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

>Osa04LNT0258000.2

GGTAGGGCAATAATTGCCATCAAACCAAAACAGCCATATATACTTCTGTTTTAACAGCAAAACTATACATCTGGGATAATTTGGAACACATGTATTTTTTTTCCTGAATTCCAGGCATTGCAGCATTTTTGCAATGAACCTGCGAAACTTTCTTCTGTGCTTTGACTCTCAGAATTTTGTGTGATCAGTAAATCCTATTGCTGTTAGAGACTATGGGTGTGCATGCTAGCATATTGCACTGGTAAGAGATACAGTTAACGCAAGCTGCCAAGGTCTGATGCTGATAGGTGCAGCAGATCATCCGTCAGATGCTACAGAATCTGAAAGAAGAGGCTGATAGGTAGCGCCCCTGTTGCGACGCGAATCGGCTAGTAAATGGGTGAGATAACTGCCAGCAGATATGATCCGTGACTCCATATTTCTGGTGGTATGGGTATGTCCATTGGATTGCTCGATTTGCTGAAGTATGTTGATGGCATTAGGTCGAAACATGTTCCTGAAGTATCTCAAAGCCAGCACCGGGCCCATTCCTACCGCAACAATCAGACCCATGGTTATCCAGTACGAAGGTTGGCTACACAGGCGGAACATTATAGTATACATTTGGAGTGTTGGTACCGCACTGACTATTAAGTTGATCATGTAGAAGGCGATAAAGTTTCCCCATATGAGAATGATTTGCGGATAAGTGAATGAGTTTGTGTCCAGTGTCACAACAAAAGCCTGCAACCAAATGCATCCAGATAGCGCAACCATGGAGAGTTCCTCAATCTCACTTTTTTCATCAGAATATGCACAGATTGTAGTTAAGAATACAACAAGTGCATGGTAAACCGATCGTCCAAACCATCCAGCAAATGTAGTTGGATTCAAAAGCCTTCCAGACTGAGAATAGAGTAAAATCTGGGGATATTGCAGTACTGTTTCCTCAGAGATATCCTTGTCAAAAATTATAGTCGTCACAGGAAGACTTGTATAGAAAACATTATAGGCCATCAGACTAATTGAGTTGAACAAGCTAGTTCCAGAGAGTCCTGATATAAAGGAGAAAAGAATCTGTATAAAGCATATCAAGAGTGACTTGTAGAAGGAGTACTGTGAAATAAATGCCGTACGATTGTATGAATATCGACCATGGACAAGTATCAACCTTTTGAGAAACTTGAATTTTCCAATGCTATAATCAGCAGCCCTTGCAGCTTGTAGCCCTTCCCTACCACTAATCCCAACTCCAATGTTTGCCTCTTGAATCATTCTTACATCATTACCACCATCACCAATTGCTAGAGTTAGGTAACCGACAGATTTCAGGAGCCCAACAAGCTGTGCTTTCTGCAAGGGTGTCATTCGACAGCATATCGCTGTTCTTGACAACATGGCCAGCTTAGTGAAGGACTCCTTGGAATGCTTTAGAATTATTTCAAGTGCCCATCCATCCAAAACAAATGCACAATCCTTTGTTACCGACATAGACTTCATTGTTGACAATGCCCTCTCTAAGCTTCTTAATACATCGTGTTCAGTTTTTCCATTGATAGACAACAATTGACCATTCGGCTCTGAAAGTGATACAAGAATTGAGTCCAGGTGCTATGAGATTACAAAGAAGTCCAATCTGAATTGCTGTGTGTTGCTTATCACCAGTTAGCATCCACACATTGATTCCGGCACTCTTTAGCAATTTAATGGTTTCCGGCACACCATCCTGGAGACGGTCTTCTATGGCACTAACACCAAGAATTTGAAGATCTTGCTCTAAACGGTGACATACTTCGGCAATTTTACGCTCCCTGTTCTCCAAGGAGCAGCTAGCATCTTGAAATGTTTTGGACCAATCTTTGTATTCATCTTCTTCTAATTCACGCCATCCCAAACATAATGTTCGCAAGCCCAACTGAGAATACATTTCTACTGTCTCAAGATAGGTTCTAATTTGCTGTCCTTGATGGCAACGAGGAAGAATAGCTTCATCAGCTCCTTTAGAAAGAAGAAGGATCTTCCCACTCTGGACATCCTTTACCACAGCAGACATTCTTTTGCGATCGGAAGTAAACTCCAAAATATCCAACAAATCATAATAGAACTTAGAACCGTTGAAAGAAATCTCAGCAGTGTTGCTGTCTTTACTCACAAGCACCATATTTAGTTTTGATGCAGCAGTGACCAAAGCTTCCTCGTCTTGTGATTGTGCTTGGTATGTTATAGTACCATCATTGCTTTTGATAGGAACAACTGTATTGCAAAGAGCCATCACCATGAGAAATTTGACAATATCAGGATCGTTACGCGAAACAGCATCTAGAAGTCTGGCATCTTTTAAAGCATCTTCATTGTTTTCTCCATACAGAATATCACTTATGCAACATCTTCTGAAAATCATTCTGTTTTCTGTCAGCGTTCCAGTTTTGTCACTCAAAACGTACTCAACCTGTCCAAGGTCTTCACTAATAGTTAGCTGAATGAGCAGGCGTACATGTTTCCCGATCAAACATTTGTTCATCCCAGTCAATGAACTTTGCATATACACCTTTAGACAGATCAAGAGTTACCTTCACTGAAATAGGAATCATTATTGAACACAATAGCTCAAAGCGCAATGGTATAATCAAGAAATCATACCATGGTCCTTCCACAGGATACAGCAGATACCATTGCTTAAGACCCTGGTTCTTCTTCCAGATATTGCCAGCAAAACCCAGAACAAGAACAACAACAATTTGGAACATAAATATTGCAACAGTGAGTTTGTCTATCATTGCATCAGCAGCAGTGAGCTTGGGCTCTGCGGTTCCCCTGCTCATTCCAGATTTTGTTTGATTGCCTGTGTAAACTGCAACTCCACACGCCCATTCTGTGTACCTTAAGTAACATGATTGAAGAAGAGTATTATTGATAGTTAAAGGACATTTTTCACTATCAATGATAGGAGGAAACAAGCGCATGTTAGCGTCAAATCTTCTTATGTCATTATCTGGGTTGGAGCACTCAACTACACCCTTGACTCTGCCTAATTGATCTGGAGAAAGGTTAGCACAGATAGAAGGAACAATTCTTGTTTTCAAGTCAGTTTCACCATCTAAAGCAGCTGTCTCAACATAACAGATGCCCTGAGGATCAGAAGTTCCTATAAGAACAAGATCACATGGTATCTCATCATTCTGATAAAGCCACACTATATTTCCAACATGGATATCTTGTGCTTTGATCTAAAAGCATGTAAATATCTGATTATTAGACAATTACATGTTCAGTGTGTAAATTCAAGTGCTCCTAAATGTAATACTTCTGGCAAATGAAGAATATCATGCACATTAAAACTCCGTATTGCATACATGTTTAGCGTTTCTCAGTATCAACAACTCCTAGGTTTAATTACAGTTTACATTTGCAGATACTGATTGGTACTTAAAATGTATCAATGGGTATACAAGTGTCAATAAAGATGAATTTGCAAATTTAAAATGGTTACAAGAATTAAGGCTTTATTTACCTAAATACGATCAATACAGTTTAGCCACTGAATGGTTATTATGGCAGCAGATCATGCAAAAAGGCTGAGTAAACTGAGCTCTCAGATAAGTTTTGCTACTACAACCTCCAAATAGAACGAGACTAAACAATGCCATTCACGAGTTCCATTATCTTTCATGTTATTTTTAATGCGAACTGAACAGCAAGTAACATGTAGGGTTTCCATCTTATCAGTTTTTGGAGTACGGTGTTGAAAACATAAGCAAATAAGGAATTATAGAATTTCCTTTTTCATATAACACCAACTAATATCAAATACAATGCCTTCAGGCAGCAGATCTCACCTAGACAAGTGAAAACACATGGCTGACAAATGACTTTCCAGCAATAACATAATGAATTCAAATATTGATGTAAACTTACAATAGATTTAGACAAAGTTTCACTACGGTTTTAAAAAACAGAAAATATAACAGAGAAAACAAAAACCTGTCTATGGTTGCCATCCTTTACCACCAAAACTTCCCTTCCGTTTGCTTTCTTGTCTGAAAGGTACCTATTGTAATCATCCCAAGCCTCTTTTGAAGCTGAAACTATGAAGATGATGGCAAGTGGACCCCATGTAGTTGCAGGACTAACAGGTGTGATACTTGACCATAACTGAAGGCAGGCGATTAGAAGAAAATACTGATTCATGAAACGCCTGAATTGCTCCCATAAGTTCTTAGGGAGAAAATTCCAGAGATTATATTTGGTATTTGATATTCGATTGTCACAATAGGAATCCTGCCATGAATCATCATTGATATAGACGAATCTTTTCATTTTGACAACGATATCAATTCCGTGCCATTTGATCACTTCAATGGCAAGAGACAGTCAAAGATCATACATCGCATCCCTCTTCCATTGCGTGGTGTCCCCGCGGCTGGACGGGAAGCGTATTCCGGAGGGAAGTGAGTAGGC

Coding Potentia
Explanation CPC Score
noncoding -1.19191
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0258000.2 4 16844100 G A
Osa04LNT0258000.2 4 16844626 C T
Osa04LNT0258000.2 4 16844669 A C
Osa04LNT0258000.2 4 16848184 A G
Osa04LNT0258000.2 4 16848194 G A
Osa04LNT0258000.2 4 16849570 A T
Osa04LNT0258000.2 4 16850875 T G
Osa04LNT0258000.2 4 16851277 G T
Osa04LNT0258000.2 4 16853720 G A
Osa04LNT0258000.2 4 16856351 T C
Osa04LNT0258000.2 4 16856523 G A
Osa04LNT0258000.2 4 16846769 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
Osa04LNT0258000.2 osa-miR812r Cleavage 5.0 12.958 1 24
Osa04LNT0258000.2 osa-miR5828 Cleavage 5.0 15.197 1 21
Osa04LNT0258000.2 osa-miR169f.2 Cleavage 4.0 17.022 1 21
Osa04LNT0258000.2 osa-miR426 Translation 3.5 15.698 1 21
Osa04LNT0258000.2 osa-miR426 Cleavage 5.0 17.246 1 21
Osa04LNT0258000.2 osa-miR1438 Cleavage 4.5 12.363 1 22
Osa04LNT0258000.2 osa-miR1438 Cleavage 5.0 12.169 1 22
Osa04LNT0258000.2 osa-miR1442 Cleavage 5.0 19.771 1 20
Osa04LNT0258000.2 osa-miR1850.3 Cleavage 3.5 13.105 1 22
Osa04LNT0258000.2 osa-miR1856 Translation 5.0 12.218 1 21
Osa04LNT0258000.2 osa-miR1860-3p Cleavage 4.5 17.002 1 22
Osa04LNT0258000.2 osa-miR2105 Translation 5.0 8.451 1 20
Osa04LNT0258000.2 osa-miR2878-5p Translation 5.0 12.03 1 24
Osa04LNT0258000.2 osa-miR5151 Cleavage 4.0 8.451 1 22
Osa04LNT0258000.2 osa-miR5487 Cleavage 5.0 13.114 1 21
Osa04LNT0258000.2 osa-miR5508 Translation 4.5 12.176 1 21
Osa04LNT0258000.2 osa-miR5519 Cleavage 5.0 13.048 1 21
Osa04LNT0258000.2 osa-miR1319b Cleavage 5.0 23.398 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0258000.2 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0258000.2 4 spp4-2 Morphological trait Panicle/flower RG449 CDO456
Osa04LNT0258000.2 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0258000.2 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0258000.2 4 An8-glum Morphological trait Panicle/flower nan nan
Osa04LNT0258000.2 4 nan Morphological trait Panicle/flower RG788 RZ69
Osa04LNT0258000.2 4 nan Morphological trait Root RZ69 RG449
Osa04LNT0258000.2 4 nan Morphological trait Root RZ69 RG449
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