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

>Osa02LNT0159100.1

GGCCATCCAGACTATCTTGACATATGTCCGTAGCCCAGCTCTCTCCTCGCTTATCTCTGATCCTTCTCCTACCTGCTGCCCCCAGGTAATGTGTCTGCACATTCTTTGTGTGTGTACATGAAGTTTGAGAGGCGTTTTGCTCAAGACCGCGCAACGATTCCATATGACACCGCATCGTTGTCCATGCCTATCATGTTCATCCAGAGCCCCTGTTGATCTTCAGATAAGAGAAAAGCTCAAAATTAAAGAAGGCTTGTTTATTGATCATGTCAAGGATAGGTATCGACGGCGATGCGCTGGCTATGGCCATGGTTGTGCGGTTCTTGCGCAATAACGTTTTGATCTCGATCTCCTCTCCTCTCTCCAAAGTTTTTCTTTCTTTACTCCTCTGATGGAACAATGCATGCATTTACTGAGTTTTTGTCTCCTGTTCTTCCTCGTCTGCATGTTCTTGAATGGTTTGGTCGCTCTTATTCTTCTGTGATTTCCTTGTCCATCATTATCTCAGGGCATGCATGAAAGCTCTATAAATTAAGATGGAACCTTTTCTTTTAGTTTTGTTGATGATGACTAATTTGGTTTGTTGCTAGCTACTAGCTGTTGTTTCCTGTCTGAAAACTATGAAGCTATCTTGTAAGGTAGGTAAGACGAATGCGGAGGTTCTTACTACTTCGGCCCTTGCCTAGAGCTTCAGAAATATAAACTAAGATTACCATGAAGAACAGGTGTGTGCAACTTTATTTATGGTATTGATGAAAACTCAATCTAGTAAACATCATGTATGATCCAGTAGATCGATCGATTAGATTCATCGTACCTGAATCTATTTTTGCTTACCGTACTGTAGCTAGTCTTTCACCTTCAGTCTTTGCAAGTTATATTTTTTTATACTAGGTTTCGTTCTTGCATACTTGCAAATGCTCTTGTAATTGAGTTTTCAGAGTTCTCCACTTGCAATAACAAATATTTTGGTTGTCTTTCCATGAAGCAGATCAGATGGCTAGATAGATGGTAAATGATCTGAAAAATATAAAAGAAGATTACAGGCACTGTTTGACAATACTTAACTGAATCTATATGCAACTTATCTTTCAGTACATTGCACTGGAATTTGCCATTTGCTAGCACTTGCTGCCTATCTGTAGTGCTTATGGGATTCATGTCAGAACTAACTACTACCTGTATTTTGTAGGTTTAAGAGTGTAAATTATTGGTCCCCTTCTTGCATTTTCTCTCAATTTATTCAGGTAACAAACGCTTGCAAGTCTGCTATTTTAAGCATTGCAAGCAGTACTAGTACTATATATATACATGCTCCGCTAATGGTCAGGCAACAGAAGACCAAACATTGTACTAGGCCAGCCATCTCGTTACATACTTACATCAATGTTTGCACTGTGATGTGACTCTTGATGCATTATTTGCTCGATCATATATATGTAAAATATAGCCAGTTCTCATGCATAATTCATGTGAGAAGATCGAGCAAGAGTGGTCGAGCCGTCCAAGAAGACATTATAAAACCACAAAAGTTCCAACATATTGATCATTGATTGCTGCTGTCCTACAGCATCCAGAGTGCTATAAATTCACATCATCAATTCATCATCTCCAATATAATGCAGCTGCAAGTTTCATACATGGATGTGGCTTGTTTCCGACATCGCAGAGGTTAACTTCTTGTTGCTATCCTCCATTATCTATTAAAAAAAAAATCTTGTTACTATCCTGATGGTCAGAGTTGCCTGATGATCGATTGATGTCTTTTTGGGGGTCTCTCCATGGAATTGCACAGACAAATACCCAGTGTTCTAGATTCCAGAAATGTTATCAGTGACAATGTGTGTTCAGGCTAGGTGCCAAAGGAAGTACAGGTACCCCATCTGTTGACTCTTGTGCTAGCAGCGTGCAAGCAAGCAGACAATCATGCATATGGTCTCAGTAATTGCATATGAGTGATGTAGGACATGGTGTTTACTCCCCTGAATGCAGGCCCGGCCTTGATCAGGGGCTAATTAACATTACTTAGTGCAATCTTTGCTCTGTTTTGTAATTACATTGATGTGCCAGATAAGCTACAGTACATCAGGAATGAGAGGAGTGCATCAAAATACTGAAGACCATGATGGATATTTCGAAATTGCAAATGAGGGGTGGCCGGTCTGTAAAAACAGTTTTCTCCTAAAAGATCGACATTGCTCAAGCGACCTTAATCTAGAAAATAATTTCAAAGGAAACTAGGAATCATGGCATGGATCAATGAGGAGGCACTTTCTAAGCCAAGTGATCAAGTCAAGGTGCAAACTTATCACGAAGGTCTTTCAGAACTCATTCGAAGTGTTTTTGCGGCCTGCAATCCTAATCGGCCAATAACACATACGCCTTCTGGCCAAACTCCTCTACCCTTACTCTCATAAATAGGAGCTAACCTTCATATGAGGTCAATGTACCAAGGAAAGGTTGATAACAATCAAAATCGAAAGGATGGAGTAACGATTGCATCGATAAAAAAAATCCCAGCATTGTAGCGCAAAAGGACATGTGAAGAAGAGATGTTGGAGAGTTTCTTCATGCCTCAGATTACACACAACACAAGTAGTAATCTGGTCTCAAAAATTTTCTTGTATTCAATCTAATATTGAGTATCAGCGAAAAAAAAAAGACTTTGTGCTTTGGTTGTGAGCAACATTTCCATAAACCAGTTAAAAGAAACTGCAATGTTTACAGTCCCC

Coding Potentia
Explanation CPC Score
noncoding -1.28705
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0159100.1 2 12452618 G A
Osa02LNT0159100.1 2 12453064 A T
Osa02LNT0159100.1 2 12453138 T A
Osa02LNT0159100.1 2 12453327 G 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
Osa02LNT0159100.1 osa-miR5526 Translation 2.5 16.123 1 21
Osa02LNT0159100.1 osa-miR5541 Translation 4.0 12.86 1 21
Osa02LNT0159100.1 osa-miR5793 Translation 4.5 11.192 1 21
Osa02LNT0159100.1 osa-miR6251 Cleavage 4.5 20.915 1 21
Osa02LNT0159100.1 osa-miR1437b-5p Cleavage 4.5 13.15 1 21
Osa02LNT0159100.1 osa-miR395f Translation 4.5 18.194 1 21
Osa02LNT0159100.1 osa-miR1861c Cleavage 4.5 16.077 1 22
Osa02LNT0159100.1 osa-miR2873a Cleavage 4.0 13.599 1 24
Osa02LNT0159100.1 osa-miR1863c Cleavage 4.5 16.169 1 24
Osa02LNT0159100.1 osa-miR1863b.2 Translation 4.5 16.016 1 23
Osa02LNT0159100.1 osa-miR3982-5p Translation 4.5 17.573 1 21
Osa02LNT0159100.1 osa-miR5488 Cleavage 4.0 11.232 1 21
Osa02LNT0159100.1 osa-miR5508 Translation 4.0 11.552 1 21
Osa02LNT0159100.1 osa-miR5517 Translation 4.5 14.784 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0159100.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0159100.1 2 np2.2 Morphological trait Culm/leaf RM324 RM262
Osa02LNT0159100.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0159100.1 2 tgw2 Morphological trait Seed RM290 RM550
Osa02LNT0159100.1 2 nan Resistance or Tolerance Drought tolerance RG83 RG171
pre-miRNA
Transcript ID Pre-miRNA Identity(%) Alignment Length Pre-miRNA start Pre-miRNA end E-value Bitscore
Osa02LNT0159100.1 osa-MIR5179 100.0 224 1 224 3.34e-116 414
GWAS
Transcript ID Chromosome Locus Trait Value Plus Minus