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

>Osa04LNT0287100.3

AGGACAGGGAATACTCTATTATGATATAATTCTCACAAAATTAATATGCTTTGCACGACTGATCATTGTTTTACATGGCATTGATCCACAGGTAAAGTATGTATGAAGAAAAGAAGCTATGTATCAACAGCTCATTCATGTTTCTGTGCCCACTGAGATCACCACCTCACCGTCAGTCCCATGATCCCATCCATCTAGATCATGGCGTCCAAGCAAGGTAGACCGCAGACATCTCTCTTCAAAACTGATGCCCCGCACATTCCTGGCGGCTACACACTGAGGAGAACATCACCCTCGTCGACCATGTTCATATGCAAAGAGCTCCTAGATCTGGTGCAACTTTAGAATCGTGATCCCGGATGGCTGGTGTTTCATCTTGTTCTTTCTTCTTTTGCTTCTTCCCCTTCTGGCCTTTCCCTTGGCCACCTTTGGTCCTGATAGTAAAGCACATTAAGCAGATAGTATTAGTACATAACACTTCCAGCATTGTGTTAAACATGCAATGCAACTAACCTCCCTAGTGAAAAAGGAAATAGTAATCAGGTCGGTGACTTTAAGGCATATGGGATAAGTGCATATTTTGCAGCAATACTGTTAAGGTTTCATAGGCCAGATACAACAGCAGCAATGCACTATGCAAATACGCTGGAAATATTGATTTCACCCCCCAAAAATTCCATTTGAAAGAATGCTTACAATGCGAACAGCAGGACATAAGTTCAGTTGTAGAATAGAATATGGTAAAAGACAAACAAAAGGACAGAAACATTATAAAGGGGATTAGCTATATTTAAGACACCACATTTTCCACCAAAAAACAAAAAAAAATTAAAACCAAATCTCAATACTTACACCATATTTTTTGCAGCACACACTATATAAGAGAATTAGGATGAAAACAATTAATTACCTACTTGAAAGAGGAGATAGTAGAGCGAAACATACTTACATAGGAGTATAAAAGAATGGTAGCAATCCGAATGGGAAAAAAATGACTGAAATCAAGTCAAAAATGTGGCGCCATATTTTTAGCAAAACCATTATAAAGCCATACTTTGGAGGTTCTCTCGATGGTGCAGTTGTTTTTGGAGGTTCTCTCGATGCTACAGTTGTGGCTAAATTACAAGAAGGCTTGTGCTTCCTAGCAGATCCACAAGAGCATTCCTTGGTTTTTGACTTTCCCTTTTTAGAATGTGAACTGTTGTGTTTCTGAGCTGTTTCGCCTTTGCTAGAACAGTCCTTTTCTTCTTTCTTGTGTTCATCCAGTTGACTCTCATCCTGCTTCATGCTAAGCTCATCCTCTATGGTCTGTACATACTCATCACATGCATAGTCCAGATAAGGATCTCCATCCGCATCATCAGAACCCAGTATTAGTTGCTCAGCTAACATGTACTCTATAGCAGCATCAATGTCACCATCCATGTCTTTCAAAACCTGTTCAACTGCAGCGATATTAGAACATCCAGTTCCAGCCATCACCAATTTAACCGATATATGATCATACTTTGATCTGTCTGAAGATTTCTTCAGGTCCTTTGCTTTTGTTTGAGCATTATTGCTTGTGCTAGCTACATTGGCATCTGCCTTGATAATAACTGGCATTGCAGGACCTTGACATGGATCTTCCCTCAGTCTGACACTATTGTAGTGCTCACCCTGATGATACGATAAATGAATCATACTGGTAGCTTCACGATCAGAAAAGTTTCTTATGTACCATCGTGGTGAGTTAAGCATGTGGATGCATATGTTTTTTCTCTTGAGAATAGAAGCTGCTTGCAACTCCATATGACCAGCCCAAGTCCCATCCTCAAGCATAGAGTCACAATATTTCTCAAACGGTTCCTCGTCCTCAATGAATGGCTCAAAATCCACACGGTGCTCCTTAATGTATTGCACAATCATTGCACGGTACTTCATGTGCTCTTCCTCGTTGCCTTCGAGCTAAAGAAGCAGTTGCCATCCGCACTAACTTCGATAATCTTCAACCCCAGCGAGTCCAGCTGCGCCCGGAACTCCGTCATGTCGGCCTTCTTCGCGAACTTCTTCTCCTCTGCATCACGCTTCGGCTTCCGGGCTTTGGGCGCCGCCACGGCTACCTTCTTCTTGTTCCGAGCCATTACGACACGTGCGGTAGTAGTGGAGTCTCGCCTAGATTTCCCCGCGGCGGCGGCGGCGGCGAGGGGGAGGGGAGGCGGAATCGCAGATAGTATCAAATCGTACTCT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.950835
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0287100.3 osa-miR159c Translation 5.0 19.541 1 21
Osa04LNT0287100.3 osa-miR159d Translation 5.0 19.541 1 21
Osa04LNT0287100.3 osa-miR159f Translation 5.0 19.541 1 21
Osa04LNT0287100.3 osa-miR167h-5p Cleavage 2.5 14.867 1 21
Osa04LNT0287100.3 osa-miR167i-5p Cleavage 2.5 14.867 1 21
Osa04LNT0287100.3 osa-miR171c-5p Translation 4.5 11.386 1 21
Osa04LNT0287100.3 osa-miR415 Cleavage 5.0 14.369 1 21
Osa04LNT0287100.3 osa-miR535-5p Translation 4.0 13.412 1 21
Osa04LNT0287100.3 osa-miR1857-3p Translation 4.5 22.802 1 21
Osa04LNT0287100.3 osa-miR2919 Cleavage 3.5 11.959 1 19
Osa04LNT0287100.3 osa-miR2926 Translation 4.0 14.173 1 20
Osa04LNT0287100.3 osa-miR167a-5p Cleavage 2.5 14.867 1 21
Osa04LNT0287100.3 osa-miR167b Cleavage 2.5 14.867 1 21
Osa04LNT0287100.3 osa-miR167c-5p Cleavage 2.5 14.867 1 21
Osa04LNT0287100.3 osa-miR167d-5p Cleavage 2.5 14.867 1 21
Osa04LNT0287100.3 osa-miR167e-5p Cleavage 2.5 14.867 1 21
Osa04LNT0287100.3 osa-miR167f Cleavage 2.5 14.867 1 21
Osa04LNT0287100.3 osa-miR167j Cleavage 2.5 14.867 1 21
Osa04LNT0287100.3 osa-miR167g Cleavage 2.5 14.867 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0287100.3 4 np4 Morphological trait Panicle/flower RG143 RG214
Osa04LNT0287100.3 4 tgwt4 Morphological trait Seed RG143 RG214
Osa04LNT0287100.3 4 np4 Morphological trait Seed RG143 RG214
Osa04LNT0287100.3 4 tgwt4 Morphological trait Seed RG143 RG214
Osa04LNT0287100.3 4 nan Morphological trait Panicle/flower RG143 RG214
Osa04LNT0287100.3 4 nan Physiological trait Source activity RG143 RG329
Osa04LNT0287100.3 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0287100.3 4 nan Morphological trait Panicle/flower RG620 RG214
Osa04LNT0287100.3 4 QGn4 Morphological trait Panicle/flower RG143 RG214
Osa04LNT0287100.3 4 QGwp4 Physiological trait Source activity RG143 RG214
Osa04LNT0287100.3 4 rpf4.1 Resistance or Tolerance Drought tolerance RG214 RG620
Osa04LNT0287100.3 4 gpps4.1 Resistance or Tolerance Drought tolerance RG214 RG620
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