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

>Osa02LNT0173600.1

GGTGATATCAACCATTTCGATAGCTTTCCCACTTGCACCTGAATACCTGGTAGTTCCATCGGATTATCTTGATTATTACAACTTATTCCATGCGGAAACCCCCTTAACGCTCTTTGATCTATCAAGCCGACGGCGCTACCAGTTCAAAATACAAGCAAGAAAAGCCAAACCAAATGGCGAGGACAAAAAGGGTATCACGTTGGATTGCTCAGCAGCTGGTAAATACGGCCAGGCAAAATGTGATACGTCGAATTGATGCACAAAATGGACACCGGTGTTGCGGTGCTGCATCTTCTGAATTAGGTTGGATTGAACCAGCTACCCATGGAACCATTCATGTGGCCATTTCCATGGATGCCTGCACCATTAGGTGCTACGGACGATGTGGGGATCAGCGAGGACGGCAGACCAACTGCCATTGAAGGAGGCGAGGAGTATAAACCTGGGACGTGCGGGAGCGAAGGGGCACTCAAGCGATGACTGCTACCTTTCCTTTGCCGAATTGCATGTATCTGTCTTAAACCCCGCTCGTGGATGTTTGTGAGTGTCTCAAGCTCATCCAGTGATAAAGCTTCCACGCCGACACCATACACGGGAGCATGCCGTGCCATCTCTTCCTGAATTGAGGTCTCCAGGGTGTGAATATATTGCTGGCAAACTTGTAGTTTTGACTCCATTCCATCTATGTAAGCTTCACAACGAGTAATTTGGTCTTCTTTTTCTTTCTTTTCTCCCTCGGTTTGTCCAACTGTCTGAGTCAGCCTTCTTACTTCACCTTCAAGTGATTTCCGAATCTCTTCACGAGTCTGTGCTTCAGCAACAAACCGTTTGAATTCATCATCAACCCTTTTCCTTGAAGCTTCAACACCCTTAAGCCTCTCTGCCAAAGCATTCTTCTCCTTGGTTATTTTCTTTAGTTCCTCGCGTTTCCATGCTTTGAACTGGGATAGTTGTGTCTCTGCTTCATGTAGACGATCATGAAGATTTTTCTTATCAGCAGTTAGCTTTACAATTTGCTCATCTTTTTCTGATCGTACCCATTCCAACTGATTCTCCATCTCCAGCATCTGCTCAGAAAGTTCCTTCTTCTCCCGGACAAAACGATCCTTCTCAGCTTTTAGCTCAGACCTTAGATGCGCATTAGCTGCCTCTGACTCAGTTAGTTGTTGCATTAACACATCTTTTTCCTTAGTGAATTTTGTTTGTTCCATATCCATGTCTTCTCGCAAACGCATATTCTCATCTTCAGTAGCACATATTTGGTGCCAAAGATTTGCACGATCAGCTTGAGCAACTTCAGCAACCTCACGCAACATGTTCAAAACAGGTCTAGCAATTCCAAATTCCTCCTTAACAAGAAATACCAAGACATCCATATCTATGTCAACTGCTCGGCAGCTATCTGAAGTATTTGTTGCTCGTTCAACAAGACCCTTCAGAATTCTATATCTATAATGATCCTCGGTATATATCTTAAAAATGATAGCATAAAGCATCCGCACAAAATCTTGCACCCTGGTTTCTGTAGATAGAGATAATACCTCACCAAGTGCAAGGACTGAAGTGAAATCATCTTCTTGGACAGGCAAATGTTCAAACTGCCCGTCTAACAGAACTTGCTTGTTCTGTGAATCATTCACCATAGTCCCAGTCCCAGACTTAAGACTTAACCTGTGAGAATGCCTTCTTTCCAACACCATGGCTACTAATTGCAGCCCAAAGGCTCCTCGCAATAAAGCCCTCTGCAAAACCTGAGAAACTTCAACAAATAATCTGGGTATCGACAGCATTTCTATCAGTATAAAAACATCTGATAGATGATCTTTTCCATGTACAGCTTGACCTTGCAAAGAATGCATCCCTTCAGCTGAAAACTCGTCTGTACTACTAGTACTACAGGACATAGAGAGGCAACTGCTATCAGGCTCACAGTCAGAATCAATATCCTTCAACAAAGCATCAGCTACATCTGACCAGCTATGCACTGTTTTAGACAAGAAATCAAGCACACACAGGGGAACTTCAGTACCCAGATCTTTTAGTCTCCATCGGACAGCTCTAGCAGCTTGAGCAATATGCTGGCATTGTGATGCTGCCTTGAGAACATATGTAATGGCCTCTACAAGTGGCTCATCATTTGAATCAGCCAACAATTCGAGTGCATGAAAAGATGCTTGTTTCCAGATATCACAATCAAATTCTAGCTCAGATAGAGCATTAAAAACCGGTAACCTCAACGAAGGCTCAGTATCTGGCTTTTGAAGATGATCTAACAGTGCACAAGCGGCAAGAGAGTGTTCTGAACTATCAACCAACTTTGGGACAAGGGCAACCAAATCTGGCTGAAGCTTCTTTGGAGATTTCTCTAGTACAAGTGCAATTTTCTGGACAGACTGAGGTCGTCTTCTTGGTTCAGGGCACCCATGTGGGACAGCACTGTCCAGTGCCCTCAATGAACTAACTATTAGTCCTAACAGCTCCTCTGATTGCTCTGGCCATTTTGTCCTGGAAGCCTGGTCAGAGCCTTCATCTTCTAGCAAATCAGCACCAGATACTTCAGGGGGAGAACAGGACTGTTCTAAAACTCTGGCAGGAATATCATTTGTACACTTATCTGTGTTTTGTACAGAAAGCCTATGATGGATATCATCATTGCCAGGTTTCAGCCTTTCATACTTATTACTGAAAGCACATTCTGTCAGTTCACCTTCAACATTGAGCTCTGGTGGAGAGCTAGCCCCATTCGAGTCAGGAGAAGTTTTGGAACTTGCTGAGGATGAGACATATGCTGGTCTTTCTTCTGAAGGTTGGCAGCACTCAACCATTATATCAAGAAGCAAGTCTATGATAGCCTGCTTCAAGACACTAACTCCCATCAGCAAACTGATGAGGCTTGTGGAACTCGAGTCGCACTTTGAAACATCTTTCTTTCCACCAGCCCTGGTGGATACTTTGGTAGGAAGTAGCATGCGCTTTACTTTTGCTGGGTTATCGAGGTAAACACGCAGACCAGTAAGAAATCCAGCAATTGCACTAGCATCTGTTAGAATTTTCTCTCTTAAAGTAACCTGCGGCTGAGTATAGTTTTCACCATATGTAAGAGAAAACCCAGCTCTCGAGAGGAGGTTTCGGAACATATCTTCCTCATCACCACTCATATCCTCGCTGTCTTCAGACTCAATAAAGTCATCAGGATCTGTTGACAAATCATCCTGGTCGTCATCTGACGCCAAAACCTCAAGATCAGAGAAATCAAACCATGGACAGCAGTCTATGATTTCACAAACAAAAACAACAGTGTCCCGGACAAGAAAACCAGCATCAGTGTCCAACAGGTCTGAGACCTTCATGAACTGAAGAACTGAATTGTTCCATGTTTTTGTGCAGATTGATGATTCCTTACACACCGTTTTTGCAGAATTCTTCTGGTTAATTATAGCCATCTTATAGTGTACCCAAAAGTTCTTATCAGGATCAAACCCAGATGGCTGGTCACTTTCCAGGTATATGCAGATCGTATCAAACGACTCATATACACCTATACGCAACTCACAACCACCAGCCTGGAAATATTTACTAAAAATCTTTCTTGTCTCCATAATATCCTTGAAGGATAAGAAATTTTCCACCTTCCACGTGAATGATGGACGTTTTGGCAAAGAATCAATCTGACATCCAGAACCTGAACTGCATGCTTCAGAATCTTCGTCACTAAGCTCTTGAATAGTAGCAGTTTCCTTCAGAATGAGAACCTCTGCAGCAAAAACAACAGTGTCCTGTACAAGAAAACCGGCATCCTGATCGAATAGGACAGTTAATGTCACAAATTCACGCCATCCCCAATCCTTTGCTGACTTAGAGTAACGGTTCTGAGATTCTTTCACTATTGTCCTCTCCTCTAATTTCTGATTGATGACAGACAATCTATGGCTCACAAAGCAGCTCCATTCACTGCTATTCCGGGGATCTGTCACTTCTAAAAACACTGACAGGTTGCATGGCGGTTGAGACTGCCCCCGTGGATACACAATAAGGCGGCAGTCTCGATTCCCGACCTGAAACTTTCTGCTTTTGATGCACAGACCCGTGATCTTTCGCTTCTTGAGCAGCTCCTTCAATCTTGTGAAGTTCTCAATCCTCCACACAAACTTTCCAAAGTGTCCATCCGACTTTCTAGCCCCAGCTCGTCCACTGCCAGCACCACTCATGCCTGCTATCATCGGTAAGCTGCGAGTGAACGAGTTTGACTCCTTGATCACATGCACTGAAGCACTAAACACCACAGCACCATCAAGCAGGTAACCCCCATCCGCAGCCAAAAAATCATCCATTTTTATGTAATCTCCCCACCCAAGGCTGGCATTGTCAGCCCCAAACCGGCCATACGAGTCTTTGTGGATGTGACTCCCACCTGGCTTCTGATTGAGGATCGAAACACGAAAAAGACACCAGCACCCACGGTCACCATCGGGCACGCCGCTGCCCCCGGCACTCGACGGCAATGCTGATGCCGAGGACCCTGATGTTGCCTGCACCAGGGGCTCCTTGCTCTCCAGACACACCGACAAATGGTCCGCGCCAGATACATTACTCTGATAGACACTAATCCGGAGCCCGCAGTCGCTCCCACCGGCATTGGCCGCCGGGAAGAAGGCAGGGCTCATGATCTTCTGCGTGCGGACCATCTCCCGGAAGGTGCCGAAGTTGAGCACCTTCCAGGTGAAGCGGCTGTCGGCCTCGGCGAACGAGGCGGCCTCGGCGAGCACCGATATGTCGGCGGCGATGACGAGGGAGTCGTGCGGCGGGAAGAGGTAGGCGGCGGCGGCGGACGGCGCGAAGTCGCACCAGCCGTGCGACCGCTTCTTGGAGGAGAAGCGGTGCCACGAGTCGCGCGCCAGGGACTTGGAGGGATCGGGGGAAGGGTGGGCGACGGAGAGGCGGTAGCTGAGGAAGCACTCCCATTTGGAGGAGGAGGAGGTGGTGGTGGCGGACGACGACGACGTCGGGGTTTTGGGGTCGAGCACCTGGAGGTAGAGGGAGAGGTAGCCCGGGAGCGCCTGCGAGTCGCCGCGCGGGTAGAGGAGGAGGCGGCAGTCGAAGCCGCCCACCTCGAAGTAGCGGCTGTAGAAGGTGCGGGCGCGGGTGCGGGGGAAGTCCGGGAGCGTCCACCGGCACGACGCGGAGGCGTCGCCGCGCCGCTCGACGGAGAACGTGGCCGACGGGGAGTCCGACGCCGACGGGGAAGGGTCGTCGGCCGCCGCCGCCGCCGCCGCGGCGGCGGGAGGGGAGGGAGTGGTGGGCTTCATGGAGGATTGGGGATTTTTTTTTTTGCTCCTCTCCTCTCTCTGATTGTTTTTTTGGGATGCTTTTCTCTCTTTTTTTTTTCTGGGGGGTGATGGTTTGGGTTTTCC

Coding Potentia
Explanation CPC Score
noncoding -1.05536
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0173600.1 2 24182308 A G
Osa02LNT0173600.1 2 24179272 T C
Osa02LNT0173600.1 2 24179332 T C
Osa02LNT0173600.1 2 24179340 T A
Osa02LNT0173600.1 2 24179633 A C
Osa02LNT0173600.1 2 24179911 T C
Osa02LNT0173600.1 2 24179954 T C
Osa02LNT0173600.1 2 24180073 G A
Osa02LNT0173600.1 2 24180468 C T
Osa02LNT0173600.1 2 24180479 A G
Osa02LNT0173600.1 2 24180758 T C
Osa02LNT0173600.1 2 24180986 C T
Osa02LNT0173600.1 2 24181048 C A
Osa02LNT0173600.1 2 24181192 T C
Osa02LNT0173600.1 2 24181243 A G
Osa02LNT0173600.1 2 24181264 A G
Osa02LNT0173600.1 2 24179206 G T
Osa02LNT0173600.1 2 24181647 A C
Osa02LNT0173600.1 2 24181783 A G
Osa02LNT0173600.1 2 24182111 A G
Osa02LNT0173600.1 2 24182468 T C
Osa02LNT0173600.1 2 24182547 T A
Osa02LNT0173600.1 2 24182552 C T
Osa02LNT0173600.1 2 24183494 T C
Osa02LNT0173600.1 2 24183667 G C
Osa02LNT0173600.1 2 24183893 T C
Osa02LNT0173600.1 2 24184020 C T
Osa02LNT0173600.1 2 24184586 T A
Osa02LNT0173600.1 2 24184798 T C
Osa02LNT0173600.1 2 24184858 G C
Osa02LNT0173600.1 2 24184862 T C
Osa02LNT0173600.1 2 24185150 T C
Osa02LNT0173600.1 2 24185440 T G
Osa02LNT0173600.1 2 24185553 C T
Osa02LNT0173600.1 2 24185972 A C
Osa02LNT0173600.1 2 24186278 T C
Osa02LNT0173600.1 2 24187139 T C
Osa02LNT0173600.1 2 24187183 A C
Osa02LNT0173600.1 2 24187199 G C
Osa02LNT0173600.1 2 24187394 C T
Osa02LNT0173600.1 2 24187551 A G
Osa02LNT0173600.1 2 24187875 A C
Osa02LNT0173600.1 2 24179162 T C
Osa02LNT0173600.1 2 24185798 A G
Osa02LNT0173600.1 2 24182072 T 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
Osa02LNT0173600.1 osa-miR5798 Cleavage 4.5 20.601 1 21
Osa02LNT0173600.1 osa-miR166a-5p Translation 3.5 18.722 1 21
Osa02LNT0173600.1 osa-miR166e-5p Translation 3.5 18.722 1 21
Osa02LNT0173600.1 osa-miR166l-5p Translation 2.0 18.722 1 21
Osa02LNT0173600.1 osa-miR166h-5p Cleavage 4.0 18.722 1 21
Osa02LNT0173600.1 osa-miR529b Cleavage 3.5 11.079 1 21
Osa02LNT0173600.1 osa-miR1424 Cleavage 3.5 14.528 1 21
Osa02LNT0173600.1 osa-miR1860-3p Cleavage 5.0 16.399 1 22
Osa02LNT0173600.1 osa-miR2863b Translation 5.0 22.055 1 21
Osa02LNT0173600.1 osa-miR2878-5p Translation 4.5 17.933 1 24
Osa02LNT0173600.1 osa-miR3979-3p Cleavage 5.0 6.186 1 20
Osa02LNT0173600.1 osa-miR3979-3p Cleavage 5.0 12.052 1 20
Osa02LNT0173600.1 osa-miR3981-3p Translation 5.0 24.884 1 21
Osa02LNT0173600.1 osa-miR5071 Translation 4.5 16.306 1 21
Osa02LNT0173600.1 osa-miR5337a Cleavage 4.0 14.398 1 21
Osa02LNT0173600.1 osa-miR5490 Translation 5.0 18.527 1 21
Osa02LNT0173600.1 osa-miR1859 Cleavage 5.0 12.595 1 22
Osa02LNT0173600.1 osa-miR827 Translation 5.0 16.877 1 21
Osa02LNT0173600.1 osa-miR2097-5p Translation 5.0 17.635 1 22
Osa02LNT0173600.1 osa-miR3979-3p Cleavage 5.0 19.166 1 20
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0173600.1 2 nan Resistance or Tolerance Insect resistance RG157 RZ318
Osa02LNT0173600.1 2 yld2.1 Morphological trait Seed RM262 RM263
Osa02LNT0173600.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0173600.1 2 qSB-2 Resistance or Tolerance Sheath blight resistance G45 RZ273
Osa02LNT0173600.1 2 nan Physiological trait Eating quality C621 C370
Osa02LNT0173600.1 2 qCSH2 Resistance or Tolerance Cold tolerance RM262 RM263
Osa02LNT0173600.1 2 nan Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0173600.1 2 qRPA-2-c Resistance or Tolerance Other soil stress tolerance C424 G45
Osa02LNT0173600.1 2 Tiller number Morphological trait Culm/leaf R26 C424
Osa02LNT0173600.1 2 Sn2a Morphological trait Dwarf C424 G45
Osa02LNT0173600.1 2 qRTT2-1 Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0173600.1 2 nan Others Others C424 G45
Osa02LNT0173600.1 2 qPTD-2 Morphological trait Panicle/flower C424 G45
Osa02LNT0173600.1 2 qGRH-2 Resistance or Tolerance Insect resistance C621 C601
Osa02LNT0173600.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0173600.1 2 qPN2 Morphological trait Culm/leaf RZ961 RZ401
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