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

>Osa06LNT0354800.4

GTCAGTGGAGCCCGGTGAGCCGAACCTGATCGAGAGATCGAGTTTAAGAGGTGAGCTTATATTAGGCACAGCACCCCACACCAACATTCACATTCAGTGCACCCCAAACACCAAGAACTCCTCCTTTTTTTCTCCTGTAATAATCCTGTACCCTCTCTCTCTATCTCCCTGCAGCTGCTGCCTAGCTCCAGTACGGCCACCGTCGTCGATCGGTCTCTCTCTCTCACCGGATCCGAGAAGCAAAGAACCGATCTTTTTTCTTCTTTTTTCCCCTGCGTGATGCTTCTTGTTTACTACTACGTGGGTGCAGTGCAGGTTTGTTGATCGATCTTGGGGCGGGGCGGGATCGAGCATATGAAAGGCGAGATTGTTGACAGAAGAGAGTGAGCACACGGCGCGGCGGCTAGCCATCGGCGGGATGCCTGCCCCCGCCGCGTGCTCGCTCCTCTTTCTGTCAGCATCTCTCATCACTCCCTCCCGCATCCCCCGCCCCGATCTCGCGTCGATCTCTCATCTCCGGAGAGGAGCCATCTTTTAATTTGTTTGATTTGATTTGATCTCGTTTCCCTGAATTTCTTGGTGGAAACCCGCGCCGACACGCGTGGCTTTTCTTTCTTTCTTTCTTTTTTTTGTGCAGAGACAGAGAGATCGAGATAGCAAGGACATGTCACTTCATTATCTTCTAGAGCCTTGCATGCCGGGGAGCTACTACCGAGGAGATCAGCGATTATTGCTGATATGATGCTGCTGCTGATGGAGTGATGGCAAGGAGGAGGAGGAGAAAAGATGAGCATTTGATGTGTGCTGCTAGCTGGGCTTGGTGAGCTCCTGCTGGCTCAAAAATGGAGCATGGAGGTCACTAGGAGGAGAACCATATTTGGCAAGGACGGTGGTCTCGCCTTTGCTTTGGCCAGATCTGATGGATGATAAACTACTACATGCATGATATAATGGATAGCAGAAGCAAGCTAAGCCACCACCACCACCAGCAGCAGGAGCACTAGCTGCAAGTCTCTGCAATATCACCAATACTAAGTACAGGTGCACACGATGAAGAGGGAACAACAGCTGAAAAGAAGTGAAACATAGGCTGCTTCTGCAGTATTGATAATTTCTAACAGTTGCTGTCATAGAAGGCAAATGCATCTGCAGCTTACATGGAGCATTCTGCAAGAGTATGTTTGGTGATAACTGAGTTTTTAGAGGATGTGTGCAACCAATTCTCGCACGCAAGTCCATCGCGATAGGGGATTTGGTGTTCACTGAATTCAAACCGTTCCTTTCAAGCAAGAAGGGTCCTGAAGGATATAACAGCTTCAAATCATACAATCTTTGCCCCTCCCTTTTATTCGGCTGGAACTATTGAAATGTCACTTTCAGGATGGTTAGAAGCTTGTGCTTTAGGGGAAAATTTCAAAACTTTTGCATTTTTTCCTTAGCCTTTCTTTGTCAGTAGTACCAAACTGCGCCTTTATTTCCAGTGTTCCTGGAGAAACGTCACGCTCAATATTAGTTGACCATATACACAAATTCTTTGCTTCCAAGGTATCATTTTCCTTTTGCAGATTTGGACATTTTTTGCCATGCCAAAGATCTCATCTTTTACAGGCTCCCAAAGAGCATTGGTAGTAGTTGGTAGTACACTGGTACTATTAGTACCAAATGACTGAAAAAGAATGGTTAGTACAGTAGTACTAGTGCTGCCCATGAGTACTTTGGTTGTTGCTCTTGTCATCTTCCATGTTAATTACTCCTATTTTGCTGTCCGGTACCTTGGATAGTTCAAAGTTTCTGCAAGCTTTGCAAACCTCCAAATACAAGGTAATGGACTACTATTATAATGGATAATCAAAGGAGCTGTCACTTGTCTAATCTCCATGAAAACAAATGCAAAGCTAGGACAGACGTGTCCTGAATCTCCAATATAATACAGGGGATTGCATAGGCAAACGTTCTATTATTGTACCTGATGAATGTTGTAAAGAACTCTAATACAGTTCAGTGTTCAC

Coding Potentia
Explanation CPC Score
noncoding -1.05272
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0354800.4 6 26555138 A C
Osa06LNT0354800.4 6 26555770 A C
Osa06LNT0354800.4 6 26557877 G A
Osa06LNT0354800.4 6 26558253 A C
Osa06LNT0354800.4 6 26559182 C T
Osa06LNT0354800.4 6 26560047 G T
Osa06LNT0354800.4 6 26555936 A C
Osa06LNT0354800.4 6 26560685 T C
Osa06LNT0354800.4 6 26560742 T A
Osa06LNT0354800.4 6 26554504 T G
Osa06LNT0354800.4 6 26555935 C T
Osa06LNT0354800.4 6 26557966 A 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
Osa06LNT0354800.4 osa-miR5820 Cleavage 5.0 18.314 1 21
Osa06LNT0354800.4 osa-miR5837.1 Translation 5.0 17.571 1 21
Osa06LNT0354800.4 osa-miR164a Cleavage 4.0 20.217 1 21
Osa06LNT0354800.4 osa-miR164b Cleavage 4.0 20.217 1 21
Osa06LNT0354800.4 osa-miR164c Cleavage 4.5 20.217 1 21
Osa06LNT0354800.4 osa-miR164c Translation 5.0 7.07 1 21
Osa06LNT0354800.4 osa-miR164d Cleavage 4.0 20.217 1 21
Osa06LNT0354800.4 osa-miR164e Cleavage 4.0 20.217 1 21
Osa06LNT0354800.4 osa-miR168a-3p Cleavage 2.0 21.896 1 24
Osa06LNT0354800.4 osa-miR164f Cleavage 4.0 20.217 1 21
Osa06LNT0354800.4 osa-miR818a Translation 5.0 22.691 1 22
Osa06LNT0354800.4 osa-miR818b Translation 5.0 22.691 1 22
Osa06LNT0354800.4 osa-miR818c Translation 5.0 22.691 1 22
Osa06LNT0354800.4 osa-miR818d Translation 5.0 22.691 1 22
Osa06LNT0354800.4 osa-miR818e Translation 5.0 22.691 1 22
Osa06LNT0354800.4 osa-miR2092-3p Cleavage 4.0 22.265 1 22
Osa06LNT0354800.4 osa-miR2097-3p Translation 4.0 14.302 1 22
Osa06LNT0354800.4 osa-miR5076 Translation 4.5 9.943 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0354800.4 6 ph6 Morphological trait Dwarf RZ667 RG653
Osa06LNT0354800.4 6 qLDLJ-6-1,2,3 Physiological trait Source activity RM217 RM3
Osa06LNT0354800.4 6 amy6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0354800.4 6 asv6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0354800.4 6 qREP-6 Resistance or Tolerance Other soil stress tolerance nan nan
Osa06LNT0354800.4 6 tgw6.1 Physiological trait Source activity RG264 RM3
Osa06LNT0354800.4 6 nan Morphological trait Root RM4447 RM5509
pre-miRNA
Transcript ID Pre-miRNA Identity(%) Alignment Length Pre-miRNA start Pre-miRNA end E-value Bitscore
Osa06LNT0354800.4 osa-MIR156j 100.0 165 1 165 1.49e-83 305
GWAS
Transcript ID Chromosome Locus Trait Value Plus Minus