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

>Osa02LNT0157100.1

ACTTGCATTTTCTCGACGGCTTCAAAAATACAATTCAACCCTGATTTGATCACTTGTTCAAACCCCGTCCAATTCAGGCAATAGCTTCACCCCGATCTTCATAAAATTTCATCAACCCAACCTCCCATGCTATATATAGTGCTTGTGCTTAGATTTCAGATGTCATTTCAAATCGATCCTGCCCACGAAGTTCCGGGGCATACCCTGGTGCCGTGCCAAAACATTCCTGTAAAGATAGATGACCAATCTGCATGTCAATTTAAACATCAAAGAGCATCTACTATATTGCTTATTGGAAAGCAGTGCAAAGACATTCCGAGAGCACTGGCAGACTCATGTATGCGTGCAAGTATGTGCATGATAACGCGAGCCGAGCTGTTCTGCTCCGAAGGAGCTTTTGCAGAAGTAGAGTTGCCCCTTGCGAAAGCTTTGTTAATACTCAAGGTAGTAGTAACATCCTGCAGCTTTCTGCTCAGCATCCTTTATAGAGCCTAGCTTGTTGATCCTAGGCCTGTAGGTTGTAGGATCTTTCCTAAATGTGACATCAAGATGCGAAAGAAAACGGTTCATCCCAGAGGCCAGGGGTTCTGGTGCATTTGCAATACAGTCAACAGAAGGTTTTCCCTCAAAAACCACCACCTTATCAGCAAGGTAGGTTGCCATGATAAAATCATGCTCAACAACAAAAGCAGTTTTCTTTTCATGGAGGATAAATCTTTTTATGACCTTCGCTGCAAGAAGGCGCTGCTCTGAATCAAGATGGGCACTTGGTTCATCTATGAGGTAAATATCAGCAGGCTTCCCAAGACAAAGACAAAGCGCAACCCTTTGCAGCTCCCCTCCAGAAAGAGTTGGAACCTGCCTGTCCATGAGTTGCTCAATTTTCAGTGGTTTCATGACATCAGATCTGAACTGGGCTTGAGTGCATGATCCAGGTACTTTCTCGAATAGAAGATCCCTCACTGTAGAGCTATATTTAGATATCAATTCCTGAGGCTTGTATGAGACAGTGTATTCAGGCACGTCAACTTCTTCGTCTCCTACTTTGTCTGGCTTCACTCGTCCTGCCAGCATACGGATAAATGTCGTCTTCCCAGTACCATTCTCACCAAGCATTACAATTATCTGGGAATCATTAAAGCTGCCTTCAGTGACTGATAGCTTAAAGCCACACCTTGTCTTTGTCATTGTAGGATATCGGTAGCATTGGTATGTCTGACCCTCTACGATTTCCTCAGTAGACTCGGTAACTCTAAATGTAAGTTTCTCCTCGCGGAAACGTAGGTTTTCTGTTGGTATAAAGCCATCCAGGAAAATGTTGATTCCTTCTCTAACAGAAGAGGGCAAAGTAACAACACCATATGCTCCAGGAGTCCCATAAAGACAGCATATATAGTCTGATAGGTAGTCCAGTATGCTAAGATCATGCTCCACAACAATTACATAGTTTTTGGGCTGAAGCAAAGAGCGAATAACTTGTGCAGCTTTCAGCCTTTGCTTCACATCAAGATAGCAGGATGGCTCATCAAACATATAAACATCTGCTTCTTCCATAGCACGGGCAGCTATTGCAAATCTCTGGAGTTCACCACCAGATAGAGCTGAGACATCTCGGTCAAGAACTTGATTCAACTCGAGAGTATCACACAGTAGGTTTTTCATATGTCTCTCATCTTTCTTGCTAAGAAGATCTCCAACCTTCCCTTCATTTTGTCTTCCAGCAGACGAGTAAAGTATTTCTGGAGTTCAGATCCACGGAAATTCCTCATAATTTCATCCCAATTTGGGGGATCTGTGAATTTACCCAAGTTGGGTTTCACCTTCCCTGCCAAAATTTTAAGTGCCGTTGATTTACCAATACCATTTGTCCCTACCAAGCCCAACACTTGCCCTGGTCTTGGAACAGGCAGCCTGTGAAGCTTAAATGAATTTGGTCCATAGCGATGTGTCGTCTCCTTGTCAAGATCACTTGGCAAGTTTATAATCTGGATAGCATCAAAGGGACATACCTTCACACAAATACCACATCCAATACATAGTTCCTCAGAAATTAAGGATACTCTCGATGATGGAGTAACTTCTATGCACTGACGCCCGGTGGCATTGACGGGGCAGCGCTTGCGGCACTGCTGGCCGCACTTGCTGGGCCGGCACCGGTCCTCCGTCACCACCGCGATCCGGCTCGACCTCCCCGACGACGACGACGACATCGCCGCCCGCCTCTCCTCTCGCGGCGGATCGATTTGGGGATTTTTGCCCGGTTCGGAAGCTAGCCGGAAACCGATCGATCGATCGCCGCGGCGCGAGGAAGGAGAGGAAATCTGGGAGAGCCCTAAAAGTAAAAAAACTACTACTCTCTTGTGTTTGTTTGGTTTGTCTTGTGTTGCCTTACGTGTTGGTGCCTTGGTGGGCCGCGCCGCACTAGCGACCGTGTCGCGTCGCGTGTGTTGTTT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.232724
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0157100.1 2 10552917 T A
Osa02LNT0157100.1 2 10552667 T C
Osa02LNT0157100.1 2 10553558 A G
Osa02LNT0157100.1 2 10554422 T C
Osa02LNT0157100.1 2 10554455 A C
Osa02LNT0157100.1 2 10554543 G C
Osa02LNT0157100.1 2 10554979 C G
Osa02LNT0157100.1 2 10555862 T C
Osa02LNT0157100.1 2 10555925 G A
Osa02LNT0157100.1 2 10556716 G A
Osa02LNT0157100.1 2 10556811 C A
Osa02LNT0157100.1 2 10557010 C A
Osa02LNT0157100.1 2 10557762 A C
Osa02LNT0157100.1 2 10558023 A G
Osa02LNT0157100.1 2 10558796 A T
Osa02LNT0157100.1 2 10558857 T C
Osa02LNT0157100.1 2 10558872 G T
Osa02LNT0157100.1 2 10558066 A T
Osa02LNT0157100.1 2 10555182 G A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa02LNT0157100.1 osa-miR812s Cleavage 5.0 13.569 1 24
Osa02LNT0157100.1 osa-miR5799 Cleavage 5.0 13.569 1 24
Osa02LNT0157100.1 osa-miR5837.1 Translation 4.0 11.338 1 21
Osa02LNT0157100.1 osa-miR397a Translation 3.5 18.711 1 21
Osa02LNT0157100.1 osa-miR397a Translation 5.0 12.517 1 21
Osa02LNT0157100.1 osa-miR397b Translation 4.0 18.711 1 21
Osa02LNT0157100.1 osa-miR171g Cleavage 5.0 13.569 1 21
Osa02LNT0157100.1 osa-miR171i-5p Cleavage 5.0 13.535 1 21
Osa02LNT0157100.1 osa-miR820a Translation 5.0 19.487 1 21
Osa02LNT0157100.1 osa-miR820b Translation 5.0 19.487 1 21
Osa02LNT0157100.1 osa-miR820c Translation 5.0 19.487 1 21
Osa02LNT0157100.1 osa-miR1423-5p Cleavage 4.0 18.219 1 24
Osa02LNT0157100.1 osa-miR1430 Translation 3.5 18.356 1 21
Osa02LNT0157100.1 osa-miR1857-5p Translation 3.5 14.141 1 21
Osa02LNT0157100.1 osa-miR1857-5p Cleavage 5.0 22.09 1 21
Osa02LNT0157100.1 osa-miR2097-3p Translation 5.0 15.837 1 22
Osa02LNT0157100.1 osa-miR2928 Cleavage 4.0 19.845 1 20
Osa02LNT0157100.1 osa-miR2928 Translation 4.5 16.834 1 20
Osa02LNT0157100.1 osa-miR5338 Translation 5.0 15.301 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0157100.1 2 qLRS-2 Resistance or Tolerance Drought tolerance RM322 RM324
Osa02LNT0157100.1 2 nan Resistance or Tolerance Drought tolerance RG83 RG171
Osa02LNT0157100.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
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