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

>Osa02LNT0148500.1

GGTCGATTAAAGTTGGACGCAAAAACTCATAGTTGCGCTTATTTTAGGACGGAGGTAGCAAGAGAAGCTCTGCAAAATGCCAAACCCGGCTGTTCTGATAGGACGGGCCCACACGACCCGGAAAACCGAGACCAGCCACAAAAACGGGAGATGCCATCCATCCGTCCTTCCGGTTCGATGCATCGGGTCACCTTCCTCCAGCAACAAGCCAACAACGACAAGTCTCGACGAGATTCATGCACGATGAAGTCACGCGTGCGATGAGAAAACCGCACGCGTGTCTGTAGCATGGCAAAACCAGGGATGCGCCACTTGTGCCGCTGCGACTTGAAGCTCACTCGCATAGTACATTCGGTTACTTCCATGTTGCTTTCAGGCCAAAGAGAGTACACGTTTGGTTCAAATTCAACCCGTTATAACTTGGGAGTTGCTTCCTGCGATGTCACGCATGATCTGCCCGCCATGATTCTGCAGGATCAGTAAAGATCCCACTATTCAGCAACCAACTAAATGAGATCCTTTTCCCTGCAGGAGGAGAATGTGCATGTCCAGTTTCACAGAAGAAAGCATATGAATGTCGAGAGGGTTCATCCGCCTCTGAACAACACCTCTACACCAGTATACTTTATGCAATTTGATAATGTCTAGGAAGTACAGGAATCTACTTGGCCCATAATGAGAAGGCCCATGTTCCCCTGGCTGTACCACTACCACCTTTCAACAGGTAAATGCGGCTCCAGAATCAACATGTACACTAAAGGACAATGCTGTCCATTATAAATACTGAAAGGATGCTCCACAGAAATGATTGTGTTTCCTCTGAATATTTTTGATAGCTGCGAGAGCTGGCTTCCTAGATGTACGGCCCCACCTTGATCTCTTCGTTACTCTGATTCCTCACTGGTAACACTTATAATCCTAGCTAGGTCTTGGACAATCTCTGACATTGATGGTCTGAATTCTGGTTCCGGCCGAATACAACGGCTGATGATGTCTGCAAAACGTGACAGTACTTTCTCAGAACACTCTCCTTGAATAGAAGGATCAACCATCTTTGATATGGACTCAATGTCATGAAATTGAGAATCAGCCCATCTAACAAGATGTTGTTCAGCACGAGGACGAGAACTGTCATATGGTTTACGGCCAGTGAGAAGTTCTAGCATTACCACGCCAAAACTGTAAACATCACTTCGGTAGGTAAAAGTCCCAGCTTCATGGATTTCAGGAGCTTCATAATTCAGCAGTGCCCTCATGCGACCTGACAACTGTGTAACAGAACCTGACAGCGTCAATTCTGCCAGTCCACATTCAGCGACACGTACTGAGAATCCATTACCAAGGAGCACATTGGCTGGCTCAAAATTCTGGTGCACTACTGGAGGTTCACAGCTCTCATGTAGATAGTCTAAGGCCTTTGCTGCACCAAGAGCAACTTGGAGGCGAGCATTCCATGATAGTGCACCATCCAATTCCTCCCCTTCATGTAGTACATCATGCAGTGTTTTTCTACTGAAATGATTATAAACAAGTAACCTCTGACCATATTCTGCACAGTATCCAACAAGCTCGAGGATGTTGGGATGCCTAATATCTGATACACTTGCAACCAGTTCTAGAAATTCATCTACCGGTATTCTATCATTGGCGTTATCAATCTTCATAACTTCCAAGAACCTGCCTTCAGGAAGTTCTGCCAGATATACTTTTCCCAACCTACTCTCTCTTATCAAATTTCCCTCTTCAAAACTATTTGTATATTGCTGAAGTGATGCAACAGAAAAGGATGTTGCAGATGTCGAGGGACCTGTCCTAGGTGGAGTACTAACTCTTTTCTCTGGCTTAACAATGGGATTTACAATCACTTTTTCAACAGGTGGTGGTGGTGGCGGCGGCGGCGGCGGCCGCGGCGGTGGCGGTGGTGGTGTCGGAGGAGGAGGAGGAGGTGGTGGTGGTGGAGGCGGCGGCGGCGGAGGTGTAGAAGCAAAAATTTCTGTTTCTGATCGCTGCAAGTTAATTACATGTTCTTTTCTCTTTTCAGGAGGCTTCTCGAGAGCAGCTGGTACCGCCAAATTTATTTCACGAACCTGCCTCCGTTCAGGAACCTCTGTTGATCCTTTTTTGGCATCATTCCTTGACTGCACTGAAGCTTGCTTAACTTTCGGCTCTTCAACCCTCTGATGAACCCTCCCCACCTGACTTGTTGTATAATCACGTCTTGACTGTCTCTCTTGGTACTTGGACAGGCAAAATATTACCAGCAGCACTGTAACTATAAACAGGACAATAGCTAGAAGAACATATCCAACAATCCTGAGGGTTGAAGACTTATGTTTCCTAGATGATGGAGAGCTGCTGTCTCGAGCAGTAGATCCACCAGAAGAATTAGAGGGCGAACTAGATGGCGAAGGAGTTCCAGAAGATGAAGGTGACGATGGTGTTTGTGTTGGTGTAGAGCCTGTAGGTGTTGAAGAGGGTGATGCAGAAGGAGCTATGCTGGTATTAAATGGGTTCCCATCCTTTTTGAAGTTTGGCACATTCAGCAACTTTGGAGGAACCGGTCCAGAAAACAAATTATTCTCTATATTTAAATCTTTGAGGGGGAGATCCTGCAAGACATCAAGGGTTCCGGATAGTTGGTTGTCTTGCATGTGCAATGTAGTCAATGATGACAGGCTTCCCAGAGAAGGTGGTAATGAACCACTGAAGTTATTGGATGAAATATCAAAATTTACAAGGCCAGTAAGGGAACCAAAAGCATCTGGCAGTTTCCCGTCGAGATGATTATCATTTAGAGACATGTCTGTTAAACTCTGAAGCATTGATAGTGACGTCGGAATGCTTCCAGTGAGCTGGTTATCAGACATAAAAAAATGCTGCAGTGTAACAGGTAGATCTTCTGGTATAGTTCCACCAATATTGTTGTTGCTAAGATTTATAGTGGTTATTGAAGTGAAGTTCCCCAGGCTGCCTAACTGTCCTTCCAAATTTGCAGCATTGAAAATTATTGAATCTATATTTGAGCCAATACATACAACGCCCTGCCAACCATCACCACAGGGGTCACCACCATTCGCAGTCCATTTAGGAAGAGCCGGTGATCCAAGTGCAACATACAGTCCATTTATAGCAGCAACATCGGCGGCGACGGTGGCCGCGAGCGCCCGCCGGGGCAATGCCGCCGCGGCGATCAGCAGCAGCAGCGGCAGCACGAGCACCGCCGCGGGAGCCCCTCTCCGGAAGCAGCACCTCCCTCCCGCTGCCATCCGCATCGACGCAAACTCTCTCTCTCTCTCTCCCCTCCAGCAATTAATCAGCGCGGCCTCCGCCGAAGCAGCATCAGCCAGATCAACCCGAAGCGATCGCGGAAGAAGAAGGAACCAAACCCCGCGTTCGCAGATCTAGCGTTCGCTCGCTCGCGCGCTCGCGAGAGAGAGATGCCGTGCCGTGCTCCGCACCACCGCCGCCACCACGGGGCTCGCTTCCCGGAGCACGCCGCCGCCGCCGCCGCCGCAGAGGCTTGTGCTTTTGGTGGGCTTCTAGTAGAATCTAGCTGTAAAACTGCAGTCTCCAGAGGAGAGAGAGAGAGAGTGAGAGAGAGAGAGAGAGGAGAGAGAGGAGAGTGAGAGTGGCGGCGAAGTGAGAGAAGAGAATGCGAGGAGGAGGAGCGTGGGAGTGAGCAACGGGCGTGAAAAGGTAGAGAGAGAGAGGGAGAGGGAGTGGGTGAGCGGCGAGCAGCGAGGGGAGAAAGAGAGAGAGAGAAGAAAAGGCGTTTGCG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.208605
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0148500.1 2 4167490 T C
Osa02LNT0148500.1 2 4165420 A G
Osa02LNT0148500.1 2 4168275 G A
Osa02LNT0148500.1 2 4165387 A G
Osa02LNT0148500.1 2 4166630 T G
Osa02LNT0148500.1 2 4167236 A G
Osa02LNT0148500.1 2 4169394 C T
Osa02LNT0148500.1 2 4166542 T C
Osa02LNT0148500.1 2 4167576 C A
Osa02LNT0148500.1 2 4167281 A G
Osa02LNT0148500.1 2 4169799 T C
Osa02LNT0148500.1 2 4170277 A G
Osa02LNT0148500.1 2 4170741 G A
Osa02LNT0148500.1 2 4172276 T A
Osa02LNT0148500.1 2 4174168 A G
Osa02LNT0148500.1 2 4174704 T C
Osa02LNT0148500.1 2 4173427 T A
Osa02LNT0148500.1 2 4173432 G 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
Osa02LNT0148500.1 osa-miR5820 Cleavage 4.0 12.898 1 21
Osa02LNT0148500.1 osa-miR156b-3p Cleavage 4.0 12.978 1 21
Osa02LNT0148500.1 osa-miR156b-3p Cleavage 5.0 7.523 1 21
Osa02LNT0148500.1 osa-miR156c-3p Cleavage 4.0 8.886 1 22
Osa02LNT0148500.1 osa-miR156g-3p Cleavage 4.0 8.886 1 22
Osa02LNT0148500.1 osa-miR156g-3p Cleavage 5.0 12.978 1 22
Osa02LNT0148500.1 osa-miR1850.2 Cleavage 4.0 11.361 1 21
Osa02LNT0148500.1 osa-miR2092-5p Translation 4.5 14.356 1 21
Osa02LNT0148500.1 osa-miR3979-5p Translation 5.0 15.655 1 20
Osa02LNT0148500.1 osa-miR156c-3p Cleavage 5.0 12.978 1 22
Osa02LNT0148500.1 osa-miR396e-5p Translation 4.5 13.166 1 21
Osa02LNT0148500.1 osa-miR396h Translation 4.5 13.166 1 21
Osa02LNT0148500.1 osa-miR396d Translation 4.5 13.166 1 21
Osa02LNT0148500.1 osa-miR3979-5p Cleavage 3.0 16.172 1 20
Osa02LNT0148500.1 osa-miR812n-5p Translation 3.0 17.44 1 24
Osa02LNT0148500.1 osa-miR396g Translation 4.5 13.166 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0148500.1 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
GWAS
Transcript ID Chromosome Locus Trait Value Plus Minus