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

>Osa03LNT0235500.2

TCAAAGCGAACAGCGAAGCTTCAATTTAACAAATTCTATAGCAACCAGCTTGTTTCAGATAGTCGGTGACAAGAATTCACTGTCACCTCATCAGAATTTAGAAAGCGGTAAGTATTTCTGGCAGTGAAGTATCTTGATGGTAGAACTTTCACGGGCACATGCACCATCCATTAGATTGGCTGTCTGCTACCTCTATCAGTAATTCTGTATATACAAAACACTTTTAGTATCTCCCAGCATTAAGCTCTAACGTCAGGATCTAACGATGTCGATGTTTCGACATAGAACCAAGTAATGTGAGTTTTCTTTCCACCAAAATATGATACGGTAATTGTAAGCAATAGATCACATATGAACTCAACAGCAGCAGCAGCTGGCCTGTTTCTCACTCGTCATCACTGTCAAAAACAACCGTCTTTCTACGATTAAGAGGCTGTTTCCTTGGTGGAGATTCGTCGTCAGAGTTGAACCCTTTGCGCTCCTTTACATGCTCTTGTTCCTCATTATTTTCATCTGACATGGAAGTATCACCTATGACTTCTTCTGGGTCTTCTTCCTCTTCATCCATGTCATCTTCCCTTCCATTTGTTGGTGAATTATCTATATCCTCGACATCTGTTTCATACTCTGATTCCTCACTTTCACTCTTGGAATACTCATTCACCTGATGCTTGGGTACACTGGGAGAAGGAACAGCTTTCCCTACATTTGCCTTCTTTGCATTAGTTACGTGTCTCTTAGAAAGTGCTTCAGCCTCCAAGCTATCCTCAAAATGTGCATGGCCTGGGCCTCGGCGCTGATTATAACCAACACCAGGTGCCTCATCCTAGCTGTTTGCTGATTCCCATGCAGTTAGTTGACGAAATGGCCGTGGCTGTGGGAGGGCACAAAGGCAACCTCTGCAATTGGAAGCAATAGTTTTGTTGCAGCCGTTGATCGAATATGCTCATGGCCATGTAGTGAATATGAAATTTATATCTCAAACAGAAATTTGGCATGTCTATCTCGTTAAATGCAAGAGAGTTACTCAAACCTGGATGGCCAAATAAGTATACTTCAATATTGGTCACAGTGGAGAAAGAAAGAAGTATATCGGTCTACGTAGACAACATCATCTCTCACACGAGGGCCTGAGGTCAAGACCATTGACAGAAAAGCACGAGGGATTAGACATAATGGGCATAAATTTTAGGTTTTAGGCCATAACTGGTGGGTATCGGATCCTACGTTACTAATTTTCCCCAAGTAATAACTAAATAACCAATTGTATTAACTTTACAGATTTGTGCAAAATTATGGTGGAACAGGGTGGGAGCACCCTAATTGCAGCGTTACCTCTTAAATGAGCAAACTCAATACTAAGGCAAGAAACCAAACCTCCTCTAATGCATCTTCCAGAAAACCTGGGGTAAGCTTCCGCCTTTTCCTAAGAGGCTGACTGTATTTGCGCTTCACCTGTTCTCTTTTTCGTTGAAGACTTGAACTAGCTCGAATATTTTCTCCTTCAGCCTTTTCTCTTTCTTCCTTCACTTTCTCGGGATCATTTTCATCAATCCATGTTTGCATCTTGATTGTTTTCTTGTTTTGAGAATCAACAAGAGCAGTTAATAAGCGATGGGATCGTGAGGACAGTGAAGAAGGCATAAACCTCATCTTCTGTAGAAGCCTTCCTTGTGATTGCATAAGCCCCTTTCCATTCCTCAGAAACAGGTTGGAATTATCATGATTTGAGTCATTTACAGATATATCAAGAACTTCATTGCCAATCAGCAGTTGTATGCTTCCATCTTTCCACTTTACAAAACGTGCATTGCTTTCACGAGATTCGGTGCCATCAGCGTTCTTAACGATTTTCCAGCGGACAATATTATCCTCCAAGCGTATCTTTTTCCTGCTCCCAGATTCATCTGTCAAAGCATCCTCCTCCACATATGTTTCAGGATCAAAAGGTTTTGGATTAACCCCCATAATATTTGAAACCTTGATCACATTCATTCTGTCAGGTTGACCAGGTGGCAGCATACGTGGAACCACCAAATTCAGCGGAGGACCAAGTGGCTTATCTTTCAGTTCATGTTCAATATTTTCATCCGGTTCATAATGCTTATCTTCATCAACCATGTCCTCTGGAAGTAATTCCTCATAGGGGCCTTCATCATTCATAAGTGATTCATGGGCATGTTTATTGTCATCTCGAGAACCATATGGAGCAAGCCCATCCTCATCGTTATCATCAAAAGCATCATGGAGAACTTCATGGTCTTCTTCGTTCTCTGTTGACCTTGTTTCGCTGGTTATTGTTCTCTTGACATGACCTCCCTCTGCAGTATTCACGCCTTTCATGTGAACTTGTGTACTCTGATTGCCAAGTTCCACATCATGAGAGTCACCCTCAATTTCCTGGGCCATGCCACTTGACCCTTGGCTTTCACCTTGCCCTTCCTCCCATTGGTCGCCGCCGTGGCCGTTGTCCTCCAACCCGTACTCCTCGACCACCTCCGCCGCAGGGGACGCGAGGCGGCGGTCCTGCAGCTGGCCCCCATCCCCGCCGCCGCCGCCGCTACCGCGATCACCGCCACTCGTCGCATCGTCGCCGTCGTGCGCCAGGTACTCCTCCGGGTCCTCCTCCTCCTCCTCCTCCACCACCACCTCCTCGCCGGACTCGTCGCCGAAGATCTTCTGCATAATCTGGTTCCGCTCCTCCT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.949407
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0235500.2 3 31226951 T G
Osa03LNT0235500.2 3 31226801 A G
Osa03LNT0235500.2 3 31227021 C T
Osa03LNT0235500.2 3 31228715 T A
Osa03LNT0235500.2 3 31229539 G C
Osa03LNT0235500.2 3 31229574 G T
Osa03LNT0235500.2 3 31229668 T C
Osa03LNT0235500.2 3 31231250 A C
Osa03LNT0235500.2 3 31231274 G C
Osa03LNT0235500.2 3 31231605 A G
Osa03LNT0235500.2 3 31227024 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
Osa03LNT0235500.2 osa-miR5804 Cleavage 5.0 11.882 1 21
Osa03LNT0235500.2 osa-miR5816 Translation 4.5 8.104 1 24
Osa03LNT0235500.2 osa-miR5819 Translation 3.5 15.485 1 21
Osa03LNT0235500.2 osa-miR6246 Translation 5.0 16.06 1 23
Osa03LNT0235500.2 osa-miR166g-5p Translation 4.5 17.918 1 21
Osa03LNT0235500.2 osa-miR1849 Translation 3.5 10.019 1 21
Osa03LNT0235500.2 osa-miR1877 Cleavage 4.5 20.165 1 24
Osa03LNT0235500.2 osa-miR2098-3p Translation 5.0 11.297 1 20
Osa03LNT0235500.2 osa-miR2099-3p Cleavage 4.0 12.217 1 20
Osa03LNT0235500.2 osa-miR5340 Cleavage 4.5 13.907 1 23
Osa03LNT0235500.2 osa-miR5497 Cleavage 4.5 16.795 1 21
Osa03LNT0235500.2 osa-miR5508 Cleavage 4.5 15.458 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0235500.2 3 nan Resistance or Tolerance Drought tolerance C136 R1618
Osa03LNT0235500.2 3 nan Morphological trait Shoot/Seedling RZ403 RZ630
Osa03LNT0235500.2 3 QFll3 Morphological trait Culm/leaf G249 RG418
Osa03LNT0235500.2 3 nan Resistance or Tolerance Drought tolerance C136 R1618
Osa03LNT0235500.2 3 nan Morphological trait Panicle/flower G249 RG418
Osa03LNT0235500.2 3 qSBR-3 Resistance or Tolerance Sheath blight resistance G249 G164
Osa03LNT0235500.2 3 qPES-3 Morphological trait Panicle/flower G249 G164
Osa03LNT0235500.2 3 QSn3 Morphological trait Culm/leaf G249 RG418
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