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

>Osa02LNT0170200.1

CAAATAAAGAAGCTCTGACCAAAGCCCTACAGGGCCACATACCTAGTACGAGGTAGTTGGGTCAAACAAGTAACCAAATTATATCTTTTAGATAAAGAAACAAGTAACCAAATTATAGTTGTTTAAGACCCATCAAACAAGATGTAAGTAAGTAGTATTTGCCTTGGGCTGGGTTTTTAGGATGTCAATACAGACTTACCTTGGGCTGGGTTGAGTAGTCGCAAGTGCAACGGGCTGAAATAAATTTAGGGCTTTCAGACTTTTGACCCACCTCAAATTGGCATGACTCTGTATCTATCAAAAATTGACTTGACAGGAAAAATAAAAGAACAGATCTCCACCAAAATGGAATCATGTACTCGATACTTACAAAGAGATGTGCATTACAATCACATGCAAACTTGGGTAGAAATTATGAAGACCAGAGTGGCAGCTCATGTTTTTCCACTTAAACAGAAATGAGGAGTAAGTCCTCCTGTTTGCTCAACTATTCAGAGAAGATACAAGGAGAACAACACAAAAAAAAATAAAAATAAAAATAGAAATAGAAAGTTCACAGTACATGCAAAAGAATAGCTAATCTTTTAACAAAGAACCCTGTTTTGCACCATCTTAGCAGCGGTTTTTATGTGGTCAGTACGGCAGTCAATAGTCAATGAATTACACCCCTGCAATCTAAGAGTAACAAACATTCAAAGAAAATGTCATGTGCCTTTTTTGTCCGCAAAGGTGAATGCTGAACATGTGAGGATACAAAAATAGTGAAATACTACATCCGTTCAAAAATGTTACTAACTACTACAGAAAGAAATATTTTATAGGACTATGAATCTAGACAGGAAATGTCCAGGTTATATTTTGGGACATAGGTGGTTCAGTAGTAAACTACATACTCAAGAAAGCACCTAGGCACTGGTTTTCCTTTCTCAAATAGTAATCCCTACAAACCTTGCATTCTGCTGAATAGGTCAACCAAGGTTTAAGACACTAACTAGGATTCTAGGAATGCACTAGGTAGCATGTTAACAGCAGAAATTAACTTCATAAAAGCTGGAATTTTTCATTTGCTTGAGAACAGTCATACACATCTTTTTCCTTCCAAAAGTAAACATATATTATTCAGTCTCATTTGATTTACAAAAGTACAAAGCTGAGTAGCATGGGACAATGAACGTTCCGCTACCAAAGCACAGGTGACAGGAAAATTATAGTGCTATTCTGATGAACAATCAACTCCAAAATTTACAGGATCACTCACTGGGCATTCCTAGAGAAATTCATGCAAACCTCATGATCAACTCAAAATTGCCCTTCCAAGCAAGCATGTCATGGGTAATAAGAGAAACATTCAGCAGTGGAAGCCAATACACAATGTAGAGACGACGTAATCTGATCAGAGTAAACAACAATAGATGATCAGGATGGACTAAACAGTTTACATGTGCAGCCTTCATTATAAGAACACTAGGAACAATTTTCATACATATTAGATGTTTGACTTCCTTACCAGACTTTACTCATCTAGCACCTTACCAGACTTTACTCACCTTGCTAGATGTTCATATGTTGATGAGTTCATTTGCAATTGCCTGGTGGCACTAGCATCCATGGAAATAAATATATTTTTGTTAATCAAAAGATTTAGAAGAACCATTAAGATAATGTCAACCTTGTCAAAACATGTACCTGCCTCCATCTAGTTTTCATATTATAACTGTTGTAAGCATCATGCTTCAATATTATCTCATGCCACAAGAGTTTTGTTATTAATCATTGTGTTTGTTGGTCAGACATGTTTATTACTTTAATTTTGTCTTGTGTGCCTGTAATTGAATAACTCTACCCTGCTTTCTCACTTGATAGTTTTGGCAAAGGGAGGCAGCAAGCTTGAGACAACAACTGCACAACTTGCAAGAAAATCATCGGTATGGTCTGAAAAACCCTAAAGATTTTCTTGCAAGATGTGCAGTTGCTGCCACAAGCTTGTCACCATCCCCTTGCATGAATCTGAGAAACCACGCGCGCGCCGCACCGGCACCGTCGAGGGGAGGGGACGGCGGGAGCTAGCGGAGAAAGGCATTGCGATTTAGGTGGTGGCTGGGGCCGGGGCCGGGAGAGTGGTCAGGGAGGGGAATTCACGAGATCGGTGCGGCTGCGCCGCGCCGTCGCGCGCGGCGGTGCCGGCGATGGCGGCTCAAAAGGGGGAGGAGCGTGCGCCGGATCTGGGCGGCGGACGCGGCGTGAGGACGGCGCGCGGGCGCGCGCGCGCGCGGGTGCCCGTGGCGCGGCATGTGGCCGTGGAAGCGAAGCAAAAGCCGCGACACATGTTGCTCCCGGCGGAGTAGAGGCGAAG

Coding Potentia
Explanation CPC Score
noncoding -1.28121
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0170200.1 2 22304262 A G
Osa02LNT0170200.1 2 22299264 T C
Osa02LNT0170200.1 2 22300804 T C
Osa02LNT0170200.1 2 22301208 A G
Osa02LNT0170200.1 2 22301738 A C
Osa02LNT0170200.1 2 22301956 A G
Osa02LNT0170200.1 2 22302040 T A
Osa02LNT0170200.1 2 22302082 T A
Osa02LNT0170200.1 2 22302205 G A
Osa02LNT0170200.1 2 22302223 A G
Osa02LNT0170200.1 2 22303305 G A
Osa02LNT0170200.1 2 22304299 G A
Osa02LNT0170200.1 2 22304318 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
Osa02LNT0170200.1 osa-miR5815 Cleavage 4.5 12.708 1 24
Osa02LNT0170200.1 osa-miR1437b-5p Translation 4.0 12.354 1 21
Osa02LNT0170200.1 osa-miR164a Translation 4.5 17.306 1 21
Osa02LNT0170200.1 osa-miR164b Translation 4.5 17.306 1 21
Osa02LNT0170200.1 osa-miR164d Translation 4.5 17.306 1 21
Osa02LNT0170200.1 osa-miR164e Translation 4.5 17.306 1 21
Osa02LNT0170200.1 osa-miR164f Translation 4.5 17.306 1 21
Osa02LNT0170200.1 osa-miR535-3p Cleavage 4.5 20.346 1 21
Osa02LNT0170200.1 osa-miR1429-3p Cleavage 5.0 9.444 1 21
Osa02LNT0170200.1 osa-miR1439 Cleavage 4.5 11.295 1 21
Osa02LNT0170200.1 osa-miR2100-3p Translation 4.0 17.865 1 22
Osa02LNT0170200.1 osa-miR2863a Translation 4.0 19.811 1 21
Osa02LNT0170200.1 osa-miR2923 Translation 5.0 17.632 1 22
Osa02LNT0170200.1 osa-miR2923 Translation 5.0 15.135 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0170200.1 2 qRTT2-1 Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0170200.1 2 nan Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0170200.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0170200.1 2 nan Resistance or Tolerance Insect resistance RG157 RZ318
Osa02LNT0170200.1 2 yld2.1 Morphological trait Seed RM262 RM263
Osa02LNT0170200.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0170200.1 2 qCSH2 Resistance or Tolerance Cold tolerance RM262 RM263
pre-miRNA
Transcript ID Pre-miRNA Identity(%) Alignment Length Pre-miRNA start Pre-miRNA end E-value Bitscore
Osa02LNT0170200.1 osa-MIR444b 100.0 138 1 138 1.24e-68 255
Osa02LNT0170200.1 osa-MIR444c 86.331 139 7 138 2.81e-35 145
GWAS
Transcript ID Chromosome Locus Trait Value Plus Minus