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

>Osa04LNT0255600.1

GGTTGACAGTTGCTTCACATGTATTCATCATAAATTTTGAGGAACAATGAGATCGGAAACTCATGAACTGACTAGTTTCTCTTACAAATGCAGTAAATCTTGGATTACCCATCGATCTAATGCCATATGGTAAATTGAAGATGCACATATATACTACATCAACATAGCTGCTACTTTGATTTCCGTGATTTGAATATGTTTTCCTTGTAGTATTGTAGCTCCTTAATGCTTTCTCTAATGTCATCCATCGCCCTGTGGTTCTTCTCCTTCCTTGGAGCATGTTTCCTTTCTTTGGGGAACCATCGGGAGCACAAAGCCGATATACTGCTTACATCAACTATCACATGAGAGAAAATGGCTGCCAGATGTGGCATGTACTTCTTCAAAAATAGTAAATCCATATAGACAGAATTCCCAGCTATCAGTGGAGTGGCTGAGCCTATATACTTCCTAATAAAATCTAGCACTTGTTTCTCAGCATCATTCTCAGAAATGTCGCTCTGCAGCACCTTTTCCTTCAGCCCGCTAGCGCTGTGATGAACTTTGCACCATTCATTCATGTCATTTACACATTCCTTGCTCTGTCTTATAACCAAGTCAGGACCCTCTATTCGTTTGGTAAGTTTACCGTCTGTTATAATACAAGCAATCTCCAGTATGCGATCTTTGGTGATATCCAAACCAGTCATTTCCAAGTCTATCCACACTAATGGCTTATCATAATCACTTGATGATGAAGCAAGGTTTTCTCCATCGTGGTTTACAATCATTGTGTGATTCAGCCTGATTTTATCAATCTCCGTGCTGCTAGTAACAGCAGCAGCTTCGGCCTTGCTGGATGTTGGTGGTTCCGCACCTTCCTCTCTATCGTCCTCAGCATCCAGATTAAGAACAGAGAACATATTCGCGAGTTTGCTCATCTTTTCCCCCAAGAAAAGAGTGACGGAGCTGTAACCGGAGGCGGAAGCGGGATGGATGGAAATCGGGCAGCGCAGGAGAGCGGAGTCGAGGGCGAGAAGACGCGGCGGCGGAAGCAGCAGGACGACGGCGGCGCCGCTGCTCTTCGCAGTCGGCACGGCAGCAGGTGTGACGGAGTCGAGATCGATCGACTCGTCGTCACGGCTCACGAAGGCCCGCGAACGTGAG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.783554
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0255600.1 4 13611168 G A
Osa04LNT0255600.1 4 13611689 C T
Osa04LNT0255600.1 4 13611942 A T
Osa04LNT0255600.1 4 13612571 G A
Osa04LNT0255600.1 4 13612716 G A
Osa04LNT0255600.1 4 13612835 T C
Osa04LNT0255600.1 4 13613019 T A
Osa04LNT0255600.1 4 13613237 T C
Osa04LNT0255600.1 4 13613312 G A
Osa04LNT0255600.1 4 13613328 T C
Osa04LNT0255600.1 4 13613941 C T
Osa04LNT0255600.1 4 13614273 G A
Osa04LNT0255600.1 4 13614420 A G
Osa04LNT0255600.1 4 13615454 A T
Osa04LNT0255600.1 4 13615732 A G
Osa04LNT0255600.1 4 13616118 G C
Osa04LNT0255600.1 4 13616264 A G
Osa04LNT0255600.1 4 13616343 G C
Osa04LNT0255600.1 4 13616131 T 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
Osa04LNT0255600.1 osa-miR5801 Translation 5.0 15.513 1 24
Osa04LNT0255600.1 osa-miR159c Translation 4.5 14.564 1 21
Osa04LNT0255600.1 osa-miR159d Translation 4.5 14.564 1 21
Osa04LNT0255600.1 osa-miR815a Cleavage 5.0 18.743 1 21
Osa04LNT0255600.1 osa-miR815b Cleavage 5.0 18.743 1 21
Osa04LNT0255600.1 osa-miR815c Cleavage 5.0 18.743 1 21
Osa04LNT0255600.1 osa-miR1868 Translation 3.0 12.013 1 24
Osa04LNT0255600.1 osa-miR1877 Translation 4.5 11.689 1 24
Osa04LNT0255600.1 osa-miR3979-3p Cleavage 4.0 13.988 1 20
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0255600.1 4 An8-glum Morphological trait Panicle/flower nan nan
Osa04LNT0255600.1 4 nan Morphological trait Root RZ69 RG449
Osa04LNT0255600.1 4 nan Morphological trait Root RZ69 RG449
Osa04LNT0255600.1 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0255600.1 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0255600.1 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0255600.1 4 nan Morphological trait Panicle/flower RG788 RZ69
Osa04LNT0255600.1 4 spp4-2 Morphological trait Panicle/flower RG449 CDO456
Osa04LNT0255600.1 4 qPEN-4 Morphological trait Panicle/flower RG190 RG908
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