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

>Osa02LNT0155500.1

GGGAGGGTTTAATAACATCATACATTGCATTCAGGGGGAAAGAAGTCTATCATACATACAACGCCCTCGTGATCAGTTACATTTACAAGGTCTTCCATTTCAAGGATTCCCCAGAGGCAGGAGTACAAGAATACAATGTGGAAGTGGAATGCTTATAATACATGCATTCCATGTACAACACAAATATTACATGTATAGATGAAGATCCAACGGTAAATCGAATTATCTTATATAAACCAAAAGGCTTGGAACCAAATGGTCTATCTATGTACAGAATTCAATCATATACTGAAAAATGGTATATCAGCAGGGGAGAGAGAACTTTTACCAGCTGAAGCATCAATTTCTGCATGTAGCAAAGTATGGACATTACTGATCTTCAGCGAAAAAGTTCGGTTCTGCAGGCTTCTGTAATAACCTTGCAGGCACTCTTTCCTGCAAACGGGCCTTTCGAGTGGCATTTCTCCGTAAGATCCGCATCATATTACCAGCAAAACGTGAAGCATATAGCGCCGCACCAAGACTGAGCGAACTCGAACCATCACTGACAATTGCCGCTTGCAACCTCTTCTCCTTCTCAAACAAAGTATCCTCCAGTTTCTTTCTGCAGTATCTATGCCAAGCTGCCTGTATAAAACAAGCTGCCCAGGTTCTCCATTGCTGTGAATAGAATCTAAATGTATGCTGGAGTTGTTTGCTGTGGAGTCTCCTGAATTGGGTGGCTACAAACTTCAAGTCATCAGCCCTCAAAGCAAAAGCTTCGACTTCAGACAGCGTTTTCACAGTCCTGGTTGAGCTGGGAAGGTTTGAAGCTGAAGTAGGGTCAAGTGCCCATGTGAGAAGCTCTTCACCACAAAAATCTCCACCTTTGATAATATTGGAGTTGAAAAAGCCAGTCTGTCCACCATTTGTCGTCATACTCTCAAGATTTCCTCTCATGATGAAGAGCATTTCATTCACTGGGTCTCCTTCGCGAATGATGCAGCTGCCTTCTGTGTACAGCATGGGCTTTAGACGATCACACATGGCATCCAAGAGCTTCTCATCCATGTTTTCAAACATTGGAACCCTCATGAGAAGCGACAGGCAAAGATGCCTCTTTATCTCTCTCCTAAGATTCTTAGGAAGATTTGAAAGAAGGCCCTCTTCATCAACCCCTCTTGTTTCTTGCCACCTATATTGTTCATGACGCAGTATTCGCTCCTTGAGGTTATCAGGAAGTAATCGATGTGCCATCCATTGCTCTGTGTCACGCCGTTTCACTCTCATTTCTTCTATACGCACAGAGGCAGATTGTAGATAGGTCTGCACATTACCAATAAGGAGTGCAAACAAAACTAGACCTGATGTCGAGACGAAAACAGCAAATAGATTCTCCCATGTATACGTGCTTGTCTTAAGATTTTGACCAAGAGAACTTAGATTTTGCAGACCCCACCAAAAGCAATAAAACAATTTTTCAAAGAAACTCGTTGATTGTGAAACATTTTGAAGAGCTGGAAGATAAATTCCGAAAGTTGGATCTGCATTGTCAGTTCCATTTGTCGGGCAAAAATCTTGTAAGAAACTGTTATTTCTAGCTGCATTACTCCCACAAAATAAAGATCCCGAATCACAGCCATCATGTCTACTACATGCATCTTTCCAACAGGTGTCTTCTCGTTGAATGGAAAGAAGGTACCAAAGAGCTCCAAGGACATGACTAGCAAGCATATAAATTAAAAGGTTAAATGCAGCACCAGCCCATGCTGTCTCTGTAATTATACCAGCCGATCTGGTGATTTGAAGGTACAATGGTATTATTCGAATCAACCGAGGTACATATTGACAAATAACTATAACCATTAATATATTTTTTGCCGTCATAACTGAGGAGCCTTGCAGACGGGGTAGAACTACCAATACGAGCACCTGAGGAAGGGGCAGAACAGCTAAGAAATCAATCAGAAAATATGTTGATAGATACCGCTTTGCTATTGCAAAGGTGTCCTCAACCAAGACACCTCGACCAAACACTCTAGAGGAAGGAGCAATAAAGCCTGTCCTGAACTGAAAAATTATATGGAGTAAATAGAATATATCTGTAAAAAATCGCAGGACACTTGCTATGATTTCCAACTTTTTGTCCAGATATAAGCAGATATTGTCACCATCAATCACTGGAATATAGAAGAATAACGGGTCCACAGAAACTGCAATAAGGCATGATATAACAAATATCTTGTTCCATCTCTGCAAGAATGGCCCTTGAGGATCAAGAACTCTTGTTTTGGACTTCTTTTCCTCAGAAGCTGGTTTGTTGAGGGTTTCAGGATGTGAGGAATTCCCTAGGAATGAAAAGGCTCCTACAGTTCTATCCATTAGCGAGTCAAACACATTATGCCTTCCTTCTAAAACTGTCTTTTCGGAACCAACAGAATGTTCTGATCTCCAGTCATGAAATCTCACATATTTGTCCTCTCGGAAAGCCATGGATTCCACCAAACACCAGCATGCAAAACGAGACCAACAAGGCAGCAGAAAGGGATCAAATCTTCAATGTCGCATTGCAGTATCAACTCCCGGAGGGGCGCAGGGCGCTGGCACGGCGGCGGAGGAGGTGGTGGTGGTGGAGAGGCTACTGCAAGCTGCTGCTACGAGGAAGCGGCGGCGGAGAAGGCCGCGAGACGCGAGGGGAGAGGAGAGAGAGAGAGAGAGAGAGAGAGAGGCTACTGCAAGCTGCTGCTACGAGGAAGCGGCGGCGGAGAAGGCCGCGAGACGCGAGGGGAGAGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGGAGAGGAGAGGCGGAGTTCAATGCT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.995689
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0155500.1 2 8749241 A G
Osa02LNT0155500.1 2 8747280 A T
Osa02LNT0155500.1 2 8747514 T G
Osa02LNT0155500.1 2 8748258 T C
Osa02LNT0155500.1 2 8749395 A G
Osa02LNT0155500.1 2 8749903 T C
Osa02LNT0155500.1 2 8750554 A G
Osa02LNT0155500.1 2 8752517 A G
Osa02LNT0155500.1 2 8752801 G C
Osa02LNT0155500.1 2 8753462 A C
Osa02LNT0155500.1 2 8754878 T C
Osa02LNT0155500.1 2 8755068 G A
Osa02LNT0155500.1 2 8750749 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
Osa02LNT0155500.1 osa-miR5527 Cleavage 5.0 22.855 1 21
Osa02LNT0155500.1 osa-miR5528 Cleavage 4.5 12.325 1 21
Osa02LNT0155500.1 osa-miR5797 Translation 4.0 10.602 1 21
Osa02LNT0155500.1 osa-miR5832 Cleavage 5.0 20.051 1 21
Osa02LNT0155500.1 osa-miR156c-3p Cleavage 4.0 4.578 1 22
Osa02LNT0155500.1 osa-miR156g-3p Cleavage 4.0 4.578 1 22
Osa02LNT0155500.1 osa-miR818a Cleavage 5.0 21.143 1 22
Osa02LNT0155500.1 osa-miR818b Cleavage 5.0 21.143 1 22
Osa02LNT0155500.1 osa-miR818c Cleavage 5.0 21.143 1 22
Osa02LNT0155500.1 osa-miR818d Cleavage 5.0 21.143 1 22
Osa02LNT0155500.1 osa-miR818e Cleavage 5.0 21.143 1 22
Osa02LNT0155500.1 osa-miR169r-3p Cleavage 5.0 18.187 1 21
Osa02LNT0155500.1 osa-miR1853-5p Cleavage 5.0 24.537 1 24
Osa02LNT0155500.1 osa-miR1882a Translation 4.0 24.354 1 24
Osa02LNT0155500.1 osa-miR1882b Translation 4.0 24.354 1 24
Osa02LNT0155500.1 osa-miR1882c Translation 4.0 24.354 1 24
Osa02LNT0155500.1 osa-miR1882d Translation 4.0 24.354 1 24
Osa02LNT0155500.1 osa-miR1882e-5p Translation 4.0 24.354 1 24
Osa02LNT0155500.1 osa-miR1882f Translation 4.0 24.354 1 24
Osa02LNT0155500.1 osa-miR1882g Translation 4.0 24.354 1 24
Osa02LNT0155500.1 osa-miR1882h Translation 4.0 24.354 1 24
Osa02LNT0155500.1 osa-miR2094-5p Cleavage 4.5 18.122 1 21
Osa02LNT0155500.1 osa-miR2871a-3p Cleavage 4.0 11.61 1 21
Osa02LNT0155500.1 osa-miR2871b Cleavage 4.0 11.61 1 21
Osa02LNT0155500.1 osa-miR5338 Cleavage 5.0 19.922 1 21
Osa02LNT0155500.1 osa-miR5491 Cleavage 4.0 13.629 1 21
Osa02LNT0155500.1 osa-miR5079a Cleavage 5.0 12.832 1 22
Osa02LNT0155500.1 osa-miR5079b Cleavage 5.0 12.832 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0155500.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0155500.1 2 qEML-2 Morphological trait Seed R2344 R712
Osa02LNT0155500.1 2 qLRS-2 Resistance or Tolerance Drought tolerance RM322 RM324
Osa02LNT0155500.1 2 qMXA-2-1 Morphological trait Root OSR9A RM71
Osa02LNT0155500.1 2 nan Resistance or Tolerance Drought tolerance RG83 RG171
Osa02LNT0155500.1 2 qLER-2 Morphological trait Culm/leaf R2344 R712
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