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

>Osa02LNT0159300.2

CCTCAAAGCAGATCCTTCCATGAAGCAGGTGGTCCCAGTTCACCAAATAATTACAAAATGTGATGCATATTTTTGTGCTGATCAATAAAACAACAAAATTTAGATATCAAAATCTGCAACAATGTAATGATGGTATGCTTACTATATTAAATGTTTGTGAAGCAACTTGTACATCCCATTGGTAGCATATAGTACATCCGTAGCTCTAGGAGGCTTTGATGGAAAAAAGACCATATCTGTCTGTGCTATGCCATTGCTTTCTAACGTTTCTGAAAGTTGAGAAATTTTATGGAATAGCCAAAGATGAGAACAAAGGCGGCCATAAAGCCAAAATGGGCAAGTATAACATATCCTAGGAAGTCATGTCGGACGCCAACATTATCTTCCAAAATTTGGCTCATTGCTACATGGCTCCCACCAGGAACTGAAATCGATCCACCGTTCCCTCCAAACTGTGATGCAATGACACCATATATTGTCCAGGATACTGGGTTTGCCCAATAGTACCACCTCCACCAAATTGGTATTGCCTTCCTAAAAATAAGGAACCCAGCAAACAAGTTCCAAAGAGGGAGTGCAAAGGTTATGAGAATGTTCGCAAGCAGTGCAGATGGGGTGCATGCCACCAACATCATTCCGAAAAATGTGAAGTAGTTGAAGCTTGAAACAATGAAGAATAGAAAATAAAAGAATTTGCTAGCTTTCCAATCGTATCCGATCATTGCATAGATGATGACCGTGTACAAAATCCCTTGTATGATATTGTAAATGAACTCCACGCTTGCCTGAGCAAATGCATAGGACAATGGAGAGTACATTCCTGCTGCGCTTTCACGATAGTAAACTGCTCTCTCAATTGATACAACAGGCTGAACTGACATGCAGTTAGTAGCCCCAATGAAGAAGATTGCAGCATAAGTGGCTCCGAGTAAATTGTACAAATCTTGCTGTGAGTCTAACTTTGTTCCTTTTTGCCAAAATACTGTGCCAAAGAAAAGGCCATAGAGAAACGTTGTTAGATAACGCAAGCTATTGTAAGATGGATTCTTCCAATAAGACTTATATTGCTTCCATAAGTTCGCAACACATTGGATATAGAAACTTTGAGAATATTTTGTAGCAAATAAGAGATCTCGATAGCCTGGTGGGGGAATGCTCAACTCCTCAATAAGTTCTTGGTTTTTCCTATAAAGCAGGGAATTGGCATAAATTTCAGCAAAATCTACGTTCATGCGAGCTTCTTCTAGAGTGGAGCTAACTTCTAGCATCCATGTTGCAGGATTATATCCTTCTGTAATACTTGGAACACCTAAAATTGTCTCAAAATATTCAACTAGTTTATGTGAGTGGTCACCAAGTTCACCAGCATAAATAACCCGACCTCCTCTTTTCAAAAGCAAAAGCTCATCAAAAGACTCAAAAATATCAATGCTTGGCTGATGGATCGTGCAGACCACAGTACGCCCAGTGTTGACAGTATTTCTCACAGTTCGCATGACAATTGCTGCAGCTCTAGCATCAAGACCAGAAGTAGGCTCATCCATAAAGATGATTGAAGGATTTGCTACCAGCTCCACAGCAATTGTTAATCGCTTTCTTTGTTCAGTCGATAAACCGCTAACTCCAGGGAGACCAACCATAGCATTGCACAATACATCAAGCTCTACAAGGGCCATGACCTCCTCCACAAACATCTTTCTTGTATTGCTATCAACATCTGAGGGAAGGCGCAACCAAGCAGAGTAGAGAATGGATTCATATACAGTAACATTTGGTGAATGGATATCAGCTTGTTCACAGTAGCCGCTAATGCGAGCAAACGTTTCTTGTTTCTTGGAGTAACCAGAAAGGGTTATGCTTCCTTCAATTGTTCCACTAGTTTTCCTTCCTGCTAAGACATCCATCAAAGTGGTCTTTCCAGCTCCACTGACACCAACTAATGCAGTTAGAAGACCTGGCCTAAAAGCACCACTAATATCAGAGAGCAGTTGGAGACGACTTTCCATGAGTCCTTGTTGCTTCATTTCTGAGGGCATGTCCACATAATAATTTAGATGGTTGAAACAAAGTGACAATGGTTGGAAAGGTAAGACAAATTGTGACTGAGTTGGCCTATTTCCTTCTCCGTTAGCACTCGTAGGTATCGATGATGTTGTGGTGGATGTTCGGGACCTATGCTCTTCATTTCTTGTTTCCGTGTACAACTCAGTTTCATTGTGTTCATCAATAACTAGTGCGTTTGCACTTCTAATAGCTAGGAGAGCCAATTTTTGAAGTATAAGTGCCCAACGTTTTTGCATCAATGGTTGTGTCATTGTTTGGAATGGCCCACCTACTGGCCAGAAATTCGTTGATCGATATTGCATTTTGGCTATACATCATAGGAGATGCCCAATAACACCAGATCCACCATGGTCTAATGTCATTTTTACGTATCACAAATCCTCCAAAGACGAAGACAATAAGCAACACAAGCATCCCAAAACTAATTGCTATAACCATTGTTTGCAAGATAGCACCAAGAAATCGAAACAGAGCCATTGCCATTAGGTGAGTAACGAAGAAAGCTAGAAACTGACGAAAGAACCTTCCTGCTGCTGGTGCAAATCCCATCACATAGTACGTGATGACAACCCAGACCGTAGCCTCCACAAGAGATACAGGAACCTTTATTAGTATATTTGCAACCCCAAAGGTCCATGGAGGGAAGAATAAAAAATCTCTATGCTTGTAGAACACAGGAAGCTTCTTTACTGTCAAGTTTAGCTCAGAAAGGCCATTGAACATGACTGTTATTAAATTGAATGTCAATGCCCCAAGAAATTTAGTGCCATCAGAAAATTGCCCATGGGGCATCTTTGTTCTAAGAAACACGGTCATAGACAAGAAAGCAAGAATGATCAATTGGGTGACCTTGAATATGTAAAGAAAAGAGTTGCGTTTCATCAACAACTTCTCTCTACAAAGCACAGCCTTCAATGACTCCCAGTTGGATAATGCATTTTTCATTGTTGTCAGTGCAGCAGGATGGATTTTTGATTTTTCAAATGGAATATGTTGCTCCTTCATCATTTGTTGGCCAATATAAAATGACTTGAAACGTTCTGCAAACTCTGGGACTGACACATAACAATAAGGCTCCTTGTCAAGGAACCAATATTGTTGCTGGTCTTTCTTGGAAGTGACCTCTTGAAGGAAGTCAGCCACTGCTTTCCTTTGAGGGCATCGAAAGCCAGAAGCTTCAAAAAATTCCAATATATTCTCGCGTGGCCCATGATAGACTATGTATCCTTCTGATAGTAGAACTATGTCGTCAAAGAGATTATATGTCTCTGGCGGTGGTTGGAGGAGAGAGATCATCACAGTTTCATTCATTATATGGACCAAATGCCTAATAAATTTTACAATATGAAATGTGCTAGAGCTATCCAAGCCAGTGGATATCTCATCCATGAGCAAAGCCCTTGCCGGTCCTGTTAACATTTCCCCTGTTGTCACACGCTTCATTTGTCCACCAGAAATTCCTCTAATCATCTCATCACCAACAATAGTATCAGCGCAAATGTCCAGCCCAAGCACCTAACAATGTTCAATGATCAT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.29847
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0159300.2 2 12663637 T A
Osa02LNT0159300.2 2 12666195 A G
Osa02LNT0159300.2 2 12667302 T G
Osa02LNT0159300.2 2 12667732 A T
Osa02LNT0159300.2 2 12668466 T C
Osa02LNT0159300.2 2 12664136 A C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa02LNT0159300.2 osa-miR5528 Cleavage 4.0 10.394 1 21
Osa02LNT0159300.2 osa-miR812q Cleavage 4.0 14.96 1 24
Osa02LNT0159300.2 osa-miR6251 Translation 4.0 13.694 1 21
Osa02LNT0159300.2 osa-miR1861d Translation 3.5 19.33 1 22
Osa02LNT0159300.2 osa-miR1861e Translation 5.0 19.33 1 22
Osa02LNT0159300.2 osa-miR1861g Cleavage 5.0 19.528 1 22
Osa02LNT0159300.2 osa-miR1861k Translation 5.0 19.33 1 22
Osa02LNT0159300.2 osa-miR1861m Translation 5.0 19.33 1 22
Osa02LNT0159300.2 osa-miR1866-3p Translation 5.0 14.81 1 22
Osa02LNT0159300.2 osa-miR1862e Cleavage 4.5 18.317 1 24
Osa02LNT0159300.2 osa-miR2874 Translation 4.5 15.811 1 24
Osa02LNT0159300.2 osa-miR5488 Translation 5.0 18.45 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0159300.2 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0159300.2 2 np2.2 Morphological trait Culm/leaf RM324 RM262
Osa02LNT0159300.2 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0159300.2 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
GWAS
Transcript ID Chromosome Locus Trait Value Plus Minus