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

>Osa09LNT0427800.2

GCAAACTTGGGCTGGTGCTATATTCATATAGAACTCGACATTACTGATCTGAGAACTCATATCCGGTACAGAATCAAAGCAGATGAAGCACCTATGCAATACAATCAATAGAATCAATGGAAGAGAAAGCCAACTTGCACAGATAATCTAAAGCTAGCGGCTAACATTTCTGGTAATATAGAGCAGCTGCGATAATATAAGTATGCCTCTTAGAATTTATATTTTCTTCTTGATAATCCATAACATCAATCAGAAAAACAAACTGTTTTGTACAATCAACTAACCACCTTCAGATTTAATTTAGGCACAATTGATCGGTGGCTGCAAGCAACATGGTCCCATACTCTGATATTGATTTGTCTTCCAACTCTTAAACTTAAGACGCACTGGAAGGAATGGCAGGTTATCCTCAAGATTTGTCTTTCCTTGAAAGATTTGAGAAACTTCTATTGCCACGGAAAGCCAGTGCTGGAAACAATGGGTAGCATACTGAGACACATCATGCTGATTTTGTTTGGGATCACAGAATGACTGAGACGAAAAACTTCAGTATGTCAGTTCAAAACTACAATAGAGTCATCTAGCCTAGTTAGAACTGCAAAATAGCTAGCAATTCTGTGACATTTTTTTGACACAATTTTTTACAAACAAATAAAATTATAGCAAGCAAAAATTATTCTAAATTGTTTTGCGCAAAAGCTGGCTGAAGACTTAATTTCCAAGCCAATGCGTCACCAGTAAACAGAGCAGAATGACAGCAACCCTTTCAATTGGACCAACCCAACCAAACCACATTAATTCTGTCAAGCAATAGAACTAAGTGAAAATTTGAAGTGGCCATATTATTCTGCCAATATTCTAATTGCAAATAGAAAACAATGATACTGGCAGCTGTTTCAAAGCTAAAATACATTGTAGATCATGCAAAGCAAATATCTTGATAATTCAAATATGGTTGTAATCTAATTGAAACCATGTGATGTCTACATAACAAAAACTATATAATATATCATATATCAACAGGCGTGTGAGGGCACTGATAAGCAAAACATGACAAATATAGATGAAAATATTAATTTAAACCAAATTGTATATAAAGAAATATTGCAATGGAAGGAAATGTTGTGAATATAAGCAACTAATAGAGTTGGGATCAACCTATCATTTGGGGTAAAAAGATTGTTTTACTTAAATGGTTACGCTGATACTTCCTCTATTAGATCAAAGCGGTAAGAAATAATTCCAATTATCTTACATTTAGCTAGTGTATGAATTAAGTTAGCGGTAAGAAATAATTCCAATATTCCAATGCAATACAGATTACATATTGTCCCATGAGTTTTTAGGTCTAGCAGAAGTGTATGACTATAACCAAGATCTGTATGGTAGATATTGTAGGAGTTGCAGGCTAGATGAATTTTCCATTCAAGCATAATGTAGACAAGTCTGTAGAATAAGCTTTATAGGGATAGACCCTTGTATAATGTAAAAAATAATAGAATGAGAGGATCAGTTGCATACCTCCAAAGTGAAAATTGCCACTCGGATCTACATAGTTTTAAGAATCTTAAACATCAAGGAAATATTCATTCAACAGCTCCATGCAAAATATTAACTTTTTTATATATGTAATTACAAACGGTGAAGAAATACCATGGTTTTGTTAATGGATTCTTTTTGAAAAAAAATGTTAATAAGTGGCAACAGAACATGGTTTTACTTAAGATAAGTGATATGGTACTACAATTTAAGAAACAAGAAAAGAATGTAACTTGTATGTAATTTCTTTTGTCCTTAGCAATTTTAATATTTTTTCTTTCCAGTATTAGATATTGTAAGCATGCAACAAATAACAACTAAAAAGTTGTATAGAACAATCATGTGGTCCAAATTATAAACGATTCAAAGTGGAAATATCACTGGGATACATTTTATATTTGTATTTCTACAAACTGGGGTTGGCACTCAACATTACTTATATGAGAACAAAATGCATAACCAGTACATATACAAAGCAAATCAAGCAACTGTGCAATTCAATCAATAGGATTTCATGGTTCATCTGTATCGGACAACCTGCATTTCTGCTCACATAGAGTAGCTGAACAATTTGAAATGACATATTGGGGACTCCCAGATTGACCTAATGTTGGATGGTGCTGTGTGATTCCCCGTTTAGTCGGTAGTTTCCTTAAGACGAACAATACTGAAGCTGAAGGTACAATCTCAACCAACCATCTAAGGAAAGTGAATGTTATCAACAAAGGATATCGGTGAGTACAATTGTTGGTTTGCACATGCTCAAAATGACACAACATAGGATTGTGTTTTGCAGTTTATTCTTGGCACATTTTTTAATGGCTAGTTGCAAAAGCTAAATAAATTTGGTAGGAATTATCTTTTATGTCGATTACTTCACAAAAATCCAAGGATACTCCAGTAACAAAAGTTCATTTTTAACTCGTTCAGCAAAATTGATATGTTATACTTTCAAATGGCTAGTTACATGTAGATCTGTTTTCATCGCTTCAACTATGAATTTGCCATGATTATCCATAGGGAAAAAGATAGTCCCATTACACAGATGGAACAATGGATTGACAATTTGTAAAAGAATCACCATATAGTATTTTTGCTAAAAAAAATGCCTATGCGCAGATACATGCACACACACGACTTTTGTGAAATGAATATTTTTTTGTTCCCTCTTATATATTCTACCAAAATCAAATTCTTTTAGCCATAATCTCGATAGCATTTTCAGCTCAGGTATTTCTCTAAACACAATTAATCTATTAGGATATAAACAAGGCAAAGGAAATATATCTTTCACAAGTTTATACTATAATCTAGCAGTATGCTTTGTTTGCTTCCACACCAATTAAAATCATGTTATAAATGATTTC

Coding Potentia
Explanation CPC Score
noncoding -1.30629
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa09LNT0427800.2 9 2399166 C T
Osa09LNT0427800.2 9 2397482 A T
Osa09LNT0427800.2 9 2397182 T C
Osa09LNT0427800.2 9 2397950 A C
Osa09LNT0427800.2 9 2398294 A T
Osa09LNT0427800.2 9 2399970 C T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa09LNT0427800.2 osa-miR5530 Cleavage 5.0 9.416 1 21
Osa09LNT0427800.2 osa-miR5543 Cleavage 4.0 17.116 1 21
Osa09LNT0427800.2 osa-miR169d Cleavage 5.0 15.18 1 21
Osa09LNT0427800.2 osa-miR171h Translation 5.0 11.743 1 21
Osa09LNT0427800.2 osa-miR171h Translation 4.5 18.767 1 21
Osa09LNT0427800.2 osa-miR1862d Cleavage 5.0 13.451 1 24
Osa09LNT0427800.2 osa-miR2122 Translation 4.0 14.588 1 22
Osa09LNT0427800.2 osa-miR2864.2 Translation 3.5 14.273 1 21
Osa09LNT0427800.2 osa-miR2864.2 Cleavage 4.5 14.7 1 21
Osa09LNT0427800.2 osa-miR2864.2 Cleavage 5.0 11.829 1 21
Osa09LNT0427800.2 osa-miR5081 Translation 5.0 10.266 1 22
Osa09LNT0427800.2 osa-miR1320-5p Cleavage 5.0 9.297 1 21
Osa09LNT0427800.2 osa-miR5081 Translation 4.0 13.097 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa09LNT0427800.2 9 qPC9 Physiological trait Eating quality RM4413 RM1896
Osa09LNT0427800.2 9 qAC9 Physiological trait Eating quality RM4413 RM5122
Osa09LNT0427800.2 9 nan Morphological trait Root C711 G103
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