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

>Osa09LNT0449200.2

ATATATAGGCCAGTATCATCATTAATCTATTGAGTCAATACATCAAAATCCTGTATACATGTGCATCAATCCACCTGAAACAAACCCTCAGTGGAATGCATTATTATGAGGTTTATACATATGAACACGTAAAAAAAATCAACTGAAAAATGGCCTCTCTATGACGATTCTTGTGAGTGTGATCTATCCTCTCTACAACTCTACAACTCCTATAGCCCTACAGCAACTACAAAAACAAGGAAGAAAAAGAATGTGATCCTATGTGTAATCAAATCATCAATACAGGATAATGGAGCTCTGAAGCTATGGTGGCTGGAGCTGAGCTGATCAGAATTCAGAATTCAGAGAACGATGAGGAATAGGAGAACAATGGTGGCGGAAACGCTCTGCGGTTGCAGCGGTGAGCTTGCTGAAGGCATCACATTGACCTGGGTGCCGTTTGGCAAAGCTCCTTTGGCTGCTTCAGGGGTGTAGCTACTCGGACCAAGACCGGGTTTCGAAGGAACAGCTGAAGGGCTGGGGTTCACCGGAAGTCTGCTCGATTCGTCGAAGTTGTAGCAGTTGAAGTTTTTCCAGCCCAACACCATTCTCTCTCGGTCAAAGACGACCTTCAGTCCAGACATGAAATTCTCTCCTATTAAGTTAACACCCTCACTCTTCATAATAGCCAAGCAGTACCCAACTGGATTAAAAGCATTGTCCGTTATGGTAATTATTGGATCGTTAACAGGAAATATGCTTCCACCTTTTGCTGTCAGACTTACATTTGGATGAACAATTCCGTTGGCACTTACTGAGTAGCAAAATTCAAACGGCATGGAAGAGTCAAGCATGTTTCGGCTCGAACGGATTTGTGCATCAAAACTGCTAGTGATTTGAGTATACATTGGATCAGACAGAGCCGTGAAAGACGTGCCAGAGTCAACAATAGCACTGAACTCTGTGCTGATCGATTTACTTCCCACCGTAATTCCCGTGATAGTTATGTTGTAATATGGATTCTGTTTATAAACATTCAATGGAGTTTCCTTCTGATCCGAGCTTCCTGTGTCCCCAAAATTGATCCTACCATGACCGTCATCGCCAAAGCACATGGAGAAAGAATTAGCAGCAAGTCCTTTGCTTGCTAGCAAGCTAGGAACCGATTTGCTGTCCATCCCAAGCCCAAGCAGACCGTTTGGCGCAGCACTGCCTAGAAACGATCCTGTCTGAACCTGTCCACAGCCGAACATTATCGGAGCTGTAACGATTTTCGATTGCGCGGAGTCAGATGTCAAGTACAAGACATCCTCCACTAATACCCCAGAGGATGAGGTGTTATCCGACAAGTACTGGATACTGTAGGGGCAGCTGTTACTCTTAGAACGGCAGGCATTTTGGAGATCACACAAGTTGCTACTGCACGGGACCTTCCGGCTAGTAGTCGATTGCGCAGGGCTATACACGTCGAACTTCAAGCTCTGTATAAATTTGTCATGTGCAGCAAATGTAAATAGATTACTCAGTAAGGTCATCATGATTCAGCAGCTTCCCATAAGCAAGAGTAAATTTCAAAATTCTGACAAGAGTGCACGGAAGAATACAAGATTCGGCTATTTTCTTTAAGCTGAACGAGGTCCCAGTTCAAGCTGTCATGCTAATAGAAAGGCTTCCAAGAAGCACACAAGCACATGCAGTGCCTTCATGATTTTCTCCTCTTTATAGACATGCTCATAATCCTGTCGTAATCTTTTCTACCAGTCTAGTAGTCTACTAGTACCACTTTCATCTTTGTTTAGCAACAAATCTATTATTATGCCATTCACAACAACTTTCCCCAATCCCTAAAGTGAAATTCTCTTCTCTACTAGACTACTACTTATCCAGTTATCCTAACAACCTAAAATATCTAACAGAACAACAAACTTTTGAAACCAATTGCAACAAAAACTAGAGGAAAAAGAAGAAGAGGGAGGAGATTACTCCGTAGTTGGGGGATTGGAAAGGAGCACACTTGAGGCAGTCGCATGGCACCCAGAAGAGGTCGCTGCCGGTGTCGAGCGCCACCAAGAACGTCACGTTCGGCGTCCCCAGCGCCACCACCGCGTAATGCAAAAATCCGAAATCGTTGAGGCGGTAGGTGTCGTTGCCGTCGGCGAAGGCGAACTCGGCGCCGCCGCCGCCGCCGCCGACGCCGAGCGACCGGCGGCGCAGGCCGTCGTGGCCGGCAAGCGCGGCGTAGTACTCGGCCGTCCCGTGTGGCGGCGCGGCGGCGGCCGCCCACCGGCGCACCGCCGCCGAGTACCGGTGGTGGACGTCCAGGCTCAGCGCCTCCGCCGCGGCCACGGCGGCGAGCAGCAGCAGCACAGCCCGAACAACCACCACACCACCACCACCACCAACCATAGCTCGCAACGAAGCAAAGCAAAGCAAACGCAGAGAGAAGAAAAAGCTAGTATCAACTTTATACGGAGAGAA

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.802415
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa09LNT0449200.2 9 21347480 A C
Osa09LNT0449200.2 9 21347763 G A
Osa09LNT0449200.2 9 21348501 A C
Osa09LNT0449200.2 9 21350083 A G
Osa09LNT0449200.2 9 21350922 G A
Osa09LNT0449200.2 9 21348485 G A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa09LNT0449200.2 osa-miR159a.1 Cleavage 4.5 10.596 1 21
Osa09LNT0449200.2 osa-miR159b Cleavage 4.5 10.596 1 21
Osa09LNT0449200.2 osa-miR159c Cleavage 5.0 10.596 1 21
Osa09LNT0449200.2 osa-miR159d Cleavage 5.0 10.596 1 21
Osa09LNT0449200.2 osa-miR159e Cleavage 5.0 10.596 1 21
Osa09LNT0449200.2 osa-miR159f Cleavage 4.0 10.596 1 21
Osa09LNT0449200.2 osa-miR172a Translation 5.0 15.689 1 21
Osa09LNT0449200.2 osa-miR166i-3p Translation 5.0 22.545 1 21
Osa09LNT0449200.2 osa-miR172d-3p Translation 5.0 15.689 1 21
Osa09LNT0449200.2 osa-miR416 Cleavage 4.0 14.11 1 21
Osa09LNT0449200.2 osa-miR444a-3p.1 Cleavage 5.0 19.296 1 21
Osa09LNT0449200.2 osa-miR528-3p Translation 4.5 24.323 1 21
Osa09LNT0449200.2 osa-miR444d.1 Cleavage 5.0 19.296 1 21
Osa09LNT0449200.2 osa-miR2867-3p Cleavage 4.5 16.332 1 20
Osa09LNT0449200.2 osa-miR2868 Cleavage 5.0 18.598 1 20
Osa09LNT0449200.2 osa-miR5337a Cleavage 4.5 18.784 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa09LNT0449200.2 9 gy9 Morphological trait Seed RM242 RM215
Osa09LNT0449200.2 9 nan Morphological trait Root RM160 RM3808
Osa09LNT0449200.2 9 Spk(t) Morphological trait Culm/leaf nan nan
Osa09LNT0449200.2 9 dhc9.1 Resistance or Tolerance Drought tolerance RM215 RG667
Osa09LNT0449200.2 9 rwc9.1 Resistance or Tolerance Drought tolerance RM215 RG667
Osa09LNT0449200.2 9 nan Morphological trait Root RG667 RZ404
Osa09LNT0449200.2 9 yldp9.1 Morphological trait Seed RM242 RM205
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