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

>Osa03LNT0197000.2

CCTGGGCAATTACGATTGCCCCAAAATTCGACAACATTTCTTTAATATTTGCCATCACGGCACGATCAATTGAAACACCAAGAGTTAAAATATTTGCCCGCCGTACACTTCGAGAGCTTATAGATAATGTCTTAAGCAAAAACGAGTGATGTATGCGAACTTAGTGTTGAATAACCCATGCTATAAAGTACAAAAGGCTGCATGACATAATGTTACAGGAGACCGTTACACAGCAATAGAGCAAGAATCTTCAGCGATCAACCGAAAGTTGCTGTCCGCTAGCTCGGGAACTTCGTTGAGTACTGCTGCGGAGACATAAATGTTGCCGTAATCATCTTTCCCGCAAACCACCTCCCATGAAGTGCTTTCTGTGCACTCATGGCAGCTGTTATACTGTCAAATCGAAGGTACACAAAGCCAGAAGTATTCTTGTCCACAAAAATGTGTTTTACTTGGCCAAACTTGGAGCATTCTTCTTGGACATCATCTTTGATATCCAAATCAAAATCAGGGTCCGTCTCCACGGATGGATCAAACATATTTTTAAGCAATAGGCATTCACTGGGTGGGGCTGTCTCAATGGCTTGGGTAGTAATTGGAAGAGACACCCCAGGAACTGAACCAAGACCAGGCACTGTAGGCAGTACAGATGCAGCGACTGGAGGAGCACCAAGAACTGATGCAGGTGGTAATCCAACAGAAGTGTTCAAACCAGTACCGGCTATCCCAGCAGTCAAACTGGTGGTAACGCCGCTACGGTCTAATTTCTGCATCAAAAGAGCTCTTGAACTAGCATTCAGTGCCAAACCTCCACCTTCATCATCATCCAAATCTCCAGTAGTTACTCCACTGACTTGAACTCCTGCTTGGTCTGTCACAGCAGAAACCTTAATCACACGTCCAGCTATATCAAGTTGCCCATTTAAACTCTGAGCAGCCTTTGCATCTTCAAGGCGTGCAAACTGAACAAAACCAAAACCTTTACATAACCCAGTAAGTGGATCTAGTGGCAATTGGACAAGCTCCACCTGACCAAACGGTTCGAAGACCTGTCTCAATTGATCTTCAGTAATATTTGAGTGAAGATTTCCAACATACAACTTTCTTGCCCCACCTGAAGCTGCTCCACTTGAAGAAGCATTTGACTGAACTAAATTCTTTTCAGCCTCTGATGGCTTAACCATCACCTGTTGACCAAGAAGCAGCTGGCCAGAAAGAGCTATTGCCATTGGTACAGACATAACATCATAGAATTCGATGTACTTCCCCCAAAAAGATCTTGTATTCCATCTTAGTCATAAGTAGCTGATTATCCCAGTAGATACACCAAATTATAAACATTCCCAACTCCTTTAGAACGGCGCGAGTTTCGGTCCATGATGAGGCGAACATCCCGGACCTTCCCAGCCCTTGAAAAGAATTCGTACACGTCTCTTTCATCCGCCTTCAGAGATAACTGGTAGGCAAATACTGTCCTTTGATCTCGTTCTGGATCTGCTTCAGGCTCTCCAGCCTCTTCTTTCCTACGTCTGATATCCTAGGTCAGGCTCAACATCAAGACCACAGAAGATGGCTCTAGCAAATTGAATCTGACATCGCGGTCACGGTAGTCTCGCTCGCGGTAGCGTTCGCGGTCACGTTCTTCGTCGTCGCGGCGGCGCTCGGACCGGCTCCGGCTCCTCCGCTCTCTATCCTTCTCCCTCTCCCTCTCCCTCTCCTTCTCCTTCTCCTTCTCCTTCTCGCGGTCCCGGCTTCTCCTCTCCTTGTCCTTGTCCCTCTCCTTCTCCCTATCCTTCTCGTCCCGGTCTCGGTCGCGGTCGCGGTCGCGACGCTCCCGGCTGCTGCGGTGCCGGTCCCGGTCCTTGTCGCGGTCGCGGTGCCGGTCCCGGTCCTTGTCCTTGTCGCGGTCGCGGTTCTCCTCCGAGCGAGAGCGCTTGGATCTGCGCTCGCCATCGTCGCGCTCTTCGTCGCCGCCGCCGCCGCCGCCGCTCCGGCGGCGAGAGCTTCGCTCCTTCTCCTCGGATCTGGGCGCGGCGGCGCCGTTGGACGGCGCCCCGGAGCCCTCCACCGTCTTCTCCAAGTAGTCGTACTCGTCGAAATCCATGGCGACTCGCGGCCGCGGCGACGCGGAAACCCTAGATGAGGAAAGAGAAAATTGGGGGAGGGAGAGAGCGCGCAGCTAAACCCCCAGTCC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.931302
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0197000.2 3 2924821 A T
Osa03LNT0197000.2 3 2923926 A G
Osa03LNT0197000.2 3 2927011 A C
Osa03LNT0197000.2 3 2927652 G A
Osa03LNT0197000.2 3 2928977 A G
Osa03LNT0197000.2 3 2923811 C 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
Osa03LNT0197000.2 osa-miR531c Cleavage 4.5 24.425 1 24
Osa03LNT0197000.2 osa-miR164e Translation 4.5 7.271 1 21
Osa03LNT0197000.2 osa-miR169i-5p.2 Cleavage 4.0 6.411 1 22
Osa03LNT0197000.2 osa-miR531a Cleavage 4.5 24.425 1 24
Osa03LNT0197000.2 osa-miR1846a-5p Cleavage 4.5 7.973 1 21
Osa03LNT0197000.2 osa-miR1846a-5p Cleavage 4.5 23.454 1 21
Osa03LNT0197000.2 osa-miR1846a-5p Translation 5.0 15.724 1 21
Osa03LNT0197000.2 osa-miR1846b-5p Cleavage 4.5 7.973 1 21
Osa03LNT0197000.2 osa-miR1846b-5p Cleavage 4.5 23.454 1 21
Osa03LNT0197000.2 osa-miR1846b-5p Translation 5.0 15.724 1 21
Osa03LNT0197000.2 osa-miR1883a Cleavage 5.0 14.932 1 24
Osa03LNT0197000.2 osa-miR1883b Cleavage 5.0 14.932 1 24
Osa03LNT0197000.2 osa-miR1846c-5p Cleavage 4.5 7.973 1 21
Osa03LNT0197000.2 osa-miR1846c-5p Cleavage 4.5 23.454 1 21
Osa03LNT0197000.2 osa-miR1846c-5p Translation 5.0 15.724 1 21
Osa03LNT0197000.2 osa-miR3979-5p Cleavage 5.0 21.36 1 20
Osa03LNT0197000.2 osa-miR5508 Cleavage 5.0 11.94 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0197000.2 3 qOE3-1 Physiological trait Eating quality nan nan
Osa03LNT0197000.2 3 qTA3 Physiological trait Eating quality nan nan
Osa03LNT0197000.2 3 rn3 Resistance or Tolerance Drought tolerance RM231 RM175
Osa03LNT0197000.2 3 qDEF-3 Physiological trait Flowering R518 C721
Osa03LNT0197000.2 3 QSs3 Physiological trait Sterility RG348 RG944
Osa03LNT0197000.2 3 QSbr3a Resistance or Tolerance Sheath blight resistance RG348 RG944
Osa03LNT0197000.2 3 qtl3.1 Resistance or Tolerance Drought tolerance RM7332 RM545
Osa03LNT0197000.2 3 nan Resistance or Tolerance Drought tolerance RG348 RZ329
Osa03LNT0197000.2 3 dth3.1 Resistance or Tolerance Drought tolerance RG104 RZ329
Osa03LNT0197000.2 3 qFDN-3 Physiological trait Flowering RZ329 RG348
Osa03LNT0197000.2 3 nan Resistance or Tolerance Drought tolerance RM231 RZ329
Osa03LNT0197000.2 3 nan Resistance or Tolerance Drought tolerance RM231 RZ329
Osa03LNT0197000.2 3 nan Resistance or Tolerance Drought tolerance RM231 RZ329
Osa03LNT0197000.2 3 nan Morphological trait Root CDO20 RG409
Osa03LNT0197000.2 3 qHEJ-3 Morphological trait Shoot/Seedling RM175 RM22
Osa03LNT0197000.2 3 S34(t) Physiological trait Sterility nan nan
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