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

>Osa04LNT0260400.1

TATACTTGCAACCCAGTGACAAGCGCCTCAACTGGACTGCTGGACCTGTTGGAGATCTGAAAGCTTGGTAGTGAGCAGCTTCCCTCTCCTTGGACGATCCCTCATACATATATTGGCGAAGAACTGGTGGCAAGAATGCTGAACTGCACATCAGGTAAGTCACAAGGTTGTAAGTAACATTAGATGAATGAAGATGTACATTTTTCATGTTTTTGGACAGATATGCTTAGATTCTGCCTTTTACGGATACATCCATGCTATTTTGCAAGCCATGTAACTGATTTATAATTAATGCAGCCTCTCCGGTGGTTCCATGACGATCATCGCATTACTCGTTATCATCATCAGCCAGGTCGAACTGCTTGAGCAGCGCGCCGCAGATGGGCAGTGGGATGTCCTTGAGGTAGCCGAGTGGGTTGGCTAAGCGCAGGTTGTCACAGATGCCGACATTCCTGGTGAGCAAAACACGGGCACGATCCCTTTCGGCCTCGATTTCAGAGCAGTTTGCAAGGGGGCTGTGGACGAGGACAACCTCGCAGATGTCCTCCTCATGGCTGTCCTTGAGCTCAATCTTGTATGTCCCGGTCTCATCAGTCACACCGTCAATCGCACGCTCGACCTTGTCGGTGCCAAAGTGCTTGCACTCCAGCCTGACCTTGGCACCCTTGATATACTCGGTGACATTGGTCTCGAACCCGGCGCGGCACGTGTCACAGTAGACACGGCCTTGGACGACGTAGTCCGGTGCGTCGGTGGCAGTGGCAGTGCTGGCAAGGACATAGAAGAGGATGCCGAAGATCACCGGAATGGTGCGGAGAGAGGCCATGGATGATGTGGCT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.874324
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0260400.1 4 19693621 C A
Osa04LNT0260400.1 4 19693931 C G
Osa04LNT0260400.1 4 19693113 T A
Osa04LNT0260400.1 4 19694235 C 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
Osa04LNT0260400.1 osa-miR394 Translation 5.0 15.686 1 20
Osa04LNT0260400.1 osa-miR169r-3p Translation 4.5 22.817 1 21
Osa04LNT0260400.1 osa-miR444d.3 Translation 5.0 14.727 1 21
Osa04LNT0260400.1 osa-miR2275d Translation 4.5 14.334 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0260400.1 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0260400.1 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0260400.1 4 nan Morphological trait Panicle/flower RG788 RZ69
Osa04LNT0260400.1 4 qNOT4-2 Resistance or Tolerance Drought tolerance RG449 RG788
Osa04LNT0260400.1 4 qFRP4-1 Physiological trait Source activity RG449 RG788
Osa04LNT0260400.1 4 An8-glum Morphological trait Panicle/flower nan nan
Osa04LNT0260400.1 4 nan Morphological trait Root RG449 RG788
Osa04LNT0260400.1 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
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