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

>Osa04LNT0266800.3

GCTTCTAATAATTTGTGTGGTTTTATTGTAACTTGGACAACAAAACGTGTAGTTTTGTGAAGTTTACTCTTGTATAGCCTAAACAAAGAAGCACATCTCAAACTCATTTCATCTGTGACACTCAATTTCGATGTTCAATGAAAAAAAAGAAGGCAATGCGTGCGACTCTTTTCATCCCTGTTTCATTTCTCGGAGGAACTTCTTGAACCAATGGGCTGAATTCTTGGGGTGTCTCTTCATCCCATCATCGTAATCCACAAAGTTTAGCCCAAACCGGAGTGTGTAGCCATCCGCCCACTCAAAGTTGTCAAGCAGAGACCATGCAAAGTACCCCTTCACGTTTGCTCCATCCCTCATAGCATTTCGCAGGGCGAGAAGGTGCTTGTGATAATATTCTATCCTCGTATTATCATTCAGGGCCTCCTTGAGTGGCATGGTCTTGTTATTGACTTCATCAACACCATTTTCAGTAATAAAGATGGTAGGATTGCCGTAGTTTTCCTTGATATAAAGCAACAATTCACGGAGCCCTTGAGGGTATATATGAAGCCAAGATGAAGCAGCCTACACACATATTGTTTATAGAGTTCAATCATGTCACCTGATCATTGTTTTGCACTTTTACTAATAATTTGTTTTGTGGGTAACAAAGCTGTAGGTCACCTGAGGACCAATGAGAGTACCGTTTCGACTACCTAGCATAATTGGGCAAGGTTAGCACCTAGTAGCAAAAAAAAAAGCTACAAAATGCATGTATCCAAAATTCCAAAAAAATTGCCATATGTTTATATTTCATGGTTCAAACGCACAAAAGAAGTTGACTGATCCCAGAATATGTTGACTCACCGGTAATCCTAGCGTGGAAATCAGTATTGTAGCTGTTCTTAAGACCATACGATGGAAGAACATTCTCAGCATAGCTTGAAGAGTAGTAATTAAGTCCAATGAAATCAAATGCACCCTTGACCATTTCAGATTGCTCTTTGGTGAACTTTGGCAAGCGATTTCCAACCAATTCTCTCATGTTTAGGGGGTAGTCCCCTCTAATGAGAGGATCCATAAGCCATCCAAGCACGAAATCTAGAACACGTCTTGCTGCATCCTTGTTGGTTTTGGATGGGGAGAAGGGAACATACCACTGTGAGTTCACAATTATTCCAATCTTCCCCTTTTGTAAGGCCTGCATTTGTCAAGCATTTTGTTGTTCCTTTTGATTTGAAAAACAGAATTGATTCTACTAAGCATTCAATCTGCATGCATGGTCAAAGGTTTTGTGTTCCCTAAAAATAATATTAACAACAAATGTATAACAATCATGTTCAAATTATAAGGCCTTGAACGTATTATCATGTAGCAGTAAATTGCAGAAGCTTTGAATATATCACTGGACTAGAATATGCATGTCTCCATTTCATAATATGCAGGATATAAATTAGCGCTGCAGTTAATAAAGTAATTAGCTAGTCAAGTTACCCGCAGAAATTGTGAGCTAGCTATCAGAAACATTTGTGATGTTGGATACTGATATGTGTTTGAATTTGAAGATAACTTAATGGGAGATGTTTTGCTTTTTATGAATTTATTGCTTTTCTTATCAACTCTAAAGTCTTTCATTGAATTTAGCATGAAAATAATAAAATAATAGGAGTATATCTTTAACCTAACCAACAGATCCAGACCTTTGTATTAGGAGGACCGAGATTAAGGCATGATGTTTTGTTTTTATGTGAGAAGGTCTTGTATAATACATAAATATTTTCTCTGACCTATTTTGACCTCTCTAACTAGGGCACATAACACATTGGGATTAAGTGCCAATTTTTATTGTTTTTTTTGTGAATTCTAGAATTTCTTTCCTTTTTTTCCTTATCAACTACTACTAGTAAAGGTTAATGTCTGTACTGGCAAACTCTACCACCAGGACCTGGCTGAAAGTGAATGCCAAGCAATAAGTAATTTTGGATTATGAAACTTAACTTTGCGGATCTTCGATGTAAATCATTATCATGGATGAACTGCGACTGCCTGACAACTTCTTCAGTGAACTGATATTTCTCTCTGTACAACCGAACAGTTTCTGCGTGGGCAAGTAGTTGGTGATGGCATGCAGTGTAAGGCTCCCTTCCTGAATCTCCAACGCTGCATTTTCCCATCTCCCAGGGTGAACACCGGCCCGGGGCATAGGTGCCAGATGCATAGGCCTTAGAGCAGAAGATCCAAGGCTCATTGAAGGTGATCCAATGTTTCACTCGGTCACCAAACTCTTTGAAGCAGATTTCAGCATAGTCCTTATAGTCATTTATGATATTAGGGCTAAGAAATCCGTTGTATTTATCTTCCAGTGCCAAGGGATGGAGCTAATGGTTTCCACAAGTTGCATCTAGCCACTGAACTTGAAACTAAACAGTGAAGATTAGACATGAATGCCTTTCAATAATAGCTCATTGATCAAATTGTTGTAGTAGTTGATGCCTTCTATGTTGACTCCACCATTCAGACTTCCATTTGGAAGAATTCTTGACCATGAGATGGAAAACCTGTATGCATCCATTCCCATCTCCTTCATCATGTGCACATCTTCCTTGTAGAGATGGTAGGTGTTGTCAGCCACATCCCCGTTGCTTTTGTCAGCGATTTTATCTGGATGCTGATATGTGAAGGTGTCCCAGATGCTTGGTCCTCTGCCCCCCTCTGCTGCTCCACCCTCGCACTGATAGGACGCGGAGGACGTCCCGAAGATGAACCCCTTGGGGAAGCTTCTCCGGCTAATCGGCGGCAGCTCGCCGGCTTCGACGCAGGCGGCAGCTAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGAATACCGCCGGACATCGCCACTGCCCCGGCAACCGCCATCTGAACGAAGCTTGACCTGCAATTCTGCAAAAGAAAGAGT

Coding Potentia
Explanation CPC Score
noncoding -1.22709
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0266800.3 4 23717180 A T
Osa04LNT0266800.3 4 23718355 A G
Osa04LNT0266800.3 4 23719966 T C
Osa04LNT0266800.3 4 23720471 A G
Osa04LNT0266800.3 4 23720507 T C
Osa04LNT0266800.3 4 23721170 T G
Osa04LNT0266800.3 4 23721275 A 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
Osa04LNT0266800.3 osa-miR5528 Cleavage 5.0 14.096 1 21
Osa04LNT0266800.3 osa-miR397a Cleavage 4.0 18.655 1 21
Osa04LNT0266800.3 osa-miR397b Cleavage 2.5 18.655 1 21
Osa04LNT0266800.3 osa-miR530-3p Translation 5.0 16.821 1 21
Osa04LNT0266800.3 osa-miR1428a-3p Cleavage 5.0 10.924 1 21
Osa04LNT0266800.3 osa-miR1438 Cleavage 4.0 18.289 1 22
Osa04LNT0266800.3 osa-miR2097-5p Cleavage 4.5 14.754 1 22
Osa04LNT0266800.3 osa-miR2866 Cleavage 4.0 15.459 1 20
Osa04LNT0266800.3 osa-miR812o-3p Cleavage 4.0 13.423 1 24
Osa04LNT0266800.3 osa-miR5083 Translation 5.0 12.832 1 20
Osa04LNT0266800.3 osa-miR5486 Cleavage 4.5 14.099 1 21
Osa04LNT0266800.3 osa-miR5524 Cleavage 5.0 15.063 1 21
Osa04LNT0266800.3 osa-miR5524 Cleavage 5.0 17.182 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0266800.3 4 qChla4-1 Morphological trait Shoot/Seedling C2807 RM241
Osa04LNT0266800.3 4 qChlab4-1 Morphological trait Shoot/Seedling C2807 RM241
Osa04LNT0266800.3 4 qPH1-4-1 Morphological trait Dwarf RM241 C2807
Osa04LNT0266800.3 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0266800.3 4 qDLR4 Resistance or Tolerance Other soil stress tolerance RM3524 RM3866
Osa04LNT0266800.3 4 qDLR4 Resistance or Tolerance Other soil stress tolerance RM3524 RM3866
Osa04LNT0266800.3 4 d11 Morphological trait Dwarf nan nan
Osa04LNT0266800.3 4 nan Resistance or Tolerance Other soil stress tolerance RM5586 RM3916
Osa04LNT0266800.3 4 nan Morphological trait Culm/leaf RM3337 RM3785
Osa04LNT0266800.3 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0266800.3 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