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

>Osa02LNT0169700.1

TACATGCTTTCTAGACCAAGAATTATTGAGTGATAGACATTACAAGTAACTTATTTCGACCTAGTAGTTATAATTTGCAGGAAAGCTACACGAGCAATAAACACTTTCAGGCAGCTTAACACAGTACAAATTTCAGGTTTTGTTTGGTCACAGCGTTCCCAAACCAGATGGAAGAAGTGTCACTTGCAGGGGATCAAGAATCACCGCATTTGCTGATGCCATCATCCCATCGGCCGTGAAATACCCGTCCTTTTCCATGTAGACGAAGTGCAAAACCTTGCTCATGAACCAGAAGAGCTTCCTGCACGGTGGAGGAACAACCCCCCCATCTCTAGTCACCAGCCTTAGGAGGTCACACCTACTACCCTGGAGAACCCTCCTCATCTCTCTCTTGGCCTCCTCCATCGATGCCTCCGGTGAGCCGCGGCCGCCGCCGCTGTGGGAAAGAGCATGCAACATGACGCTATTGACCTTCCCCATTTTGATTTCCTTCTCGTATGTCTGCATGTCATTGAGAAGGCGGCCGATAGTGTTCGCAAGGTTCATTAGGTGGATGTACTCCTTGCTCCTGAAAACCTCTTCCGAGAGCTCTGGTCCGACGAACAATGCCGCTGAGGTGATGGTGGGGCCTAGAGCAAAGGAGTCCACGGCAGCTGACATGTACTCCTCCACTGTTGTTGGCACATACTTGTCCATCCTCCATTCTGCCTCGGTCAACATGCCCCTCACTGTGAACCACCACGATTCGGCGATATGATCCACGACATTGCGTTTCTGCAGCGGCACGGCCTTTTCCGCAATCTGCTTGCTCGTGTTGTAAATAGCATAGAATAGAATCTCTACACACTCGGAGGAGAAGCCAATCTCACCGTGCCCGTCCCACTTCTCTATTAATTTGACCAAGTTCTCCATTTCTTCTTTTGATCCATCACCGTCAAAGAAGTCATCGACTGTGGTCGTCAAGATGCAGTTCTGGGTCCATGCAATGCGGGCTTCGGATAATTCAGAAGGGAACATGGTTGCAGCAGCACTGAAATAGGTGATCGATGGCATTAATCTTGCAAATTTCAGCTCATCCAATCTGGTCTGTGCCACCCAACTATTAAGGTCTTGGAGTTCTTGTTGGTAGACAGATTGAGAGGAATGGAATTCGTCAACAGCCAAAGCTAGAATTTCGTCATGTGTAATAGCGCCACGGTATCCTGATTTCAGCAGCTTGAAGCCCTCAATTTTTAGTTGTTCCTTGGTCTTGAATTGTTCTATGTTCCTCTTCTGCTCTAGCCTTTCCAAGGTGGCATAGACTGGGAATTTCAAGGCATACTCCACCTCTAGCATTTCTGATTTGTGTGTCATTTTGGAAGATATTTTTTCCTGTAGTACTCTTGCTGACCAAGAACCAATATCTTGTAGAATCAAATCATCTTCCAAGCAACGAATTTGTGAACTTCTGTACAACTCCAGCAAAGCCTTAGTATCATTTAGATATCCATGAATTGAGTCATCAAAGCTGGATTGTTCCACAAATTGAGCCATTCCATCTGAACTGATGTCATAACCATGCATACGTAGTAGGCGAAATGCCATCGCACATGTTCCCATGTCCAACATTAGCTCCTCCTCGTTGTGTATCCATAACCTGTATATCATGTCCAATATATCACTTATTTCACAAGAAAAATTATTAGAGATACCCATCTTTTCAAGAGTATCCACCATGCCAAGCTGTGAGTAAGCATTTTGCGGATACATCACTGGGACTGGGCCATCGAGCTTGCTTACAAGTGAATCCAAGTAACAGAGGGCACTATCGTTGTGGCCATGGATTACTGTAGCAGCAGCTGCAGAAGGTGAGTTGAAAATCGATCTGTTCTTCCTTTGATATGCCATTACCTGATCCCAATCTTGTAGGCTGCCCAACCCTTCAGACACATATGCCATGAAGGCTCTTCTTGATGAAGCTGTACCATAAGCATCCCTTTCCAATTCAATCTTCCGCATGTGAAAAATCCCATCAATATCTGTTTGCATAACAGGGAATTCCAAACCCGTTCCAGTGGCAAGGTTAAGCAAGCCAGAAAAGGTAATGTTAAAACCCACAGGAGCAATAGTTTGCTCATCCATGGCAACCCAGAAATTTTTTCCAATAAAATTCAGTCCTCTGCTGATGTGATCTCGTCCAGTATTCCATCTTTTCAGTGCAACAACACATGCCAATGTACACAAAAGAATGTCTTTGTTGACAACCGAACCTGGCAGGTTTGTGCCCCAAGATCCATCATCATGTTGGTTTTGCAGTATCCACTCGATACATTGCGGGAAGCGTGGAGTTTGATGAGAGCCCTGCACTGGCACCATGGCTACCCATGCCGTGTCGTATGAAGATGGTGATAATTGAACTTCCCGAAGTTGCTTCCTTATCTTATCCTGCAGTTGGTTCTTCTGCATGCCTTGTTGGCTTCCCGCATTCCTCCCTAATCCCAGGCTCTTCTCAACACCTGCAGCTCCTCTTATGCTCACACGAAGAGGAGGTGCTCTGTTGAACTGCTCTATCATCCCACGGGGTGAAGCTCTGAGGAATTGTCCTAAGCATGCTGAACTCATAGGAAGTATCATCCACAACTACCCTATAACGATACTACACAATATGATTCTATGTTACATGCAACATGGGTTTATGCTGAAAAAGTAATAATAATATAAGCGAAGTCATCTAGATCTAGTTTATGATTCAGCTATCTATATCACTCCCTTTCATCGTAGGTCCAGTTCACCACCTCAACTATTACAAAAAGTACAATAATTAACCTCTTCAATTATGAAAGAAAAAAAATACACCACTCATATATTTAATCCGGACTCTTAAATCCCTCGTACCCTATTTTAGGTGGTTTAGGGCTAAGCTATCTTGATACATAACCAAATCTTGCAAAGTAAACTTTATGCAGTCTCTCGTTTCTTACCTGTGCCATTTCTAAGCCTGTGGGATAGACGGTGGGTTGTTCTACTAATATGAAATATTAACTGTGTACTTGTGTTATACTCCATCCGTCCCATAGTATAGCAACTTAGGGTGGGAGGGAGTACTATCTTCCAAGTCAAGTTAAACGATTTGATTATTGCTAGCTAGCATTCAGCACGTGCGTACGTACAGTACGCCCTTGAGGACTTGGGTTTGAGAAATTATGCATTCTGAATTTATGACTGGCTGCACTGCCACTCACATGTACACCACGAGAAGAAGAAAAATATAAAAAAAGAACTAGGAAGAGAGAGAGAAAAAAAGTTTCATGCAAATCGGGAGAACGTGTCAGATATTAATTGAAATATGCAGAAGTTTGAATCCGTTTGTTTTTTCTACGGAAATATGTATCAGTTGTTTGATGTCATATTGTTTTTGTGCAATGAGAGATCTGTGCAAACAAATAGAATAAAGCATAAGGAACAAGTAATATACTCTATTCCACAAAAGTTATGTACGTACGTATTACTTTCGTCACCAAAATTAAGTAGAAGTTAACTCATATTGTATCTAACAAAAATCAAGAAGTATATACACGCATGCAACAATGAGTATTAATATGACTACTCGGATTCTGATCAAACATTTAATTTTACCTCTCTATTTAAATTTTAGATGAATAAAGACTACCAATAGAAACAACTTATTTAGAAAAAAAAAATAAAATATGAAATAGTTTACTCTTGTGGATGGAGAGAGTAAGCCTTAACAGCACAGGTTTTGACACTACGTCAAACGAGGTTATTTTCTGTATCAGAACACAAACGGTGGTGTACGAAGCAAAGTGTAGAGCACTGAAAGGACACGGATGTTTAAAAGGGGCAGTCTGTTTAGATTCATCGGAGAAAGAAACCCACCTTACAGAAACGAGAGAGGCAGGACGCAGGAGAAGCAAAACCTGGCAGAACAGGGTAGGCTAGCTAGGCCGCAGCTCGATCTCTGAACGAGAGAGACCAAGGGGGCAGGAGGAACTAGCTAGCAGCTTATCGTTGATCAGCTATCGGCCGTGCCTGCATG

Coding Potentia
Explanation CPC Score
noncoding -1.01811
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0169700.1 2 21855840 C G
Osa02LNT0169700.1 2 21854293 T A
Osa02LNT0169700.1 2 21855576 A T
Osa02LNT0169700.1 2 21855735 G A
Osa02LNT0169700.1 2 21855884 T C
Osa02LNT0169700.1 2 21856195 A G
Osa02LNT0169700.1 2 21856204 T G
Osa02LNT0169700.1 2 21856921 A G
Osa02LNT0169700.1 2 21857029 T G
Osa02LNT0169700.1 2 21854347 T C
Osa02LNT0169700.1 2 21857623 A G
Osa02LNT0169700.1 2 21857709 A G
Osa02LNT0169700.1 2 21858086 G C
Osa02LNT0169700.1 2 21858223 T C
Osa02LNT0169700.1 2 21858517 T C
Osa02LNT0169700.1 2 21858819 T C
Osa02LNT0169700.1 2 21858978 T C
Osa02LNT0169700.1 2 21859301 A G
Osa02LNT0169700.1 2 21859347 G A
Osa02LNT0169700.1 2 21859728 A C
Osa02LNT0169700.1 2 21860560 T C
Osa02LNT0169700.1 2 21860726 T G
Osa02LNT0169700.1 2 21860877 C G
Osa02LNT0169700.1 2 21861523 G A
Osa02LNT0169700.1 2 21861899 A G
Osa02LNT0169700.1 2 21861927 C T
Osa02LNT0169700.1 2 21857580 T G
Osa02LNT0169700.1 2 21855520 G A
Osa02LNT0169700.1 2 21863539 C G
Osa02LNT0169700.1 2 21853711 G C
Osa02LNT0169700.1 2 21856489 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
Osa02LNT0169700.1 osa-miR5543 Translation 3.5 7.867 1 21
Osa02LNT0169700.1 osa-miR5807 Translation 4.0 16.761 1 24
Osa02LNT0169700.1 osa-miR5837.1 Cleavage 4.0 9.505 1 21
Osa02LNT0169700.1 osa-miR818f Translation 3.5 14.852 1 21
Osa02LNT0169700.1 osa-miR1861o Translation 3.5 15.677 1 22
Osa02LNT0169700.1 osa-miR159a.2 Translation 4.0 19.676 1 21
Osa02LNT0169700.1 osa-miR439a Translation 4.0 12.924 1 21
Osa02LNT0169700.1 osa-miR439b Translation 4.0 12.924 1 21
Osa02LNT0169700.1 osa-miR439c Translation 4.0 12.924 1 21
Osa02LNT0169700.1 osa-miR439d Translation 4.0 12.924 1 21
Osa02LNT0169700.1 osa-miR439e Translation 4.0 12.924 1 21
Osa02LNT0169700.1 osa-miR439f Translation 4.0 12.924 1 21
Osa02LNT0169700.1 osa-miR439g Translation 4.0 12.924 1 21
Osa02LNT0169700.1 osa-miR439h Translation 4.0 12.924 1 21
Osa02LNT0169700.1 osa-miR439i Translation 4.0 12.924 1 21
Osa02LNT0169700.1 osa-miR1428a-3p Translation 5.0 11.234 1 21
Osa02LNT0169700.1 osa-miR444d.3 Cleavage 2.5 12.413 1 21
Osa02LNT0169700.1 osa-miR1435 Cleavage 4.5 18.561 1 20
Osa02LNT0169700.1 osa-miR1436 Cleavage 3.0 19.846 1 21
Osa02LNT0169700.1 osa-miR1441 Translation 4.5 23.857 1 21
Osa02LNT0169700.1 osa-miR1851 Cleavage 4.0 14.824 1 21
Osa02LNT0169700.1 osa-miR1852 Cleavage 3.5 16.92 1 21
Osa02LNT0169700.1 osa-miR1861a Translation 3.5 15.677 1 22
Osa02LNT0169700.1 osa-miR1874-3p Translation 5.0 16.111 1 24
Osa02LNT0169700.1 osa-miR1846e Translation 4.0 18.487 1 20
Osa02LNT0169700.1 osa-miR2097-5p Translation 4.0 16.256 1 22
Osa02LNT0169700.1 osa-miR2097-5p Cleavage 3.0 18.885 1 22
Osa02LNT0169700.1 osa-miR2100-5p Translation 5.0 21.008 1 22
Osa02LNT0169700.1 osa-miR818f Translation 5.0 16.389 1 21
Osa02LNT0169700.1 osa-miR1850.1 Cleavage 3.5 14.219 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0169700.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0169700.1 2 nan Resistance or Tolerance Insect resistance RG157 RZ318
Osa02LNT0169700.1 2 yld2.1 Morphological trait Seed RM262 RM263
Osa02LNT0169700.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0169700.1 2 qCSH2 Resistance or Tolerance Cold tolerance RM262 RM263
Osa02LNT0169700.1 2 nan Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0169700.1 2 qRTT2-1 Resistance or Tolerance Drought tolerance RG157 RZ318
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