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

>Osa04LNT0256500.1

GCACAGTTGAAATTCAGCGTCACTAAACCAATTTTGCCACAGAACAAGATACTACATACAGTACCACATGGTGACAAGAATTGAACACAATTCCTTCAGCTTAGTCAAGACGTCCATAAGAGGATTGTGCATAGGTGAGTTCTAGGCAAAAGGAACTGAATCTGAGATATATACAGGAATCTATATGCAGGGCACATATTTCATAACTTGGATTAGTCGGTCACACCATCCAGAACGGCTCTTGCGGTTTTAGGCAAAATGGAACTGAAATATGAACAGGCAGAATAGCTCCAAGATGGCATCTATATAGACAGACACTGCACAGATTTCGCCATCCAGAACTCAGCTCTTTCTTGGTCCGTAAAATACTGATTACGACCATGTTAAGTAGAGGATCATCTTCATTAATTTGATGGACACCTCCAGATGAACAAAGAAAAGATATATACTGATTCAGAGCGATGCAACCTTGTAGGCTGTTCATCGGGTGGAACGAGTCCACGATTTATAGGCTTGTGTGTTGCAATTTGCAACTGAAGGACTGAGGCTTTTCTGCAAAGAGGTTATGTGCTGTGGCTGACGGGAGCTGCCCTGTGTACACCGTGCTAACTTTTTCGGGCTCAAGGTGGCAATTTTCCCAGCCGCTTACGCGCACGAGAAGTGAGCCGGTGGTTTCGGTGGAAATGCATCCGATTTCATTTAGCACGGTATTGTATTTCTCTTGGATGACGAAAGAATGGCTGCTTGCAGCTTTGTGAACATCCTGGAATGGCTGTCCAAGACTTCCTTCATCACTTCGGTCTTCTAGCATGTCGGGGGATGCATCGGGGTTGTAGTCTTGCTCCTCAGCAATGAACTCCCATTTTTCATCCTTAAGAGATTGCCGTACAACATCACCATGATCATACACAATCTCGTGTGTTTCTGAAGAAGCATCAAATGACTTAACCAATCCATTGTAGAACATTTCATCAGCAGGCCACCGTACTTTGATTCTCGAGCCGACAATGCTACCGTCAAGAGCTTTTTTATTTGAATTAGGAGCCTCTTTAGTTCCCTGTACAATTTCCGGTTTCAACTCATCCCCACTATCTGCTGGTTGTCCTATAGTTTTACCCATCATGGTCGAAGATTTAGGAGACACTACTTCCTTCATGTCATGCATAAAAGCACCAACATTGTTATCTCCAGCAACTATAGCATCTTGGAGAAATGATGTAACAAGATTGCTATACTCGGTTATGGGAGCACCCTGAAGTAGTTTGATGAACACTGGCTTTAACTTTTCATGGCAGAGTCCTATTACCCTCTCTGCAAGTACAAAAGATGCTGGAGGAGTTTCTTTTTCTTCCTTTTTAACATTCTGAAGCAGGCAGGATGCCAGATCTTTAATTAGATCTTGTTCCATATCAGTAATATCTTCGATCACAAACTTCATTATGGTTTCCATATAGGATATAACATGCTCCTGATGAGTATTGGATACGGTGCGGAAGAAATGGTGAAACATATCCCGTATCAGATCATTGCAGTCAAGATCTAACAACAAGGCACAACCCCGTATCCTTGCAAAAGTTCCAAGCATTGAAACCCTTGTTCCATAGGAGGGGCAGTCCACATCATCCAGTTCACAGAAGACCCCAACAACAAGCTTGAGAACATCCTTCATCACATCATCATCATAAGGGGGATCCGGCGCGCGGATCTTGATCAGCGTGGTTAAACACGACGCTACGGCGAGCTTCACTCCGGGGTCAGTGTGATCCAGTAGCTCTTTCTTAATCAATGCTCTCATAACAGGGATAAGAGCACTGTGAATTCTGTCTACCTCACACTGATTCACTCTGTACAACAATTTGGCTGCTTCCTGGAGCAACCTGAGCAGCTCGCCGTCGTCCGGAAGCGAGCTCAGGCGGGCGCCGACGTCGCGCAGCCGCCGCCGCACCTCCACCTCCGCGGCGTCCCGCTCCATTCGGCGGCGACACAGTCGGAGAGAAGCAGTAGCACTGTTTGAGTGAAGGGGACTGTGGTTGTAGCCGGTGCAGCGGAGAGACTGACAAC

Coding Potentia
Explanation CPC Score
noncoding -1.24751
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0256500.1 4 14698819 G A
Osa04LNT0256500.1 4 14699051 G A
Osa04LNT0256500.1 4 14699424 T C
Osa04LNT0256500.1 4 14700425 C T
Osa04LNT0256500.1 4 14701687 G A
Osa04LNT0256500.1 4 14702258 T C
Osa04LNT0256500.1 4 14702390 G A
Osa04LNT0256500.1 4 14701068 C G
Osa04LNT0256500.1 4 14701369 G A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0256500.1 osa-miR5823 Translation 4.5 17.516 1 24
Osa04LNT0256500.1 osa-miR5179 Cleavage 4.5 17.261 1 21
Osa04LNT0256500.1 osa-miR5083 Translation 4.5 13.096 1 20
Osa04LNT0256500.1 osa-miR5150-5p Translation 3.5 22.451 1 24
Osa04LNT0256500.1 osa-miR5518 Cleavage 5.0 21.619 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0256500.1 4 An8-glum Morphological trait Panicle/flower nan nan
Osa04LNT0256500.1 4 nan Morphological trait Root RZ69 RG449
Osa04LNT0256500.1 4 nan Morphological trait Root RZ69 RG449
Osa04LNT0256500.1 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0256500.1 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0256500.1 4 nan Morphological trait Panicle/flower RG788 RZ69
Osa04LNT0256500.1 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0256500.1 4 spp4-2 Morphological trait Panicle/flower RG449 CDO456
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