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

>Osa01LNT0004300.1

GACATCGAAGATCTTTATAAATTCTTACATTGAGCGTACTCCAAAATAACTTCGCAAAGTAGCTGAACCAAAACAAAACATTTCGATGTCTCTCCTCTCTCGACCATGATAAATTCAAATGCAACCAATTACACAATTCGAAATTTAAGAAACACGAATCAAAGATCCTGAACCATTACACCCGAGTACCCGATGGCCGGAAAAGCAGATCGCATTGTATAATTGTATTAGCACACTTGATTATTTTGCACCATTGGCGACGGCAGGAGAAGGCAGCAAGAACTTGAGCAGGATATCGTTGAACATCTTGGGATCCTCCTGGTGCGCCAGGTGCCCCGTGTTCGGTATTATCTTCACCGTCGCCTTCTCCCCAAGCATCTCTTTCACTTTGTGTGCTTTCTCCACAGGGAAAATCTGGTCGAACTCCCCCCAGATGATCAAAATTTCTTGAGGGAGAGGAGAATTAAGCTGCGAGTCTTGTTCCTCGGTGACGATCTCTTTGATCAGCCGGATCTTCTCCTCTCTTTTGTCCGCGAAATATTTCTGCACCACACGCAGTTTGCAAATTTGCAAATCAAAATTTAACGAAAAAGTTATCTCTCGTTTCTTAATTTCTATCTGCATCCAATCTTCTCGGTGATATCATACAGTTGAAACACAATTTCTGCAAATCCGATCGAATTGAAAGAGTCAGGGCATGAATGCAAGATGCTGACGTCACGCTCACGCCATGGAGACGAGTCCTAACCTTTTTCGTGTGTAAATGCAACTATTTATATTTGGCGGGAAAAGTGCGATATGCCGGTGGGTGATATGATTTGCCACCAAATTTGTCGGTAGAAAAGATTTTAATTGGACGATGTTTGTATGATTAGTCATCTACTACTAGTCTACTAGCTTTTGGGACAACTCGCCAACAAATCCAAAAATTCCTAGCTTAGCTAAGAGTCCACTACACTATCATGGCATCCACTGCAGAATACGTAATGAGAACGGTTTAATCATTCGGTGGACGTCTACCCATTCAACTAAATAATTATGAAAAAAATTAAAAAGAATGATAAGATAGATACACCACTCTCAAATTTAAATTCAACTTCTATAAATTATAATAGAAAATAATAAATTTGTTATTAAGTTGTAGTTATATACAGAAAACAAATATAAACCTTCATGCCTGTGAGATGATATATCTCATATTAATTTATCTCATTATCTTTTAAAATTTTTATAAATATATTTAGTCGACATGCAATGAACGGGTGAACATTCACCCGGGTTATTAAAAGAGTTTTCGTATACGTATACGGTGAGGTACGTATACGTATGTATGTACGTAGGTACCCGGAGGAGGTCGCGGACGAGGAAGTCGGGGATGTACTTGGGCGGGCGGTGGACGCAGAGCGCCATCAGCCGCCGGAACGCCTTCCCGTCCGCCGGCGCCATCAGCTCCGTCACCTCCGCCACGCCGCCCTTCGCCGCCAGCGCCGCGTCGTCCTCCGCCCCCTTCGCCAGGTCGGCGTCGCACAGCACCACCTTCCCCACCTCCACCTGGCCGTCGCCGGCCGACGTCGACAGCGCCCGCGCCAGGTGCCGCGCCACCAGCCCGCCGTAGCTGGTGCCCACGATGTGCAGTTCCCGGCGTTCGCCGCCGAGGCCTGGGAGGTGCGCGCCGCCGCTGGTGAGGAGCGCGGCGATGGCGGCTGCCTGGAACGCGTCGGAGCGCGGCGCGGCGCTGGTGGTGGAGGCGCCGAAGAAGAGGAGGGTCGGGACCACCAGGTCGAAGTGGCGGGAGAGCGGGCCCACCTGCGCGCCCCACTGCCACGTCGGGTCCGGCCCGAAGCCATGGACGAGCACCACCACCGGCCGCCGCCCCGCCGCCGCGGCGGCGGCGGCGGCGCCATTCTTGGAAGGGAGGATCAGGAGAGAGGAGTGCGCCCAGAAGTGGAGCGTCGTGCCGTCGTCGTCGACGACGGCGGAGCCTGGCCGGAGGCCGGCGGAGGCGAACATCCGCCGGAACATGGCGCTGATGAGAGACACGGCGAACCCCATGGCCGCCGCTCTCTCTCGAGAGCTCTGAGCTGTGTCTGTGACTGAACGATCAGTTTGGCTCC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.258716
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0004300.1 1 3517821 T C
Osa01LNT0004300.1 1 3517927 A T
Osa01LNT0004300.1 1 3518057 T C
Osa01LNT0004300.1 1 3518147 A G
Osa01LNT0004300.1 1 3518140 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
Osa01LNT0004300.1 osa-miR416 Cleavage 4.5 18.81 1 21
Osa01LNT0004300.1 osa-miR535-3p Cleavage 4.5 17.455 1 21
Osa01LNT0004300.1 osa-miR1428a-5p Cleavage 4.5 14.231 1 21
Osa01LNT0004300.1 osa-miR1428b Translation 3.5 10.563 1 21
Osa01LNT0004300.1 osa-miR1428c Translation 3.5 10.563 1 21
Osa01LNT0004300.1 osa-miR1428d Translation 3.5 10.563 1 21
Osa01LNT0004300.1 osa-miR1428e-3p Translation 3.5 10.563 1 21
Osa01LNT0004300.1 osa-miR2099-5p Cleavage 4.0 7.671 1 22
Osa01LNT0004300.1 osa-miR2925 Translation 4.5 19.013 1 19
Osa01LNT0004300.1 osa-miR2927 Cleavage 3.5 18.749 1 23
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0004300.1 1 qFLL-1 Morphological trait Culm/leaf RZ543 RG532
Osa01LNT0004300.1 1 qFLP-1 Morphological trait Culm/leaf RZ543 RG532
Osa01LNT0004300.1 1 nan Morphological trait Root RM7383 RM243
Osa01LNT0004300.1 1 nan Morphological trait Root RM7383 RM23
Osa01LNT0004300.1 1 gp1a Morphological trait Panicle/flower RM1 R753
Osa01LNT0004300.1 1 nan Physiological trait Source activity RG532 RG472
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