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

>Osa01LNT0008200.2

TAACAGCAGCGAACTTGCTTGATTTTTACACTGATCAAACTTATAAATATTCATACAAATCACATTCCATTCTTGTGTAAAGATCAATGCACATTAGACCCAATAGTTGCACATCTGTCACACGACATTTTTTTTCATAGGATCAAGAACATGAATTCTGCACATAAACAGGCTTTTTCCTTTAGCCTTGTGAAGAGGGATGCTGCCGCGAGTATTGGTTCACCAGCAACAGTATACATCACTGATCAATCTACTAGGTTGCCTCTGCAGAGAGTATCTCGAGCTCAGCCCACCAGAGAGGCGAGAGCCGCGGCGTCGCTGCCTCCGGCGAGATGTTGAGAGCTTGTCTCAGCTTGCGGGTGGCGTCTCTCATCGTCGGCCTCTGATCTGAGTCGGGATCAATGCACTCCTGAATCACCTCGCAGACGGCCTCCAGCTCGTTGGCGTTGTGTTCCTTCAGCGACGCGTCGACGAGCTTGCTGTAGCTCTTGCCCTTCAGATACTCAGCGGCCCAGTTGCACATGGATTTTTGGTCGTCTGCTTCAGGGAGCTTTCCGGATATGATCTCTATCAGAAGCGTGCCAAAGCAGTAGACGTTGCTCGCGATATCAGGAGGACATTCAGAACGGCTGCTGCTATCCTCCTTTGCAGTCTTTGCTTTTATGGCGACTTCTTTCCAGATACCAACATCAGCAATCTTGGCAGCATAATCATCTGTCATGAAAATTGTGTCGGAGCGCATGTCGGTTATCGCAACAGGTGGATTGAGATCATGGTGCATGTATTGGAGACAGTATGCCACACCCATGATGATCCTCATCCTTGCAGCCCAGTCCAGATGCTCAAATTCTTTGAGGTGGAGATGCTCAGAGAGAGTGCCATTTGGAGCATACTCGAACACCATCATTCTCATGAAGGGTTGATTTTCCAGGCAATAACCTAGGAGGTTGATGAAATTCTTGTGGTTTACTCTTGATAGTGTGTCTATCTGTTTTCTGAAGCATGTCTCTGAACTCTTAGGCCACTCTTTGAGCGACAAAATGGCAGTGGAAACAACACTGATCTCAACTCCGCTAGATAATGTCCCTTTGAACACGGTGCAGCTAGGGAAAGTGTTGATTATGTTACTGAAATCCTCACAAGCGGCTTCGAGTTCAGGTCTGTTTAGCTTTGGAACACCTGTTACAAATGCTTTCTGAAGTGGGCCACTTAGACCCGTTTTCCAAGGTCCTATTGCCGCACGCCCTCGCTTCCGCCAGACCAAGATTGGAGCCACAATCAGGCTAATCAGCAATATTGCAGCTGGAATTATCATAAAATATGCCCACTTGCTGTGCTTTGAACCAGACACTTCATCGGTTGATTGATTTGCTGCTCCAGACTGCATTGCAGCAGCATCAGTATTTACAGCTGATTCCAGAACTTCGGCCTCTGAATTTGGGAATGCAGAGAATGAACCACTCCCTAAAGAGAGAACATCAATAGCCCTTTGGATCTCTTCTGAATTTACAGGGCCAGAAGATTTAGCATAATTCCCTGAAAGGGCAGGCAGATTGCCAACTTCACCGAGCAGCCTGCGGCCCACGGCACTTGCAAAGGACTGCAAATTTTGCATAATGTGTGGCTCGCCTAGACTTGCTAGGTTGGTGGAGTATTTCTCTCGGAGATCACTGAAAGAAGTCCAATCCTTAAACCCCGCCCAGCAACCTAATTTTCTGCTCAAGCATCCTGCCTGCTCATCAGATATATCTTGAATGTGCAAAGAAGAGATATCATCTTGGAACTGATTGTCATGAAGTGACAGCTGCTTGAGCAGTGGCATTGCCATTAATTCTTCTGGAATCGTTCCATCCAAGTTGTTGCTGCTCAAATCCAGTACTTCAAGGGCAGTTAACCCTCCGAACTCTTTGGGAATTTTCCCACGGAAATTGTTGTTTCGAAGAATGAGAGATTTCAAAAGTTGAAGACGTCCAATCTCAGGTGCGAGAGTTCCCACCAATTCTCGGCCGTCAAAGCAATGCACGCCGGACCATCTGCAGGGCGTGGCGTCTGCCGGATCCCAATCCCGCAAGGCGCCATGGGGGTCAGCCTCCACCCTCTCCCTCAGCTCGAGCAACGCCATTCCTTCGCCGTTGAGCGTGGCGCCGCCGCGCCCCGCCTGCGCCTGGAGCAGCACGAGGAAGACGAAGAGCAGGTGACGCAGCGCGTCGCGGAGGTGGGGCCCGACGGTGGCGCGGCGAGGCCCCCACCGCGCACCCATGGCGACGGGGGAGGAGCGCCTCCCGGACAATGGCAGCCCGGCGGCCACCCGCCGCTGCCGCCGCCCTCTTCCGGCCGAGAATGTGGGGGAGGGAATCAAGAACCAGACGAAGCTTAGCGAAACAACCGCGGCGAGCAGAGGCGCTGGCTCCGGTCGATCTCTTCCTCTCCGGCCTCGTCACGACGCCGGGAAAACAAGATCACAAGAGGACGACGACGACGACGACGACGACGACGACACGACGCCGCGGGCGCTGGCTTAGCCCGGCAAAGCCCCGAGGGAGGCCGAGCTATCCGCCGGAGGATCCCATGGGTCGCCTCGCCCGCGCCGGGACGGTGTCTCAGCGGCGGCGTCGGCGAAGAGCTGGTGCTGTCAGCGGCGGAGATGGACGTGGACGGGTTCTCGTCGGGATCGGGTGGTCGGACGACGACGAGGGCGGCGGCGCGAAGGGGGTGGTGGGGGG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.971936
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0008200.2 1 5818287 G T
Osa01LNT0008200.2 1 5814924 G A
Osa01LNT0008200.2 1 5815218 T G
Osa01LNT0008200.2 1 5816960 G A
Osa01LNT0008200.2 1 5817021 T C
Osa01LNT0008200.2 1 5817344 A G
Osa01LNT0008200.2 1 5817441 T C
Osa01LNT0008200.2 1 5817442 A G
Osa01LNT0008200.2 1 5818018 T C
Osa01LNT0008200.2 1 5819113 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
Osa01LNT0008200.2 osa-miR5539a Cleavage 5.0 16.453 1 22
Osa01LNT0008200.2 osa-miR5539b Cleavage 5.0 16.453 1 22
Osa01LNT0008200.2 osa-miR172a Cleavage 4.5 22.08 1 21
Osa01LNT0008200.2 osa-miR172b Cleavage 4.5 22.08 1 21
Osa01LNT0008200.2 osa-miR172c Cleavage 3.5 22.08 1 21
Osa01LNT0008200.2 osa-miR172d-3p Cleavage 4.5 22.08 1 21
Osa01LNT0008200.2 osa-miR5489 Translation 5.0 18.284 1 21
Osa01LNT0008200.2 osa-miR5509 Cleavage 5.0 21.775 1 21
Osa01LNT0008200.2 osa-miR5519 Translation 5.0 19.934 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0008200.2 1 nan Physiological trait Source activity RG532 RM472
Osa01LNT0008200.2 1 gp1 Morphological trait Panicle/flower RG532 RM259
Osa01LNT0008200.2 1 nan Resistance or Tolerance Other soil stress tolerance C955 C885
Osa01LNT0008200.2 1 nan Resistance or Tolerance Other soil stress tolerance C955 C885
Osa01LNT0008200.2 1 nan Resistance or Tolerance Other soil stress tolerance C955 C885
Osa01LNT0008200.2 1 nan Resistance or Tolerance Other soil stress tolerance C955 C885
Osa01LNT0008200.2 1 nan Resistance or Tolerance Lodging resistance R1944 C955
Osa01LNT0008200.2 1 ph1.1 Morphological trait Dwarf RM220 RM272
Osa01LNT0008200.2 1 nan Morphological trait Root RM7383 RM243
Osa01LNT0008200.2 1 nan Morphological trait Root RM7383 RM23
Osa01LNT0008200.2 1 Rf3 Physiological trait Sterility nan nan
Osa01LNT0008200.2 1 Rf Physiological trait Sterility nan nan
Osa01LNT0008200.2 1 ppp1.1 Morphological trait Panicle/flower RG140 RM243
Osa01LNT0008200.2 1 prg1.2 Physiological trait Source activity RG140 RM243
Osa01LNT0008200.2 1 spp1.2 Morphological trait Panicle/flower RG140 RM243
Osa01LNT0008200.2 1 nan Resistance or Tolerance Salinity tolerance RM1 RM5
Osa01LNT0008200.2 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0008200.2 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0008200.2 1 qHUS-1-1 Others Others RM151 RM3746
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