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

>Osa04LNT0263200.3

GTCGTTGGCAAATATTTACTGTAGCATAATATTGTCAAATCATGGCGTAATTATGCTCAAAAGATTCGTCTCGCAATTTACATGCAAACTGTGTAATTGTTTTTTTCCCCCACATTTAATGCTCCATACATGTGTCCAAACATTTGATGTGACGTTTGAGATCTAAACAAGGCCTCACACAAGAAATCAATTACTTTGTAGATCGTAACTAGCTGCCCTAGCTAGTCATCGCCTGCCGTGGACATGGCAAAGCGTTCGCCCGAATATGTCCATTGTGAAGTTGCTATACGAGGTTGATCCAGGCACCAACGATTTGCCCGTCTATTGTCACCCAGTCAACGCCTATTGCTGCTGGTTGTTCATGCCATTCATCAACCTGCAAGTAAAGTAAAAATAAGCTGATGGAGAGGAGCATAAAGGAAAATATAAACCGTGGGGAATGGACTAATCAGGCAAATGCTATGGTACCCCTTCATACGGATTGGGATCCTCTGACGTGAAGTCAGAGGGACGTGGTGGCTGACATGTGGGCCCCACCGCTTGCGGGCCCACCTGCCAGTGACCACGTCATGTGGCAGTTCACGTCAGAGGAACCACTTCCCCTTCATACATATTTGAGCTGACTGACATGATTATTTGTGCGTATGGGTGGTTCAGTAAGAGTTTCTAACTAAGGTTTACCTTACCATTTTGGAAGTGAAAACTGCTCCCCACCTGTTTGCTGAGAACCGAGTGGAAAACAGTAAAAACCGGCGACGTTCAGTCAACTCTGTACGAAAACCAGCTAAAATCTATCAGTTTCTACAAACTAACCACCAGCGGTTTCACAAAAACCGAGCTCAATTTTGTTAACCCTGTTCTAACACAATGGATAATTTGGATAATAGAATAAGAACTGAAATGAGTTCCCTCAAGAACAATGCGTGGATGAGAACACCCACGCCAGGACTGGACTGAGAATCCTTTCTAGGCCATAATCATTGTTCTCATTCAATCGCAACATGACCGCATTGCCATAATCTAATTGAAGTCTGGCCCTCGGATTGTGTTCTTAAAGGGTTTGTAATGAAGCAAGAAACTTGTAAATACAAGGTAGTTATATACTTACCAAACCCCTAACAGGTTGGCAATCCTCAAAACATCTGAGCCTCTTGAACTGCATTTCTCAGTTCTGACAAACACCGTTCTGATACCATCTTTTCTTGTTCACCACTAAGACAGCAGCTGGCCACCCTTTCATATTCCTGTTGAGCACGATGTGCAGGGTTTAGCAAAACACGATCATTCTCAACCAGATTTCTTCGCGTTTGCACCAAATTAATAGCTTTTGATAAATCCTCTTCAATTCAAGTCGTGCAGAAATCAGGAAGGATGACAAGTCTAAATGACAATGAGTGCGGGCAGATTGGAGTAAACAGCAAACATGGGACATTTGGATGGACCTAGAACTCTGCATTGCAACAAGATTTGCCTAACCGAACTGATCCATGGAAGCAAACCTGCTCACGGCCATCAAGAAAGAATGTCGACGGCAGTGGCATGCATGCCAGGAGATACTTAACGATCTTCTCCACCGAGCAACAGCACAACCCAAGTCATATTAACATGTCGCATGAATCTGGCGAAACCATTGAATGAAGAGCACCCTGAGTTAAATCATTAGCTTCCAGGTGTTGATGATCCATCAATATGACCTGTTTTTTTCTCTCCAGATAAGGGATACCGTTCCTTTCAGCAGATTTTTGTGATCCAAGCTGAGAATTGCCTTTAGAATTGCTGGCATCAGATGTCCTAGGATCAACTGTTGCCCCTGAAGCTTCGATTTACCTTTCCTCAACAGATGTGGTGGCTCCATTGCTGGATGGTTTTCCATTAGTAATACCAGAAGCAACTGATAGAATATAATCACTATCGAAGGATGCCCCAACTTTTCAAGACCATAAAATCTCAGCTGCTTTATAGTCAATGGCTCATTTTGTTCAGCGCTGAGACTCTGTTTTGTCCTTAAGTGGTCAGTAAACTACTCGACCGTCACTGAGGGGTCAGAACAGATTTTGAATATACTCCTTTGCTTCTAAAAATGTCAGGCATCCCATTTGTTTGGGGAAAACATCTCAAGAAGGAAACTGTGCCTCAAGGGGATTACTCTCTAGACTAAAGTTTGACTGAAGTTCTGTCTTGGTGCCATGCAGTTCACCTTGCTCAGTACTTTTGGATACACTTCTATGCCACATCCAGATTATGCAGTGCTGCTTCAATGTCTATGTAACATGTTTCCCTCACCTTCACTGTTCCATCAGATTACAGAAGTGCTGTTTTTGCTACCTTCTGAGGAGAAACCTGGGCTGTTTGTGAGCTCATCTGTAGAGTACTATCAAACTGTTCTACTAAATGCGCCCCCCCCCCAAAGACCCAGAGTCCCAAACAATCTCTCGGTGAACAAGCATAAGTCGTCAGCCATATGTAGCAGAAATTGATAACTACAAATCAAGAACCACCCCGCAGGCAGCGCGCCAAGGACCACTCCGCAGATGTTCGACGAAATGCTCACAAGCTGCAGGCGATCGAACCAACGAACCTGGCAGTCGAGCCCGATCCGCGAGGGGAAGAACGACGCCCACGCGGCGAAGACACCATGCCGCGCGCCGCCGCCACCTCCCGGCGACCCATGAGGCGCACGAAGGGAAGGAGAAGAACGCGGTGGCGACGGGGAAGGGGACGGAGTTGGCCGCGACGGCGTAGACGAGTGAGGCCGTGACGCGGAGGGGATCGGGAGGCGGCGCGGCGCTTCCGCCTCAACTCCGAGCGCCTAAGCCACAGCCGCCGCCCCACCACGCTCGAGCGCTGGCCCTACTCGCCGCCGCATCCACTCGGACTCGCCGTAGCAGCCGCCACCTCGGCCGCCCCGCCACCGCCGGCAGCAACGCCGCCGCGGCGACTGAACGGGGAGAGGGGAATCCACACGTCACACGCCACACGCCTCTCCCCC

Coding Potentia
Explanation CPC Score
noncoding -1.21024
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0263200.3 4 21706220 A G
Osa04LNT0263200.3 4 21706233 T C
Osa04LNT0263200.3 4 21706248 A G
Osa04LNT0263200.3 4 21708107 T C
Osa04LNT0263200.3 4 21708264 A C
Osa04LNT0263200.3 4 21708499 T G
Osa04LNT0263200.3 4 21708860 T C
Osa04LNT0263200.3 4 21710120 G T
Osa04LNT0263200.3 4 21710470 G C
Osa04LNT0263200.3 4 21710542 T C
Osa04LNT0263200.3 4 21711379 A T
Osa04LNT0263200.3 4 21711989 G A
Osa04LNT0263200.3 4 21706817 T C
Osa04LNT0263200.3 4 21706284 T 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
Osa04LNT0263200.3 osa-miR5789 Translation 4.0 14.49 1 21
Osa04LNT0263200.3 osa-miR5796 Translation 4.5 20.216 1 21
Osa04LNT0263200.3 osa-miR5829 Cleavage 4.5 19.14 1 24
Osa04LNT0263200.3 osa-miR2873c Cleavage 5.0 15.435 1 21
Osa04LNT0263200.3 osa-miR6252 Translation 4.5 11.328 1 23
Osa04LNT0263200.3 osa-miR6255 Cleavage 4.5 22.618 1 22
Osa04LNT0263200.3 osa-miR818f Translation 5.0 13.601 1 21
Osa04LNT0263200.3 osa-miR167a-5p Translation 5.0 12.55 1 21
Osa04LNT0263200.3 osa-miR167b Translation 5.0 12.55 1 21
Osa04LNT0263200.3 osa-miR167c-5p Translation 5.0 12.55 1 21
Osa04LNT0263200.3 osa-miR167d-5p Translation 5.0 12.55 1 21
Osa04LNT0263200.3 osa-miR167e-5p Translation 5.0 12.55 1 21
Osa04LNT0263200.3 osa-miR167f Translation 5.0 12.55 1 21
Osa04LNT0263200.3 osa-miR167g Translation 5.0 12.55 1 21
Osa04LNT0263200.3 osa-miR167h-5p Translation 5.0 12.55 1 21
Osa04LNT0263200.3 osa-miR167i-5p Translation 5.0 12.55 1 21
Osa04LNT0263200.3 osa-miR393b-3p Translation 5.0 18.16 1 21
Osa04LNT0263200.3 osa-miR167j Translation 5.0 12.55 1 21
Osa04LNT0263200.3 osa-miR435 Translation 4.5 20.216 1 20
Osa04LNT0263200.3 osa-miR1423-5p Translation 4.5 16.82 1 24
Osa04LNT0263200.3 osa-miR5081 Translation 4.0 11.934 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0263200.3 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0263200.3 4 nan Resistance or Tolerance Other soil stress tolerance RM5586 RM3916
Osa04LNT0263200.3 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0263200.3 4 orl1 Morphological trait Culm/leaf S10628 C377
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