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

>Osa04LNT0251300.1

CCGGCACCTATAGTGCCGGCATCTATTTGATGTTTTGTAGTAGCGCTCGTCGAATCTGATTTGTATCCCTCAATAGAAAAATTAGGTGTAACCGTGTAAGGGCTCCTCCAACTATTAAAACCATGCAAAATAGCTTCCTCGGTAGTGTTAACGGTGGTTCTTGCTCACGTGGCAGTCCAGTCTCCTCCAACTATTAAAACCGAGCAAAACGGCTCCCTCGGTTGTATTGTTAGTGGTTTTTACTGACGTAGCGTCCACGTGGCAGTCCAAACATCAAGAAATTAAAAAGAATGTAGGCTCCGCCTATAAATGACAAGAGAAAATAAAAATAAACAACACTTGCCTATCCGCTCGTGCCGCCGGCTTCTGGCGAGTATGCTTAGCCGCCCATTCGGGTGCACGACGGTGTCCGTCGGCGACCTCCCCAAGCGTTGAGCTTCCACTCCTCCTGCTGCTTCGCCGCTGCCTCCTTTCCCCTTTCCCCCACGCTACACCCGTGATCGAGGATGACGGGGCGGGAATGAGGAGTCAGCTAGCACGGGCAAAAGAGGAGTCGGCTAGCATGGCCCCAACTTTGTCGTCGTCGCCCTCCCAACCTCATGTCGATGCCACCGCCCTCCCAACCTCGTGTAGCCGCCACCTTTGGAGAAGACGAAGCCGCAACGAGTCAGAGAAGCAAAACGGCAGTGGAAAGGTAGCAGCAGCGGTAGAACGGCATTTTGGAAGAGTAGCGACCACTGCCTCATCCTTTTGCGCCTTCCGCTCCCTCCCCGCCTCTGATGGCCTCGCCGTGCCAACCATAGGAGAGAAAGGAGGGAGGCCGCTCCTCGCCGCGGCCTTCCGTGCCCTCCCCACCTCTGATGATCCCGCCACCCAACCATGGGAGAGAGAGGAGGAAGGCC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.874456
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0251300.1 4 7498653 A G
Osa04LNT0251300.1 4 7498851 A G
Osa04LNT0251300.1 4 7498867 A G
Osa04LNT0251300.1 4 7498790 A 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
Osa04LNT0251300.1 osa-miR5803 Translation 4.5 16.703 1 24
Osa04LNT0251300.1 osa-miR444a-5p Cleavage 4.5 18.987 1 21
Osa04LNT0251300.1 osa-miR2097-5p Translation 4.5 19.863 1 22
Osa04LNT0251300.1 osa-miR2919 Cleavage 5.0 21.625 1 19
Osa04LNT0251300.1 osa-miR2930 Cleavage 3.5 20.496 1 22
Osa04LNT0251300.1 osa-miR5504 Cleavage 5.0 17.876 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0251300.1 4 spp4-2 Morphological trait Panicle/flower RG449 CDO456
Osa04LNT0251300.1 4 An8-glum Morphological trait Panicle/flower nan nan
Osa04LNT0251300.1 4 nan Morphological trait Root RM261 RZ69
Osa04LNT0251300.1 4 nan Morphological trait Root RM261 RZ69
Osa04LNT0251300.1 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0251300.1 4 qSNP-4a Morphological trait Panicle/flower RM401 RM335
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