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

>Osa04LNT0271300.2

GAGCAAAAGGGCATTGCCCTGACTAGAACATATATAAATACATCATAAGTTATCCTTCTTTGAAGAATGATCAGAAGCAGGCGAGGATGAAGAGCTCATCCTGGCCCTATCTCTAGACTCACTTAACATAACTACAACATTCCGCATCGGTGGTCTGTCATATGGAGACATACTAGTACATAGCAATGCAATTTTCAAGACCTCAATCATATGATCGACAGACGTTTTGTCTTCCAAATTCAGATTCTTATCAAGAATCCCTGGACCCAAAGAATTGTCCCTGATGTAATTCTTTACCCATGTTACCAGATCACCTCCCAGTTCTAATGGTTGTACAGGGGCACGTCCGGTTAGCAGCTCCAGCAGTACGACGCCGTAACTGTATATGTCACTTTTTTCAGTAACCTTCATGGTGTATGCATATTCAGGTGCTATATATCCATATGAACCAGCAATTGCAGACATTGATTTTGAGTATGGCATGTCTATCACCTTTGCCAATCCAAAGTCACCAACATGAGCTTCAAAGTTCTCATCAAGTAAAATGTTATTTGATTTTATATCACGGTGGATGATGCGAGGTTTGCAATCGTGATGCAAGTAAGATAGCCCTTCAGCTGATCCTAGGGCTATCATGAAGCGTGTCTCCCAATCAAGTGAAGACGAAGATTGCCCATGAAGTAACTCCCCAAGGCTTCCTCTTGGCATGTATTCATACAACAGAAGGTTGGAACCCTGGTGATAGATGAACCCATATAACTTCACAATATTACGATGCCTTATCTTTCCTAGAGTAAGGATCTCTGCACGAAAACTATTGTCTGTGTTGCTTCCCTCTCTGTTAGAAGCCAGCTTCTTTACAGCAATTGTCTGTCCAGCTTTCAAGATGGCTCTGTACACTGTTCCACATGCACCTCTTCCAATAACACAACTCTCGTCAAAATTATTTGTGGCAGAAACCAATTCCTGAAATGTATATGCATCCTTGGTAGAAACCTGCATGTTAGACCCAGCAGAAAATATTTGCTTGTCTTGCAAAGGAGCTACTGTTTCTAGTGGTTTTCTCATATGATACACAATTATAACGATAAGAATAAGTGAAATTCCTCCAATAACAGCAGCAACAATTGCTATGACCTTGCCCAAAGGGGGGCTGCCTGAATTGGATGACTGGGAAGAAGATATTGACTCAGACCCACATTTGCCAAGTTGTCCGCCACATAGTCCTTTGTTTCCAAGAAAGCTGGTTGACGCCATGTTATCAAAAAGTGGTATAGTGGGGAGAGCGCCGGTGAGATTATTGTAGGAGACATTGAACTCAAGCAAACTAGACAGATTTGCAAAGGTATCTGGGATTTCACCTGTCAGCTTGTTATTATTGAGAAACAAATTTTCCAATAATGCAAGATTACCAAGCTCTGATGGTATGTTGCCAGAGAGATTGTTATAACTCAAATTCATGGCGATCTGCAAACTTGAGAGTAGTCCAAGCTCCTTCGGTATTCCACCAGAGAATTGATTGCCACCAATCTGTAGAGCTGTCAAATGTGAAAGTTTACCAAGAATAGGTGGTATCTCTCCAGAGAGCCTATTGTCAGCAAATGATAGCAGCTCCAGCTGAGGCAGGCTGCCAACTTCATTTGGCAATGAACCTTCGAAGCTATTTTGGCTGAGATCTAGGCGTTGCAACATAGTGCAATTGAAAATTTCTAATGGTATGCTTCCGCCTAGTCTATTGGATGATATATTGAAGACGACGAGCTTTGACAGATTACCTATTTCTTGAGGCAACTCTGATGTGAAATAGTTATTTGTTAGGTCAAGCCTTTGGAGAGACTTGCAATTGCCTATCTGAGGAGGAATAGGACCATTGAACTTGTTTCGACCCAGCTCAATTGTTGTCAAATTCACCAGATTGCAGAGATCAGTTGGGAAGCTTCCTGTCAGACTGTTATCAGCGAGACGAAGCTGCACCAAGGATTTACAACTGGTGATTCCATGGGGGATGTTCCCAATCAGCTTGTTAGCCCCCAAATTCAACAAAATAAGGTTCGACTGCCTGCAAAGATCTCGAGGTATCTGCCCGGTTATATTATTATTTGAGAAATCCACCACCCAAAGCCGGCTATAGATACCAAATCTTGGAGGTATGTCACCTGACAGCATATTGTTGAATAGTTGCAATTGGATTAGTCTGCTCATGTACTGAAAACAGGCTGGAATTGGGCCACTGAGTGTATTGATCGAAAGATCAAGCTTACTCAAATTCCTCAATACACACAACTCGGTAGGAATAGGGCCAGTGAGTTGGTTTTGGAAGAGATAGAGTAAATACAATCGTGGTATCTTGCCAAATTCCTTTGGTACCCCTCCAGTTAAAACATTCTCTGAAAAGTCAATCTCCTCTGCAAGAGAAAGATTGCCAATTTCTAACGGAATCGTACCATTTAATAAATTCCTGTAGAGGTATAGCCTCTGAAGGTTCTGGATGTTCCCGATTGTTGCAGGAATAGGCCCAACCAGATTATTGTCATAAAGGGCAATTGTCCTAAGATTTATGCAGTTTCCAATCTCTGGGGGAATCACACTAGAAAGCTGATTTCCCCACAATATTAAGTCTGTCATATTTGTCAGTTTCCCAATCTCCTTAGGCAATGGCCCTCCTAACTTGTTTTGTGCAAGACCAAACACCACCAGGTTGAGGCATTCACCTATCTCGACAGGAATGTTACCAGATATTGCATTCTGACCTAACCGGACGGTTTTCAGGTTCTTAAGCCTACCAATAGTATGAGGTATAGAGCCAGAGAGATTATTGCTGTACCCTACCAGGTCCTCGAGTGATGCCATATTACCAATCTCATCAGGTATTGCACCAAAGAGCTTGTTGTTGCACAGGTTGAATGTGATCATCATAGCCAGCTTCCCGAGCTCAGCGGGGATTGTGCCCTGGAACTGGTTGTTGTTCAAGTTGAGCCCCGTCAACTTCGAGCAATTCCCAATCTCTGCAGGGATAGTGCCAGAAAACCCATTGAATGACAGATCAAGGTTAGTCAGCTCAGCCAGGCCACCAATGCTCGGGTCGACGGTGCCCGACAGGTTCATGTTGCTGAGGTTGAGGGACACCACCGCCGGCGTAGACCCCGACGAGCAGTTGACGCCCTTCCACCCGCACGGCGATGGATCCTCGGGGTTCCAGTCGTCAAGGTGGTGGAAGGTGTCAACTATCTGCTTCCTCAGCGTCAGGAGAAGCCAGCCTTCATGGTTCAGGCCATGGCAGGTAGTGGCCAGCAGGAAGGCCAGCGCCACGCCGAGCTGCAGAGCCCAGGGCGTGCGAGCCGCCGCCGCAGAGCCCATCTTCCCTTCACAATGGTCGCAGTGGAACCAGAGCCGAACCCCCCCTCCCTACGACCTCGTGCGCTGCCGCATCTCTACGACCTCGTCGTGGCTCGCCGTGGAGGGAGGGGGGAGAAGAGGTGGCGGAGGTGGGAGATGGAGATGGAGATGGAAGGGGGAGGAAATGGAAGCTGGAAATGGCAGGCAAGCACGCTTTCAAGCTCTTGCGAGGCGTAGCGATCGCGGGCGGTCCCTC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.896569
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0271300.2 4 25254368 T G
Osa04LNT0271300.2 4 25255268 C T
Osa04LNT0271300.2 4 25255785 A G
Osa04LNT0271300.2 4 25258248 G C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0271300.2 osa-miR5788 Translation 4.0 16.726 1 21
Osa04LNT0271300.2 osa-miR2873c Cleavage 5.0 23.781 1 21
Osa04LNT0271300.2 osa-miR399e Translation 4.5 14.249 1 21
Osa04LNT0271300.2 osa-miR399f Translation 4.5 14.249 1 21
Osa04LNT0271300.2 osa-miR399g Translation 4.5 14.249 1 21
Osa04LNT0271300.2 osa-miR399k Cleavage 4.5 14.249 1 21
Osa04LNT0271300.2 osa-miR399k Cleavage 5.0 17.491 1 21
Osa04LNT0271300.2 osa-miR444a-5p Cleavage 5.0 21.774 1 21
Osa04LNT0271300.2 osa-miR1432-5p Cleavage 5.0 19.567 1 21
Osa04LNT0271300.2 osa-miR1428e-5p Cleavage 4.0 16.967 1 22
Osa04LNT0271300.2 osa-miR1873 Translation 3.0 23.048 1 24
Osa04LNT0271300.2 osa-miR1428f-5p Cleavage 4.0 16.967 1 22
Osa04LNT0271300.2 osa-miR1428g-5p Cleavage 4.0 16.967 1 22
Osa04LNT0271300.2 osa-miR2866 Translation 4.0 22.873 1 20
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0271300.2 4 qPH1-4-1 Morphological trait Dwarf RM241 C2807
Osa04LNT0271300.2 4 nan Resistance or Tolerance Other soil stress tolerance RM5586 RM3916
Osa04LNT0271300.2 4 nan Morphological trait Culm/leaf RM3785 RM1388
Osa04LNT0271300.2 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0271300.2 4 nan Morphological trait Culm/leaf RM3785 RM1388
Osa04LNT0271300.2 4 nan Morphological trait Culm/leaf RM3785 RM1388
Osa04LNT0271300.2 4 qChla4-1 Morphological trait Shoot/Seedling C2807 RM241
Osa04LNT0271300.2 4 qChlab4-1 Morphological trait Shoot/Seedling C2807 RM241
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