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

>Osa04LNT0256900.2

GGCAAAAAAGAAAGAGTATTATTGCACGTAAGATGGCATGTTGTTGAACTATTGTCTATCAACGGTATTTTACAATCGTACACTTCAGTTCTAATTCAAAAAATTTCACATACAAAAATTTCTTCAATGGACACAACTCACCCGAATGTGAGGCTGGTGTTAGTTGATTGAGTCAGCCCATTCCCAGAGAGTTGATTATAGTGCACAAGATCAGTGACAAAGGCGCCTATTGTTGATCCACCATCAGCATAGGTCGCGATGAATGGACAAAGTAAGCTTGTGTTGCATTCTGGCTGCACATCCCTATCGGGCGAAGTGCAGAACATATCATCACATTTCACCACTTTTTAACTTACTGAGCTCCTAGGGTCATATAATGTCAGCTTTTTCAATATATCGCTCTTGCGAGGGCATTGCTTGCAGGGGATGCAGTTAACCCAAAATGCACTGCTGCCAGTGTCCACCTGCACATAGTATTCCATTGCGGGTGTCCCAATCCCTATCTCCGTGTAGTATAGTCCTGTGCTGGATGTGCTGATGCCACCAAGGCCACCAAGTGAGAAGTCCGCAGCCACAAGGCGACTAAGATGGCGGTTCCTATCGTGGGTTTGTAATGCACCTATGTCACTCCCCTTACACCCACCGCCCATGATAGAGAATTTGCGGCGCACCTGGAATAACCCAATGGCCACGGTACCACGAGTAGAGGATGCTACCAATAGGGCCGAAAGGATTGCTTGCTCTGCGGCTAGAGGGACCTTGGCGACTATCTTGAAATACACCGGAGCGTTGGGAGAGCCGAAATCTTGTTGGATTAAGCCTTCAACATCTTGATCCTATACATGCACCATGTGTCTGTCTTAGTCCGTCCATATGATTCAGCCAGGCAATTAGCTTGGCTGATGGATACGGATCAATTCGAAGCATAATGTCACGGATCTTGCTTATCCAACAACTTGTTTGTGTTTCTTCGATTTGTCCTATGTAAGATGCTAAGCCAACAACATCAGATAAATATGTTTTGCTGTATACTCTTTTGGAAAGACTCTCAATGGTTGAAAATCTAAAGGTTTGTTCTAGTTTTGGTTTGTTTTCTAGGGTTTTGATCTCCTGAACTTTGGCAGTGTTTTGAGAAGTTGAGAATTTTGTCATTGTGAACTGGACGATATTCTGCTACTGAAGAAACCTTGAAATTAGATATCATGGACACTGATCCTTCTTGAATGCCCTGAACCTATTGACCTCTTCATCAATCAGTATCATGTCAAGGCTAATAAGCTCGTTGCTGTTAGGATTTATGGCAACCCAAAGTCTAATTACCCATTGTTAACAGCTTTCCATGTTTCCTTTTCATTGTTAACAGCTTGAAGCATATCACATGCCATTGTAGTTATCCTTTGTGTATTACAGATGCGGCGGAGACGGATGCAAGTATGCTCCTTTTTGCCAACGCAACGACAAATATGCGATAGTTGGGAAAACGGATGAACTGTGGAACAAACATACTGATCCCAGAGTTCCAGTCGGAGACGGTTCGCTCGTTGATAAAAGTCATCGCCGCGAGAACCGATGATCTCCAACTCGCGCTCGCCGACTATCCCGCGAACGGAGAGACGGAGAGCTGGATGCGGCGCGTTGAAGATAAGGTCGACCAATGCTTCTC

Coding Potentia
Explanation CPC Score
noncoding -1.24957
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0256900.2 4 15388482 A G
Osa04LNT0256900.2 4 15388639 T G
Osa04LNT0256900.2 4 15389035 T C
Osa04LNT0256900.2 4 15389153 C T
Osa04LNT0256900.2 4 15389164 T A
Osa04LNT0256900.2 4 15389229 G A
Osa04LNT0256900.2 4 15389292 G A
Osa04LNT0256900.2 4 15389588 C A
Osa04LNT0256900.2 4 15390119 A G
Osa04LNT0256900.2 4 15390131 A G
Osa04LNT0256900.2 4 15390445 T C
Osa04LNT0256900.2 4 15390462 T G
Osa04LNT0256900.2 4 15391826 C T
Osa04LNT0256900.2 4 15391859 A G
Osa04LNT0256900.2 4 15392121 A C
Osa04LNT0256900.2 4 15392368 T A
Osa04LNT0256900.2 4 15392628 A G
Osa04LNT0256900.2 4 15393133 A G
Osa04LNT0256900.2 4 15393195 G A
Osa04LNT0256900.2 4 15393255 G A
Osa04LNT0256900.2 4 15393704 C T
Osa04LNT0256900.2 4 15393846 G A
Osa04LNT0256900.2 4 15394256 A G
Osa04LNT0256900.2 4 15394368 T C
Osa04LNT0256900.2 4 15394617 A G
Osa04LNT0256900.2 4 15395750 G A
Osa04LNT0256900.2 4 15395955 T G
Osa04LNT0256900.2 4 15396060 G A
Osa04LNT0256900.2 4 15396632 C T
Osa04LNT0256900.2 4 15396740 A G
Osa04LNT0256900.2 4 15397108 C A
Osa04LNT0256900.2 4 15391611 C T
Osa04LNT0256900.2 4 15398458 T A
Osa04LNT0256900.2 4 15390247 T A
Osa04LNT0256900.2 4 15390630 A G
Osa04LNT0256900.2 4 15396302 G 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
Osa04LNT0256900.2 osa-miR6251 Translation 4.0 22.31 1 21
Osa04LNT0256900.2 osa-miR7692-3p Cleavage 4.5 17.083 1 24
Osa04LNT0256900.2 osa-miR166a-5p Cleavage 3.5 18.069 1 21
Osa04LNT0256900.2 osa-miR166a-5p Translation 5.0 14.069 1 21
Osa04LNT0256900.2 osa-miR166c-5p Cleavage 5.0 18.069 1 20
Osa04LNT0256900.2 osa-miR166e-5p Cleavage 3.5 18.069 1 21
Osa04LNT0256900.2 osa-miR166e-5p Translation 5.0 14.069 1 21
Osa04LNT0256900.2 osa-miR164c Cleavage 3.5 14.799 1 21
Osa04LNT0256900.2 osa-miR164e Cleavage 4.5 14.799 1 21
Osa04LNT0256900.2 osa-miR415 Cleavage 5.0 14.337 1 21
Osa04LNT0256900.2 osa-miR2091-3p Translation 5.0 22.914 1 22
Osa04LNT0256900.2 osa-miR2097-3p Translation 4.5 24.468 1 22
Osa04LNT0256900.2 osa-miR2877 Cleavage 5.0 22.547 1 24
Osa04LNT0256900.2 osa-miR2877 Cleavage 5.0 23.427 1 24
Osa04LNT0256900.2 osa-miR2275c Cleavage 4.0 15.643 1 23
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0256900.2 4 An8-glum Morphological trait Panicle/flower nan nan
Osa04LNT0256900.2 4 nan Morphological trait Root RZ69 RG449
Osa04LNT0256900.2 4 nan Morphological trait Root RZ69 RG449
Osa04LNT0256900.2 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0256900.2 4 spp4-2 Morphological trait Panicle/flower RG449 CDO456
Osa04LNT0256900.2 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0256900.2 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0256900.2 4 nan Morphological trait Panicle/flower RG788 RZ69
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