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

>Osa09LNT0451400.1

AGTGTTAAGCATTTCTTCTCTATTATTCTTGTTTTTTCCCTTACAAACACACACACACACACACACACACACAAAACTGTACAACAAGCTCTATTCTTCTATTTCCCCCAAAGCCGGCAGACTTTCGCCTTTACCCATGGGAGAACTAAGGAGCAACAAAAATATGCTTTCCTCTATTGTATCGAGATGACAAACTACAGAATAGATGGAGATTATCCTGCAAAAAGCTTGAAAAGGAACTTCTACTTGTCATCCTGATTCCTGGGGCGGCAGAGTCTTGAGCACATCCCTCAGGGCGTAATATATGCTTTCACATTTGTGATCGGATATCAGATTGCCAGATAACAGTATCCTCTGAAAATTCTCCCCGGCATCACCTCTCCAGAGTGTATACGACTCATCTTCTACACCGTTTATATCCTCAATGTCCCTCTTGAGGTAATACAGAGTCCCAGGAAGGAACAGATCTTCTGGCACAAATACATCCTCTTTACTATCCGGTGACAATACTTCACTGGTGCTCAGGGGGCGATCTTGATCTTTGATGGCATCAGAACTAGTTGATACTGTGACAATTTTAGCATAATCAGCAAGCTTGCGCGCCACATCTTGAATTGACGAAACTACAAGCTTAGCATTAGTCACAATGTCCACTATATGCTTCCAGTCTTCTTTTTCCAAAACACTTACCCAATCTGTTTTGAGTATTTCGGCTCGCAATCTTGCCAGTGAAGCTGCACTTAATCTAGGGATGATATCATCCTGCAGTACAACAGTTGAAACATAGCTTGCACAACTTTGAGCAATTTCTCTTGAGACACAAGGCGGGGTTCCATATCCAACAGCTGATATAACGTCAGGACTAAATCCAAGCTCTTCCTTTGACTTCTTCCTTAGCATTATAGCAAGCAACGCGGCTGAAGCACCTCCAAGGGAGTGCCCTACCAGGCGCAACTTGTAATCCTTATGCTTTTCCAAACACTTTCTGATAAGTCCCAACTCATGGCGAAGGTACCAACGGGCGGCCTCATATGTTCCAAAGTGTGTCGAGAAACCTTTAGGTGATACCTTCTTATCGCTTAGAGCAATCAAATCGGTAACTAGGTCATAAACAGTGTGAGTCCCACGAATCCCAAGGATGACCAATTTAGTGCGTGGATCAATGGCAATGTAATAGCCAGGTCTGAGAATACTGGAGTCCTTGACGAATTTGAGAACGTTCCTCTTGCGAAGCATAGAATGGCGTGCAAGGCCAGTGGCATTGCCCTTATAGCAACCTCTTGCAAGCTCAAGGTGATAAATTAGTTGTTGAACCTAGAAAGTGTTAGTTGGAACTTAGAAGAGTGTATGATAAACAGTGGAAAGAAAGGAACATTTAATTGTATTGTATAGTATAAATGGGTTGAGAAAGAAGCAAGATTATAGATTGTTTTTTTTTGAACTAGGAGAGCAAAGCTCTCCCATTTCATTAAGAGAAATGAGAGTTACAGAAGTCTAGCAAGATTATAAATTGTGAAATTGTGATAGGGAAGAGAAGAGAAGGGGGGCTAGCCTTGTTGTTGCAGGAGATATGAAGACCCTTGAAGGCTTGAGCATCCTTTGCAGAAGCTTGGCTGAGGTAGATGAGGTAGAGGCCGATGGTGAGATCAGTGAGACTCCAGTCCTTAATGCTGACCTTGCTCCGCTGGAGGTCGCTTAGGATCTCGCTGAAGGTGCGGGTGCTTGCGGGGATATTGTCAGTAGGCGCACTAGTGAGGAAAGGCTTGTATTGGTTGTAGAGTTGCAGTGCGGGCTCCAGGGCCTTGGGGAGCCAGGCCACGTCAGGCCTCCATCTCCTCCACGGGAAAGCTTTGCCCTCGTCGTCTTCCTCCTCCTCCCCCGACGATGCCGTCCCCATGCTACTAGTATTCTTGGGGTTGGGGTTGGGGCTGGATGGGGAGCCGAGGTAGCGGGCGAGCGCGGGCGGCAGGAAGGGGATGTGGCAGGAAGGGCGGTGGGCAATGAGGCGGCAGCGGGAGAGGAGGAGGAGCCTCTTCGCCGCCATCTCTACCGCCCCCCGGACAGTGGAGGCGGCGGTTCCGTCGAGGGTTCCGTTC

Coding Potentia
Explanation CPC Score
noncoding -1.15772
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa09LNT0451400.1 9 22811872 A C
Osa09LNT0451400.1 9 22811942 G A
Osa09LNT0451400.1 9 22811972 A C
Osa09LNT0451400.1 9 22812349 T A
Osa09LNT0451400.1 9 22812767 G 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
Osa09LNT0451400.1 osa-miR5797 Cleavage 3.0 15.894 1 21
Osa09LNT0451400.1 osa-miR818f Cleavage 5.0 20.159 1 21
Osa09LNT0451400.1 osa-miR156f-3p Cleavage 3.5 20.749 1 22
Osa09LNT0451400.1 osa-miR156h-3p Cleavage 3.5 20.749 1 22
Osa09LNT0451400.1 osa-miR156j-3p Cleavage 4.0 20.749 1 22
Osa09LNT0451400.1 osa-miR395t Cleavage 5.0 14.608 1 21
Osa09LNT0451400.1 osa-miR156l-3p Cleavage 3.5 20.749 1 22
Osa09LNT0451400.1 osa-miR167e-3p Translation 5.0 20.859 1 21
Osa09LNT0451400.1 osa-miR167i-3p Translation 5.0 20.859 1 21
Osa09LNT0451400.1 osa-miR395o Cleavage 4.0 14.608 1 21
Osa09LNT0451400.1 osa-miR2118f Translation 4.5 23.616 1 22
Osa09LNT0451400.1 osa-miR2118h Translation 5.0 23.616 1 22
Osa09LNT0451400.1 osa-miR2118j Translation 4.5 23.616 1 22
Osa09LNT0451400.1 osa-miR2118k Translation 5.0 23.616 1 22
Osa09LNT0451400.1 osa-miR2118m Translation 4.5 23.616 1 22
Osa09LNT0451400.1 osa-miR1863b.2 Cleavage 5.0 18.59 1 23
Osa09LNT0451400.1 osa-miR395x Cleavage 4.5 14.608 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa09LNT0451400.1 9 qTN-9-2 Morphological trait Culm/leaf RM215 RZ404
Osa09LNT0451400.1 9 yldp9.1 Morphological trait Seed RM242 RM205
Osa09LNT0451400.1 9 nan Morphological trait Root RM215 RM205
Osa09LNT0451400.1 9 nan Morphological trait Root RG667 RZ404
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
Osa09LNT0451400.1 9 22811972 Lemma-and-palea-pubescence 8.48714447 -