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

>Osa04LNT0255300.2

GAGTAATTTCCGCGCTCAACTACTCCCTTTCTCTGCAACAAGTTATAAGCTTATCATTCTTACATGGCAACAAGCCAACAGCAAAATCGCTGAGGATGAATACCAATGTCATACAAAAAATTGTGTTGGAATTGACAGCAAGTGAGACCAATCGAATGGAGAATATATCCACATCTACAAAATTGTTACTCTAAAGTGAAAGCCCTTCTGGGTTGTGTGCTTCAATGTCAACATGTTTAATCCCAGGCACAATCTTTTGGATCTCTGACTCCAGCCGATCCACTTCATACCCAAGAGCTTCGACTACATCCTCACCGTAGTTAGACATGACCCTTATTAACTCCGTATCATCCTTGGACAATGAAGCCTCCCGGAACTGTTTTGCCCATTCTCCACGTCCAGTCCTTTCCAAATAATTCTGCACCAGGACTACTCCATTGAAATCAATTTCAGCTTTGAATCTAAAGAATCCTGGTCCAATCACCTCACTTTTGCAATCATAAAGAGCATCTACAACCGGATCAGCCTTCAGAAACTCAAGAACACGCTGCATGTCATGATCATCAATAGCCCTTCCAATTAAAGCATGCCTGTTTCTCTGGATTAGAAAAATAGCAACCATTCCCAGTAAGTTGCCAACAATGATGGAGCCAATTGGATCATACATAGCATTGCCTGTGGTTTGAACAGCCACCAAAGATGCTCCAGCAATTGCAAGACCTGTAACAGCAGCACCATCTTCAGTCATGACAGCAACTGAAGTTGGATCATGACCACGCCAGATGTAGTCCCTGATACTCATTCCTTCTGCTGCTGCACCCTTCCTAACAGCCTTTATAGCAACCAGCAGTGAAGCACCTTCAATTAGGAAGGACCCACCAATCACTAATGCAGCATAGTGGATGTTCTCAGGGGGTTGCGAATTCCATAAGTTTTGAACTCCATGCACAATGGTAGCACCTGAACCCAAACAAAATATTCCAACTGCAGATATCAAGGACCATACAAATCTTTCTTTTGAATAACCATAGCTGCAGAAAGAGAAATTAAGACATGGGGCAGGCAGCATGTCAGTTTATGGCATATCACAAATAGCCTTACCACTGATTCTATTGTGAGTAGCATTTAGTGGTATACTGGCATGACAATGAATAACAGGATTCCCTGTTTATCTTCAATTCAAGACAATTTTACTCTGGTGAAAATAACTGATTTTCCATGCAGAAATGGGACTAAATTTATGGTACAGAGAAAATAACAGTAATGAAAGAAAGTGATATTTATATGTCAACAAAGCAGCATTTCCAAATTGACAATCGATACATACGGGTGTAGAGCATCTGGAGCACGTCTTGAGCTGCTCAAGCCATATGCAAGAAGAGCCTGGTTAGCGAAGTCTGCAACTGAGTGCACTAGCTCAGCTAGCATAACATGACTAGATGTTGAAAGCCATACACCAAACTTCAACGAAAAGACAAGAAAATTACACCACAGTGCTGTGTTAACCGCTCGATGGCTGTGCTCATCGTCAAAGTGCGCCTTCTTCTTCGCCTTGGCGACACGAAGAGAATAACTGCGGGAGAGGGTGAGCCGTACGGGAGGCGCGTCGGCGACGGGGCCGCGCGGCGGCGACGGGGCCGGGGGGAGGGCCCGCGCCCGCGCCCGCCACCGGCTTAGCCCTAGGACCCCCGAGGCGAGGAGCGGGCGGGGCGAGAAGGGAGGAGGGGGCGACGGGTGGTCGTGGTCGTGGTGGTCGCCGCTGCGGCGGGAGAGGAGGAGGAGGTGGTGGAGAGGGTAGGGCGAGGAGGGGAGGCGGGGGAGGGAGGAGGAGGATGAGGAGGAGGAGCTAGACGAGGAGAGGAGGCGGAGGCGGAGGGCCGCGGCGGCGGCGAATGGGCGGCGCATTTAGGGGTAGGGGTGACGGCGGCGGCGGCGAGGCTGCTGCTGCGGCGGCCGCGGGCGGGGCGCGGCTTCCATGCGAGGGAAGCGATAGAAAAAGGAAGCGGGGGGAGTTTGGGCTTGGTTGGGGCGTGGAGAGTGGAGAC

Coding Potentia
Explanation CPC Score
noncoding -1.28993
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0255300.2 4 13178222 G A
Osa04LNT0255300.2 4 13177181 G C
Osa04LNT0255300.2 4 13177372 A G
Osa04LNT0255300.2 4 13177679 A G
Osa04LNT0255300.2 4 13178063 A G
Osa04LNT0255300.2 4 13178089 A G
Osa04LNT0255300.2 4 13178519 G A
Osa04LNT0255300.2 4 13178561 A G
Osa04LNT0255300.2 4 13179056 A G
Osa04LNT0255300.2 4 13179522 G T
Osa04LNT0255300.2 4 13179805 T C
Osa04LNT0255300.2 4 13181836 T C
Osa04LNT0255300.2 4 13181886 A G
Osa04LNT0255300.2 4 13181937 T G
Osa04LNT0255300.2 4 13182282 A G
Osa04LNT0255300.2 4 13182293 T C
Osa04LNT0255300.2 4 13181557 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
Osa04LNT0255300.2 osa-miR5537 Cleavage 5.0 12.088 1 22
Osa04LNT0255300.2 osa-miR156c-3p Cleavage 5.0 21.997 1 22
Osa04LNT0255300.2 osa-miR156g-3p Cleavage 5.0 21.997 1 22
Osa04LNT0255300.2 osa-miR168b Translation 4.5 18.614 1 21
Osa04LNT0255300.2 osa-miR169p Translation 4.5 12.356 1 22
Osa04LNT0255300.2 osa-miR172a Translation 5.0 22.63 1 21
Osa04LNT0255300.2 osa-miR172d-3p Translation 5.0 22.63 1 21
Osa04LNT0255300.2 osa-miR414 Cleavage 4.5 4.144 1 21
Osa04LNT0255300.2 osa-miR2093-5p Cleavage 5.0 14.985 1 20
Osa04LNT0255300.2 osa-miR2878-3p Translation 4.0 10.671 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0255300.2 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0255300.2 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0255300.2 4 spp4-2 Morphological trait Panicle/flower RG449 CDO456
Osa04LNT0255300.2 4 nan Morphological trait Panicle/flower RG788 RZ69
Osa04LNT0255300.2 4 qPEN-4 Morphological trait Panicle/flower RG190 RG908
Osa04LNT0255300.2 4 An8-glum Morphological trait Panicle/flower nan nan
Osa04LNT0255300.2 4 nan Morphological trait Root RZ69 RG449
Osa04LNT0255300.2 4 nan Morphological trait Root RZ69 RG449
Osa04LNT0255300.2 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0255300.2 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