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

>Osa09LNT0428200.1

GAGAATCTCGTACGAGAAACATTTCCTTCATTTCAAATCAACACACAAACACGCAGCAACTTCACAAGTCAGTTACACGGGAGAAGGGAGAGGCAAAGAAAAGAGAAGGAAAATAGTCAAAAAGAAAATAGAAGCTCAAGGATACTTCCTAAAATGCTGCATCCAATGCTCTTCTATTTTGTCAATATACTACAAATACCAGCTACTGCCCACCTTTAGGCCGCAGAGAAACAGAGAACTCCTCGCTCTCTTGCTCGGTGGTCTTGTATGATGACGACTCCTAATTTAAATACTTGAGGGTTCTTCTATAATTATAAGCACTCCACATTGGGCTTTCTTCAACCCAACATGGCAGACTGACTAGTTGTTCCATCCTCTAGAGAGTAAGCTCTTGAGTCGATTGCCAGAAATCCTCTGCAAAGCCTTCTTTGCACCAGGCACCTCAGCCTCAGCCAACTTCTGTAAATGCTGGCAAATGCCAGAATCCGCAAGCCGCCTCCGTGTCCCATTCCCACCACCCAAGGCTAGAGCTAGAACAACTGAGACTGGATACTTTTTATCAATCTCTTCATTCCTCGGATCAAGCATGTGCAATAACCTAGTCACACTCTTCTCATCCCTGACCAATTCCTTCCGGTTAAACTTCAAGGTCATCAAAGCAAGCAAGGCACGGCCAGCTGACTCCTGTACAGTAGCTGGCTTAGCTGTCTCCATCATCTTAACCAGCATGCAAATGCACGGTGCCATGCACCGCTTGGTGTCGTCGCTCACGCCAGGTGCAAGTTCAGCAACCATATCAGCGGCCATCTGCTGCAGCAAGATGCTACCACCACGGCACATGAGGTCTGTAAGTTGCGCGAAGAAGAGCGGCGATGAGCAGAGAGTTCTAGCAGCAGCAGGGACCACTGCGAGTGCGTGGATAGCGCGTAAGACAGTGTCATGGAGATCTAGGCCAGAAGCAGTGTGCAGCGCCTGCAGTAGTGGCAGCAATGCACCTGCTTGGACAATCTGGTATTGTATCTCATGGTCTCCCAAGGATGCTAGAGACCATATGCAGAGAGCAGAACCCTTCTGTGCGTCAATAGTGCCGCTTGCAAGCAGATCAACAAGAATTGGCAGTCCACCCTCTTCAACCAGTGCTGAGCGCACATCCTCGATGGAAGCCACATTCTTGAGCGCCGCTACAGCGAGAGCCTGTACCACAGGGGACCCGGAGCCAGGTCGGCACGCATTAATCAAGATGGGTACCCCTCCGTATGCCGCAACAGCCCACGCGCTGCCGACGTCCGCGGTGATGGCTTCAATGGCCGCCACGGCGCGTTCCCGCGTGGCTGGCGCTGAGCCGGAGTCGAGCACGCGAAGGAGCGGGCCAAGGCCGCCCTCGTCGAACACAACCTTCCGCGAAGCCACGCAGGCCGTGGCGAGGTGGGCCACGGTAGCCGCCGCACGGTCCCGTAGCGCGGAGTGGGACGACGCGTCGAGCAGGCGGAGCAGCGCGGCGACATCCCCGTCGGTGGCAACGATGTGCGCGGACTCCGCGGCGATGTCGTTGGCAAGCAAGTCCAGTAGCGAGGCGAGCGCCTTGAGCTTGAGATCGAGCCCCCCGATCTGGAGCCTCGCGAAGGCGTCCCGGATGAAGAGAGACTTGTCCGCCCGGGACGCGGCTGGCGCGGGCACCTGCAGCACAATGGCGTTGGGGGACGAAGCCGACGGATCGACGTAGAGGATCCCCGAGCGAAGGAGCAGCGAGAGGTCGTGGAGGAGCAGAGAGAGCGAGGAGGCAGCGATGTCGAGGTCGCTCTGGAGGCGGAGGCGGCCGCCAGGGAGTGACGGGTCCTGGCAGCGCGCGGACAGCGCTTGCAGGGAGCGGAGCGCCGGGAGGAGCGAGGCCACCAGGTCGGCGAAGAGAGGGTGGGAGACGGCCGAGTCCGGTGCTGCGGCGAGAGAGGTCTGGAGCGCGAGCAGCGTGCCGTGGACCGCGCGCCACCGGGCGTGGAGCGCCTTCACGGACTCCGCAGCCAAGAGCAGCGCCGGGAGCAGAGCCTGCAAGATCTGGCCGAGCGCATCCGCGGCAGCCGGTGGGGGCGGGGAATGCGGCAGCGGCGGCGGCATGGGCGGCGGCGAGTGGCGT

Coding Potentia
Explanation CPC Score
noncoding -1.09477
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa09LNT0428200.1 9 2703802 A G
Osa09LNT0428200.1 9 2704424 T C
Osa09LNT0428200.1 9 2705335 A G
Osa09LNT0428200.1 9 2705347 G T
Osa09LNT0428200.1 9 2705719 T C
Osa09LNT0428200.1 9 2706289 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
Osa09LNT0428200.1 osa-miR5143b Cleavage 3.0 14.444 1 24
Osa09LNT0428200.1 osa-miR159a.1 Cleavage 4.0 15.719 1 21
Osa09LNT0428200.1 osa-miR159b Cleavage 4.0 15.719 1 21
Osa09LNT0428200.1 osa-miR159c Cleavage 4.0 15.719 1 21
Osa09LNT0428200.1 osa-miR159d Cleavage 4.0 15.719 1 21
Osa09LNT0428200.1 osa-miR159e Cleavage 4.0 15.719 1 21
Osa09LNT0428200.1 osa-miR159f Cleavage 4.0 15.719 1 21
Osa09LNT0428200.1 osa-miR413 Translation 3.5 16.709 1 21
Osa09LNT0428200.1 osa-miR815a Cleavage 4.5 16.411 1 21
Osa09LNT0428200.1 osa-miR815b Cleavage 4.5 16.411 1 21
Osa09LNT0428200.1 osa-miR815c Cleavage 4.5 16.411 1 21
Osa09LNT0428200.1 osa-miR5081 Translation 5.0 16.357 1 22
Osa09LNT0428200.1 osa-miR5143a Cleavage 3.0 14.444 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa09LNT0428200.1 9 clr9 Resistance or Tolerance Cold tolerance RM285 RM434
Osa09LNT0428200.1 9 qPC9 Physiological trait Eating quality RM4413 RM1896
Osa09LNT0428200.1 9 qAC9 Physiological trait Eating quality RM4413 RM5122
Osa09LNT0428200.1 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