGAAGCAAAAGATGAATCCAAAACAAGTTCTAGCGTCTCATACAATACAAAAGCAGGGAAGTGCAAAAACATCTTAACTCCCAAACCACAAAAGGAACAACAGACAGTAACACCGGTATTACATATCCAGCCTTGCAAAGCGGCAGAGCTCAAGCGCCAGGCAACAAGTAAACATGCTTCTGCCTCTTTTGGCAACAATGACGAGCACCTAGAACAACCGTTCAAGCAGTGCAGCAATCAAATTTCAGTTATTGTGCTCATCAGCAGCTTGGTGATACTGGTAGTCACCTTCATCATATGCCTCGCCCTCTTCAGGGCCTTCAGGTTCTGTGTTGTTAGGTTGCATCTGATAGTACTCATGCTCATGTCGCTTTGAGCGCTCCGTCTCATAAGCATCATGGCTTTTGTGTTGCTCATAGTTATAGCCATATTCCTGATCATGTTTTGGCTCACCGTTGGCAAATTCAGCATCTCTCTCATGCATGTGACCACGGTCCCGTTCATGACTTGCACGCTCGTAATCTCTCTCACGGTCCCTGCCTCTCTCACGATGGCGATCATGACCACGGTCACGGTCTCTCTCATAATCCCGACCACGATCCCTGTCCCTATCTCTATCACGACGATCACGCTCACGGTCACGGTCACGACCATGATCTCTCTCCCGGTCCCTTCCTCGTTCCCTGTCCCGAGTCCTGTCCCGATCCCTATGGTGGTGTCTATCTTCTTTTGAATCACGCTCGCGAGTACGGTCATGGGATCGTTCACGAGTTCTCTCATCACGATCTCTTTCCCGTGGCCTTTCACGAGACTTCTCGCGGTCCCTATCTGCACGACGCTCATCTCTCCTAGGCTCCTCCGATCTTGGGCGTCCAGCGTGCTGCTGATCCCTAGTGGAGAGCTTCTGTTCAGCATTTTCACCACCAATTCTGCTTGATCCAAGTCCACCACCCAATCTCCTGGGACGCCAATTTGGAACAGTTCTACCACGCTCCACATCAACTAGCACCCTCCTATTGTCCACTTTTCTCCCATCTGCTTGCTTGTAAGCATTTTTCATGTCCCGGGTGTGCATATACTCGATGAATGCATATCCTCTAGGTTTATTTGTTTCCTTGTCGGTCACAAGCCGTACCTTGCATATGTAGATCCTTCATTACGAGGAGTGAAATCCAGCACAGATCAACACAGTTGGAGGCAAAAAGCAGTCTGGCTGATTGGCGTTTGTGGGAAATACAGTGATACCCCCTTACCAGGGAATTTACTAGATTAAGAAAAGAAGATGGTGGTGGACTAAATACAATACCCATTTACCCTCTCCATTGCATATAGTTCGTTCAGCCTTCGTCGGTAAGACCATCAAAATAGACAACGGTTACATAAATGGAGGTGACAAATAGCAAGTCAGTGATGTCTATTCCTTACGCTGTTACGCATCAGAAAATGGAGCCATCTTCAACTCTAAAAGTTGAGATGTCATTTGCATTATATTTTGCTGTTGTTTCCTCCAAGAGAAGCAGCACTTGAAAGCAGAACTAGCTTTAACAGCTCAGGGAAAGTAACATAAACACTGTACTCACCAGCAACCTAATAAATCCCAGAATGTAGAAACCCCATGCCTGCAGATAAGCTGCTTTTAAAAGCATAAAGTGATCTAAGCTTACTTGTGCCATCGCCAACATTCTTCAAGCTTGTTTGCTCCAGTTAATACACACGAGAAGCAAGTTCATAGAATGGGAAAACAAATGATACATTGTGCCTACTGCAGAAGCAAATGGTTTGATCTTTTCCGAGAGTAAAAGGGAAAAGATGTTCTAAGAAAAAAAAACATCAAGGCTGCATGCAGTAAAAATACCTGCTTGTGTGTATTTGTATTTCCCAGGATTTTTTAGTCTTCTAATGGTTGTACCAACCATTCGCACATTAAATTGCTCAACAGTAACTCAGATAATATGTCTAACAAAAATTACCAGAAGACATAATTTCTGCTGGAGCTCTATATTACTTATCCACTAAGTACATCAACAGAGCCCACATGTTTAGAAATGGATAACAAAGAAAAGACTGTCCGAACCACCCAAACCAATACATGTCAATACAAGATAAAAGTGTTATTTAAATAATTTGAGAAGATTATTTGGTTATTTTCTCCTTGGTTTAGCAAAATGCAACCAACATCATTATTGAGAAGCAAACAGCAAATGCATGCTTACACACAAAACAGTGAATGTATTGCCCAACTTGAAAATGAGAGTGCTATGAATACTGTTTGACAAAAACAAGAAGTTATTTTTGTTTGCTGCAAAAAAAAAGACTTGACAGAATAACTTATTTTTGTTCTTTACAAAAAAGAAGACTTCACAGCATTTTGTTTGATTTAGAAACAAATACTACAGACAATTCTGCCCATTGAAAATCGGAGAGAGATAGAAGATATCCCTTTCATCCTTTAGCACCTTGTTGTGAAATTCCAAGTAAGCAATATATAATGGCAGTGAACCAGCTTTTTCTTAAAACATGTTTTTGTAGATGAATTAGAACAACCAAACACCTTACCAAAGAGGAATAAGTCCACCTGCACTGGAATTTACCACATGTACTTACCCTTTTAATAGGCCCATAAGCTTCAAACTCCCGCTTGACCCTATGCTCAGACGTCTCATAGTTAAGTCTTGCAACAAAGAGTGTTTTGTATGGATCTCCAGTGGCATTGGGGTCACTCTGTGGGTCATATTTCTGAAGCTCTTCAGCCACCTTAGCCGCACCTTGGTCAAGCTTACTTTTGCGGATCCTATCCTTCTTTTCAGCCTTGGTCTCGCATGTGGGGACGGGTGGCGCGTACTCAGGGTCACCGGGCTCCGCAAACTGCGACACGAACTGCGCCATCCCAGTGTAGGCCGGCAACTTGCGCTTCTCGACGGGCGGCTTGAAGTCGAGCGGCGGGCGGGGCTCGAAGAGCTTGAGCAGGTTGGGGGTGAGGCCCGTCGGGTGTCCCTGCCCCATCAGCTTGAGCTGCTGCACGTTGACGCGCTGGCCCTTGGTGCGGGACTGCATCCCGCCGCCGTCCGGGTTCCCCCGCATCATCCCGCTGCCGTAGTCGCCCATGGCCGCGGCGCCGGCGGTGGCGGCGGCGGCGCGAGGAGAGAGAGAGAGAGAGAAGCGAGAGGGATTTGCGATTCGCGAAGCGTT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.891343
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa10LNT0059300.1 10 1007784 G A
Osa10LNT0059300.1 10 1008471 G C
Osa10LNT0059300.1 10 1008916 C A
Osa10LNT0059300.1 10 1009988 G A
Osa10LNT0059300.1 10 1010616 G A
Osa10LNT0059300.1 10 1011101 G A
Osa10LNT0059300.1 10 1011414 T C
Osa10LNT0059300.1 10 1011505 T C
Osa10LNT0059300.1 10 1011613 T C
Osa10LNT0059300.1 10 1011693 A G
Osa10LNT0059300.1 10 1012641 A G
Osa10LNT0059300.1 10 1012283 T G
Osa10LNT0059300.1 10 1010705 A G
Osa10LNT0059300.1 10 1010987 T A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa10LNT0059300.1 osa-miR5543 Translation 4.0 14.91 1 21
Osa10LNT0059300.1 osa-miR5837.2 Cleavage 5.0 19.163 1 21
Osa10LNT0059300.1 osa-miR6253 Cleavage 2.5 11.27 1 22
Osa10LNT0059300.1 osa-miR156c-3p Cleavage 3.5 20.256 1 22
Osa10LNT0059300.1 osa-miR156f-3p Cleavage 4.0 20.256 1 22
Osa10LNT0059300.1 osa-miR156g-3p Cleavage 3.5 20.256 1 22
Osa10LNT0059300.1 osa-miR156h-3p Cleavage 4.0 20.256 1 22
Osa10LNT0059300.1 osa-miR397a Cleavage 5.0 13.32 1 21
Osa10LNT0059300.1 osa-miR397b Cleavage 3.5 13.32 1 21
Osa10LNT0059300.1 osa-miR156l-3p Cleavage 4.0 20.256 1 22
Osa10LNT0059300.1 osa-miR164e Cleavage 5.0 16.307 1 21
Osa10LNT0059300.1 osa-miR166h-5p Translation 5.0 18.351 1 21
Osa10LNT0059300.1 osa-miR171h Translation 3.5 12.419 1 21
Osa10LNT0059300.1 osa-miR1850.3 Cleavage 5.0 14.414 1 22
Osa10LNT0059300.1 osa-miR2055 Translation 4.5 14.858 1 21
Osa10LNT0059300.1 osa-miR2055 Translation 4.5 10.325 1 21
Osa10LNT0059300.1 osa-miR1862f Cleavage 4.0 13.568 1 20
Osa10LNT0059300.1 osa-miR1862g Cleavage 4.0 13.568 1 20
Osa10LNT0059300.1 osa-miR5339 Translation 5.0 15.794 1 21
Osa10LNT0059300.1 osa-miR169p Translation 5.0 15.735 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa10LNT0059300.1 10 hwd1 Physiological trait Lethality nan nan
Osa10LNT0059300.1 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