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

>Osa04LNT0255100.1

AAAAATAGGCTCAGTGATTAGTTGATCAGACAAACAAAATTTTTGTTTACTTGATTCCCTACAGATTAATAATCCACTAAAGTGTCAGGAAACAAATGTATGATACACGAGGATGCATTAGCTCTCTAATCCTTTAATCTTGGCAAAGCAGCTCTCCATGGTCTCCACAAACTTGGGCGTGATACGATCACCAGCAGCCAGTTTGTAATACTCGAACTTAGCTTCTTCACACTCCAACGCAGCCTTCTTGCAGGCCCTGATACTTCCACTCATATCCCGCAGGTTGAATGAAACTGGGATTTTCCCAATGTTCCTCACCATGGTGATAGCAGCCCACACTTTCTGGTGATCTTCACGGGAAACTCGGATCACGCAAAGCTTCGTTATCGGATTTACATACTTCACTTGCAACGACCCAAGACAAGCTGCTAGGCCACACTCCCCAAAGTTGAGCTGGATGCTGTCTTTGATAGCTTTGGTGATATTGATCTGCGTGAGAATGAGAGGGTCGGGCTGGCCCTTGACTGGTGTATCGATGAACACCTCCATCACCATGTACCTGTTCTTGAAATGAACCATATCGTCGACGAATGCTCACTGTACAGTAGAACTCCTTCAAGTAATTTTTTTGTTGATTGTGCCTTCGAGACTCGGACGACCGGGCGGCGTCGCTGGCGTGTGGCCGGTGGACTGGAGCCCGGAAGCTTGCCTGCTACTGGAGGGATCGGGGCGCCGGGGCG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.982449
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0255100.1 4 12956035 A T
Osa04LNT0255100.1 4 12956306 G A
Osa04LNT0255100.1 4 12956403 T C
Osa04LNT0255100.1 4 12956954 T C
Osa04LNT0255100.1 4 12958062 T C
Osa04LNT0255100.1 4 12958569 T C
Osa04LNT0255100.1 4 12956148 C T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0255100.1 osa-miR171d-5p Cleavage 4.5 22.701 1 21
Osa04LNT0255100.1 osa-miR171e-5p Cleavage 5.0 22.701 1 21
Osa04LNT0255100.1 osa-miR413 Translation 4.0 14.996 1 21
Osa04LNT0255100.1 osa-miR416 Translation 4.0 20.678 1 21
Osa04LNT0255100.1 osa-miR1866-5p Cleavage 4.5 19.74 1 24
Osa04LNT0255100.1 osa-miR2094-3p Translation 4.5 12.119 1 22
Osa04LNT0255100.1 osa-miR2867-3p Cleavage 5.0 17.948 1 20
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0255100.1 4 An8-glum Morphological trait Panicle/flower nan nan
Osa04LNT0255100.1 4 nan Morphological trait Root RZ69 RG449
Osa04LNT0255100.1 4 nan Morphological trait Root RZ69 RG449
Osa04LNT0255100.1 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0255100.1 4 qSNP-4a Morphological trait Panicle/flower RM401 RM335
Osa04LNT0255100.1 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0255100.1 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0255100.1 4 spp4-2 Morphological trait Panicle/flower RG449 CDO456
Osa04LNT0255100.1 4 nan Morphological trait Panicle/flower RG788 RZ69
Osa04LNT0255100.1 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