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

>Osa02LNT0148600.2

CTCCAACAAACAAGCTACTATCAAAGTCAAAACAGGCCTATAAAGGATTATATAATTTGCGCCAGAACATACCTAAATAAAAGTACAGCATTCAAGTACAAAATGTATGTTGATCCTGAAAAATATGAGCAGCTCTCAAAAATCAAAAGCAGTAACACTAATAAACCTCCCAGTCATTTAGCTCAAATTTTTAGACATCTCCGTGTAATACTTTGAAAGAAGATGTGCTCAGTAGCGTACTATGATGCATGAATGCGGCCAAGACTGGCCACGGGCCAACCCATAGGTACTAATTGACCCACTCTAGTCCAAATAAACGAACTACATTTCATTTTTTGTGATTCTAAAAGTGAAATTTAGTTCATTTAGTTGAACTAGTGTGGGTAAAAGAGTATCCACGGGTCAGCCCACACTCATCCCTAGCCAACTAGTGAAGTGTATGTCTAAGTTCCTAATCTTTGTTTACATCGGCGTCAGGCCCAATTCATGAGTAAGAGAGGATGAAACATCTGTCGGATTGGCTTCAACCTCAGTATACAGTCAGCCTAAGAGGTAGCATGGTTAGAAGTCAACCTTCAAAATTATACAAGCATCTATGTGCACCACCACTAATTTCAGAGCTGATAATTTTGGTCACTTGGACATGCACAATCACACAGGTGGAGGTGGAGGTGGAGGTGGAGTTGATCCTTCGTTATCTTTCTTTCCCGGTAAACACCTTGAGATGTAAGTTTTCAATTCAGTTCGGGGAACCGGTATGAACTTTCCAGCAAAAGCCAGGGGCCAACTCACAAAACCAATACCAACAGAAACAAGCCAAAGCTTCCAACTGAGTCTCACAGTTGATGTAAATTTCCCAAGAAACTCAATGATTATTACCTGCAGCACGACAGTTATGCTCACTACAGCCAAAAAAAGATGGTTTCTTGAAACCCCATCAAATATATTCAGTTCATATGGTTTACGAGAATTGAACTCGTTAAACACCTGACAAAGCACAAATGTATTAAATATAAATGTATTTTTCACTTTATTGGCATGATCAAGAGTATCTTGAGTCAAATGCAGAAGATCCCGGCCTCTAAAGTTGAGTGTCAGAAGAACAGTAACTTGAAAGACAGCCTGAATGAACAAGTTTCTCCACATAATGTTAGTCACAAGTGGTTCTTTCCGTCCAACAGGTGGCCGCTTCATAAGTTGGTCTGTTGGTGGTTCAGTAGCCAATGCAAGTGCACCAAGTGTGTCCATAATGAGATTGACCCAAAGAAGCTGAACGGCGTTTAGAGGAACATTTCCTGAAGAAATAGCAGCAACCACATTGATTATAAGAGCCGCAACATTTACAGTAAGCTGGAATTGAATAAACTTTTGGATATTTGCATAAACCGAACGACCCCAGCGGACCACCTTTACAACTGAAGCAAAATTGTCATCCAGAATAATTATATCTGAGCTTTCTTTAGCTACTTCTGTTCCTTGGATACCCATAGCAAGACCAATGTCTGCCTCATGCAATGCAGGAGCATCATTCGTTCCATCTCCAGTAACAGCAACAACATTGCCTTTCTTTTTCAGTGCTTTTACTAGGAGAAGTTTGTCACTTGGAGAAGATCTTCCCATGACACTAATCTGATCAGCAACTGCCTCCCTTTCAGCGTCACTGTATGCCCGGAAAACTTTTCCCTCTATTATAACTGGTTGAGATGCCTGGGAGTCCGTGAGTATTCCACACTCAAGTGCTATTGCTCTGGCCGTTTGTAGGTTATCTCCAGTTACCATTCGTACCTTTACACCAGCATTTTTGCACAGATCTACAGCATTTCTTACCCCAGGGCGACAGGGGTCCTTCATCCCTACGATTCCAATGAGAGCCAGTTCATTATCTGGTAATTCCCAGTTGATTCTTTCTTCCTCATTTGGAACATAATTCAGATCAAGATTTCTATAAGCAAAAGCAACACATCGAAGACTTTCCTCGGCCATCTCCTCTATGTATTTCTTGAACTGATTAGCCTTATCAGGTGTCATTTCATGACTAATGCCATTTACATCAAGCCAATTTGTACATAAGGCAAGAACAATTTCAGCAGCCCCTTTCCAGTGCACATGAATATCTGAATCATCCACAATCACTGCAACACCGGCACGTTTCTTTTCTGAGTTGAATGGGGAGACATGAATAATAGAAGATTTTGATTTCTCCTCCGCAAATTTCATATGAAGCTCAACACCCCAAGAAAGAATAGCCTTTTCAGTTGGTGAGCCTGTTATCTCAATAGGACTACCATCCTCTGGCTCAAAAACGCTGCCTGAAGAATTCTGTGCGATTCCTTCAAGTATAAGAGAGGAAACAACAGGCGACAAATTCTCAATATCAGCTGGAGATTTCAGCTTTATCCCCCCAACAACAGATCGGACAACGGTCATCTGATTGAGTGTTAGTGTACCAGTCTTGTCACTACAAATGGTTGTAGCTGAACCCATTGTTTCACAAGCTGAAAGCCTCCGCACCAGAGCTTTGTCTGCCATCATTTTTTGCATCGAATAGGCCAGCGTTAGAGTTACGGCAAGTGGTAGTCCCTCAGGTACAGCAACGACAACAATAGTCACCGCGATAGTTAGTATCTTTATTGTCCCAAAAATTGTAGATTTCACACTTGTTTGCCCCTTAACAAATTGAATAGAGCCATCTGGATTTGTAGTATGCCCTGTAAAATATCTTGCAACAAGGACTATGAGAACCATTGCAGCAACAGAAAGCCCCACAATACCTATGAAAGTTGCCACTCCATTCAACCGTACCTGTAGTGGAGTTTCTTCATTGTTGTCTTCTGAGATGCTGGCCATCAATAAGCCCCACTCAGTGTTTAGACCGACTGCAGTTACCAACATGGTACCATAACCATCAGCTACTTTGCATCCTCCCATTAAGAAAGGTGATTTATGGTCCTTGACAACGATCTTGCTTTCCCCAGTCATACTGGATTCATCAATGGCAAGAGAATGACCACTAACCAAAACACCATCAGCCGGGACCTGGTCACCAATTTTTAGAGCCACTACATCACCAACTACAATATCAAATATTGACACTTCAATCCTTCTACCACCTCTAATAACCTCCACTTGTATATTTTGCTTCTCTTCATTAAGGTGCTGGAACTGAAGGGACTGTTTGTAGTCACTCACAGCAGTAACAAGTATGACAAGAAAGACCGCAAATGCAATGCTTGCACCGTCGTACCATCCTTCTTTGATGCCCTAATGAATTTTTTTAAGACAGAACTTAGAACTAAAGAAAACACTGATCAAAAGTTTTGCTGGCAGTGAGGGTGCTCAACTAAACCATCGTTTGTGGACATTAATGAAATTGGATTTCAAGATCAGAAGGGAAAATAATATTTAACCAATAGTTAGATAACATACAGTGCATAAGAAATATAAGAAAGGAGGATGGTTATAGGAGTCACCTCTGTTGCAATGCCCAATACCAGAGAAATTACAGCCGCTATGATAAGGATAACTAGTGTCAAGTCTTGGCAAGCTTCCCAGAGGAAAACCTGTTAACCCCCGGACCCCAAAGAAAGAAAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGATAGAGAGATAGATAGATAGATAGATAGATAGAGAGAGAGAGAGAGAGAGAGAGAGATATCAGTACTGAAACTAAGACACGCTTACTAGTTGAAATGGACAAATAAATTTACCAAAAAACTTCTCCCCTTTTTGCGAGGGTATCTGTTAGCCCCAAAAGCATTTGCCCTGCATGCCAAATCTACCTCATCTCCATGGACTCCCTTCTCCGTGTTTGTTTTCAGTAAATTTGCGAGTCCTTTAACCCCTCCATATCCGTGCAGAGAAGAATAATCATGATCCCTTGTCATAGCTGTAAGCTGCTCCTCTCCAATTCCGAACCCGCGAGGGAGAATTTCTGGTAATTCCCTATCAACATCATGCTTTTGTCCAGCTTCCTTGAAAAGTAATGCGGCCCGGATGACTTGAGCATGAGCCCTAATTTTCCTCCTTATTTGTTCCTTTTCCTCCTCTTTCTTCAGATCAAGAGTATATCTGAATCGCCGAGAGGCATTGAGCACAAGAGCAGCTTGCCTCCACCGGCGAAGCCGCTCGACGGAGGCGCGCTTGGCGGGGATGTCGAAGGGGTCGGCCCCCTCGTCCAGCACGTCGACGCCGAGCACGTCGCTGCAGTCGTTGCCGTTGCCATCGTCGTCGTCCCGCCGCCGATGGTACCTCCCCGGCGACGCCTCGGGCGCCTGCACTCCCACCGGCATGATTCCTCAGGAGAGATGACACGGACACCACCAGGCGGCGGCCGCCCCCGATCTCGGGTAGGTGATCGATCCGCCGTGCGCGCGCCCCGAGACGACGACGGCGAGCGGCGTACAGAGTGAAAACCAGCTCACAACCCCAAACAATCAAGCACGATTCGATCGCCGGTCGGCTGAGAGCTTCCTAGCTCGCTCGCTCGATCCGCCGGTCCTCTCGCCGCGCGCCGCTGCTAAGCTAGCTTCTCCGATCCTTGCTACTCTCGATCGATCGATCTCTTGCCGCTCAACTAGGCCACCAGCTACCGTTTTTTCACGCCGCCCTCTTTAATTTGGCTACATATATGAGATGATCTCTACGGCTACACGCTCTGCTAGCTCCATCCGTCCAAATTAAAGGGGCTTACTGGAGAGAGTGGAGACACAAAACGCTTGCTTC

Coding Potentia
Explanation CPC Score
noncoding -1.05098
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0148600.2 2 4195712 A G
Osa02LNT0148600.2 2 4195630 T C
Osa02LNT0148600.2 2 4195661 A G
Osa02LNT0148600.2 2 4197348 T C
Osa02LNT0148600.2 2 4197505 A G
Osa02LNT0148600.2 2 4200468 G T
Osa02LNT0148600.2 2 4202062 G A
Osa02LNT0148600.2 2 4202154 T C
Osa02LNT0148600.2 2 4203235 T A
Osa02LNT0148600.2 2 4204599 G A
Osa02LNT0148600.2 2 4205198 A G
Osa02LNT0148600.2 2 4205243 T C
Osa02LNT0148600.2 2 4205616 A G
Osa02LNT0148600.2 2 4207645 A T
Osa02LNT0148600.2 2 4207950 A G
Osa02LNT0148600.2 2 4208720 G A
Osa02LNT0148600.2 2 4210086 T C
Osa02LNT0148600.2 2 4210287 T C
Osa02LNT0148600.2 2 4210313 C A
Osa02LNT0148600.2 2 4210409 A T
Osa02LNT0148600.2 2 4210438 T C
Osa02LNT0148600.2 2 4203125 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
Osa02LNT0148600.2 osa-miR6251 Translation 4.5 20.096 1 21
Osa02LNT0148600.2 osa-miR156b-3p Cleavage 4.0 3.012 1 21
Osa02LNT0148600.2 osa-miR156b-3p Cleavage 5.0 3.783 1 21
Osa02LNT0148600.2 osa-miR319a-3p.2-3p Translation 4.5 20.442 1 20
Osa02LNT0148600.2 osa-miR319b Translation 4.5 20.442 1 20
Osa02LNT0148600.2 osa-miR160f-3p Cleavage 5.0 15.803 1 21
Osa02LNT0148600.2 osa-miR164d Translation 5.0 15.623 1 21
Osa02LNT0148600.2 osa-miR530-5p Cleavage 4.5 22.129 1 20
Osa02LNT0148600.2 osa-miR1431 Cleavage 4.5 9.096 1 21
Osa02LNT0148600.2 osa-miR1432-3p Cleavage 5.0 22.618 1 21
Osa02LNT0148600.2 osa-miR1847.1 Cleavage 3.5 13.082 1 21
Osa02LNT0148600.2 osa-miR1871 Translation 4.5 16.534 1 24
Osa02LNT0148600.2 osa-miR2870 Cleavage 4.5 20.599 1 21
Osa02LNT0148600.2 osa-miR2863b Cleavage 5.0 8.979 1 21
Osa02LNT0148600.2 osa-miR2871a-5p Translation 5.0 17.858 1 24
Osa02LNT0148600.2 osa-miR2919 Cleavage 4.0 13.589 1 19
Osa02LNT0148600.2 osa-miR2919 Translation 4.0 19.384 1 19
Osa02LNT0148600.2 osa-miR5490 Cleavage 4.5 8.71 1 21
Osa02LNT0148600.2 osa-miR5499 Cleavage 4.5 15.762 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0148600.2 2 qWIJ-2 Morphological trait Seed RM233A RM8
pre-miRNA
Transcript ID Pre-miRNA Identity(%) Alignment Length Pre-miRNA start Pre-miRNA end E-value Bitscore
Osa02LNT0148600.2 osa-MIR2863b 100.0 101 1 101 3.15e-48 187
GWAS
Transcript ID Chromosome Locus Trait Value Plus Minus