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

>Osa06LNT0348100.2

CCGAAAGAGATTATAAGGCAATGATTTGTTGTATCTGAAGCCTTTAAAGTACAACAATTGATCTCTCCCTTCACTTGCAGCCATATGTCTATACAATTGTCCACGCCAGAGTGCAATGAAAGTGGATTTTGTGGTGATGGTGATTCTTCTCCTACTGACAGTATCCCCAATCATCAAAGCCCAAGTTGTCATGATGTTACAGAGTTATAGAATACGCAGTGATGCATTTGAATTAATAAGGATCAGATAATTGCTAAGATTCCAGTGCATGTCACTGGGTAGGCCAAGGGGAATTGGTGTGCATCACCTGTTCATGCAAATGGATTTGGTGTAGAGTTTCCAACAACATTATCCATTGCAATAGGCCAAGGGGCACCGATCAGTGGCCACCTGCATACATACACATATTGAAATTAGTTCATCAGTCAAGATGATCACTGGTTATCTTGGGCTCTATCAGTTGTTCATAGCAAGAGGACAACTCATGTGCATGATCAAATTATCATGTAGACGATGGAAATAAGTGTCCCACCAGCTTTAGGCTCTATCATAATGCATGTTTACCTGCAGGAAAGTGTACTAAATTATTGAAAAGTTTGAAGTGAATCTTATTTCCATATTCTACTGCATAGAAACAAAATTCAAGGAAGAAATTCATATAACAGTCTTCTCCTTTTTGTCTCTGCCTCCATTAACAGAAATTCCAAAGCTCCATATGAATGCCCTATAGGACAATAGGACACTGCACATAAATATGTCATCAATTTCTCATATTCTTATTTGTAGAACTGCATTACAGGGAGGAATACAATAGCCCATGGCTAGCATAATTCTCATGGAGGTAGATTTCAAACAGATCAAAATAGCAGAACTATAATGACTCATATGAGCAAGCCCGTGATTAGTCGATGGAGAGCATGTTTTGGAATATATATCACAGGAAATAATATATAATATCTATTGTAATATACAATGTGACACCCAACTATTAGTCCATTTAAGTCAGTAATTCATGGAAAAAAAAGGTGCATACACTGTCTAATTATAGCTCACAGTCCACTTTCCCTGTCTCTTTGCGCCCTTCCTCTTCCCCTGCTTTTCCTGTGAGCCATCGAGCTGCCACCACTATTACTCTTTACGTCGGCTCCATCTGTGGCCGATGGGGAAGAGGGACGACCTCGTCTCCAGCGTGGCCAGCGGTGGAACCATATCTTGCACACCATGGCGAGTGAGACCAACAAATCGAAGGGCGCAGCACGACGGTAAGTCGTAATCACGAAAGCCAATAGAGCAACTCAGTCGTCAGAAGCAGTCGGCAGACCACCAATCACATGAAGGGTGGAAGAAGCAAATTCCATCTGAGGGTGAGAAGGGAGGAGATCACCGGCGAGGAGACCCATGCGACAGGGAAGGAGCAGGAAGCCCGACGAACTTCTTGTGTGGCGCCGCGAGTGACGACGATCTTCCTGGGCGGCACCGAGGTCAAGGGATCCCATCGAAGTCGAGCTGAGCCTTGATCGCCTGTGGGAAGGGGGAGGGGGGTGCGACACGGGGATTCCGGGCACGACCTGCACACTGCACAGGTAGGGTAGGGGTAGGCAGTGGGCGATGAACGGCGCCGAGCTCCGCTGAGCCATCGGAGTGGAGAGGATGCGCAAAGAGCGCATGGCCGGCGCGGCGGAGGGGACGGCTGAAGTGGAGTCGGAGGGATGACGGGGCGACGGCGGAGGGATGACGGGGCGACGGCGGCGCGGCGCGTTGGCAGCGTTGGGGGTGGTTGGCGTGAGGGTGGGGATTTTTGGGTGAGTGCAAGAGAGAGAATGGGAGAGGTGGCGTGATTTTCGGG

Coding Potentia
Explanation CPC Score
noncoding -1.1541
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0348100.2 6 20822204 C A
Osa06LNT0348100.2 6 20823850 T C
Osa06LNT0348100.2 6 20824821 A G
Osa06LNT0348100.2 6 20824848 A G
Osa06LNT0348100.2 6 20825024 A G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa06LNT0348100.2 osa-miR5541 Cleavage 3.5 17.719 1 21
Osa06LNT0348100.2 osa-miR5834 Cleavage 5.0 14.912 1 21
Osa06LNT0348100.2 osa-miR5079b Cleavage 4.5 13.009 1 22
Osa06LNT0348100.2 osa-miR1859 Translation 5.0 11.404 1 22
Osa06LNT0348100.2 osa-miR1865-3p Cleavage 3.5 18.939 1 24
Osa06LNT0348100.2 osa-miR2868 Cleavage 3.0 13.201 1 20
Osa06LNT0348100.2 osa-miR5079a Cleavage 4.5 13.009 1 22
Osa06LNT0348100.2 osa-miR5150-5p Translation 4.5 18.746 1 24
Osa06LNT0348100.2 osa-miR5160 Cleavage 4.0 14.032 1 22
Osa06LNT0348100.2 osa-miR5502 Translation 4.5 14.126 1 22
Osa06LNT0348100.2 osa-miR166g-5p Translation 3.5 9.206 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0348100.2 6 amy6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0348100.2 6 asv6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0348100.2 6 tgw6.1 Physiological trait Source activity RG264 RM3
Osa06LNT0348100.2 6 qLDLJ-6-1,2,3 Physiological trait Source activity RM217 RM3
Osa06LNT0348100.2 6 ph6 Morphological trait Dwarf RZ667 RG653
Osa06LNT0348100.2 6 gw6 Morphological trait Panicle/flower RG424 R2549
Osa06LNT0348100.2 6 nan Physiological trait Eating quality RM253 RM162
Osa06LNT0348100.2 6 RPLD4 Physiological trait Eating quality RG424 RG172
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