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

>Osa04LNT0275600.1

CACCGGTGTATGAAAAAATGAATTTAAACAGGGAGAAGCGACAGTTGACTCTGGCATCTTTAGGACCTGACTAACAAAACAAATCAGCTGCACCTGCATGAGGAGAATTTCATGTACAATATTGTGGTACCTTGGGCCTAGTTTGAAATTATTTTTTCCAAAACTTGAGTTGAATCTTGAAAGCTTGTAAGCAATCCCTTATTTAGGGTGATTTCTGTTTTCCTGCAACTGATAATCGTCTGGAAGGACCATACATTGGAGTTTTCAGCAGCACACACTGAAGAGCACTTCGGACGCCGTCCACATGTCATATATATCATTCTGAGGTGTCATCCGCTGCTCAATAATATCGGATCGGCTACCAGCAAATAATTGTGCTATTGTCCCAGGAATATCTGAAAGTACGGTATTAGTTTGACTGCCTTTACTTGTTAGATTGCTGGGGGGTAGGATCATGGCATTTCATTTTGCAGATTGACGTGCCAACCACTCTGATCTGGTTAAACCACAGTACCTTGTGCTACTTCCAGGCCACATAAGGAAATTCCAGCCAATGGGAGATCCACCGACAATATAAGATCCTTGCAAACATTGTCCTGATTTCTTTGTAGAATCTGTTACACTCGGTTTGGCATCATGCTTAATGTCCACAGGATTGAGTGGTACCTTCTCACCAGAACTATGCATAAAGGATGCAGCCTGGTCTGCTGGACGAACTTGATTCTTCTCTCCGGGTGGGATTTTCCCTGCAGGCATATTTCTGGCATCTCTTGATGTAGGCTCATCCATCAGTTTTACAGGCCCAGCTGCAGTTGGGAGATCAAGTCGCATTTCCTTGGATAATTCCATGAGAACTTTTATCTCTTTCAGGATCTCAAGAGCGGCATCTTTCTTTTGGGTATCAGTGCCTTTGCATAACTTCAAAACAACAAGGAAAAAGTAAACATTTTAGAGCGGATTCATGTTCTTCCCAGAACAAACTGCATTTACAATTGTCAAACCAACAGCAAGCAGGGATATCAATTTGGTGTAAGTTATGATACAATAATATGATTTTTCTCTGGTCCTTGGGAGGTAGAGAGGTATTTTTAGTGTTAATCGGGAAGTATAGTCTCTACTGAGAGCGAGGTATACCTCTTGATTAACAATATGGGGTAAAACTCTCAATACCTCCCAAAGCCACACATCAGCCATGAAAATGTTCATTTGCATAGTAGGACAATGGTGGCATTAACAACTCAGTTCAGAATCATCACACCATAAATTTCAGCTAGAAAGAGATTACGCGCCTAATTGTATTGAGACTTGGCCCAAAATTCAACTTCAACTTTAATTTAAATTCTCCCAGAGTTTCACCAGCAAGCACAGCACGGAGCAAATAGCTTCGAGCTCTCGAACTCGAACCATTGATCACACTTATCCACGTCAAGCAAAATCATCCCATACACGTTGCGCTAGAACACGGGAACATGACCTGTTCAGTTGATTGTGCTGCTGCTGCTGCTGCTGCCATGGCAGAGCAGAGAAATGCCACTCAACAAATATCTTAGGGTTCGAGGTGGGGGAGACCTGAATGAAGCGGCCGCGGAGGTTGGCGACGGCTGCTCTGATGTTGTAGTAGGGTGAGTGATGAAACCCCACCTCCTCCAGCTTCCGCTTCTTCGGTGCCGCGGTCGAAGACGTCGGCGGCGGAGGCGGGGGCTTTGGGTCGCTGGTAGGCGTGGACTCTGACGGCGGCGGCGGAGGAGGAGGCGGGGTGGTGGTCGTCGGAGCGACCATCGCGGTAGCGGCGGAGCGTGGGGTTTTTCTGCAACCTTCCCT

Coding Potentia
Explanation CPC Score
noncoding -1.13388
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0275600.1 4 27863858 T G
Osa04LNT0275600.1 4 27865762 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
Osa04LNT0275600.1 osa-miR5537 Translation 3.5 15.541 1 22
Osa04LNT0275600.1 osa-miR5791 Translation 3.5 16.254 1 21
Osa04LNT0275600.1 osa-miR2873c Cleavage 5.0 9.945 1 21
Osa04LNT0275600.1 osa-miR166a-3p Cleavage 4.0 24.269 1 21
Osa04LNT0275600.1 osa-miR166b-3p Cleavage 4.0 24.269 1 21
Osa04LNT0275600.1 osa-miR166c-3p Cleavage 4.0 24.269 1 21
Osa04LNT0275600.1 osa-miR166d-3p Cleavage 4.0 24.269 1 21
Osa04LNT0275600.1 osa-miR166f Cleavage 4.0 24.269 1 21
Osa04LNT0275600.1 osa-miR166k-3p Cleavage 5.0 24.269 1 21
Osa04LNT0275600.1 osa-miR166l-3p Cleavage 5.0 24.269 1 21
Osa04LNT0275600.1 osa-miR166g-3p Cleavage 4.0 24.269 1 21
Osa04LNT0275600.1 osa-miR166h-3p Cleavage 4.0 24.269 1 21
Osa04LNT0275600.1 osa-miR166i-3p Cleavage 4.5 24.269 1 21
Osa04LNT0275600.1 osa-miR166m Cleavage 4.0 24.269 1 21
Osa04LNT0275600.1 osa-miR166j-3p Cleavage 4.0 24.269 1 21
Osa04LNT0275600.1 osa-miR5081 Translation 2.5 11.438 1 22
Osa04LNT0275600.1 osa-miR5156 Translation 5.0 19.538 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0275600.1 4 pss4.1 Physiological trait Source activity RZ740 RZ590
Osa04LNT0275600.1 4 qCTS4-3 Resistance or Tolerance Cold tolerance RM241 RM317
Osa04LNT0275600.1 4 nan Resistance or Tolerance Other soil stress tolerance RM5586 RM3916
Osa04LNT0275600.1 4 rfw4a Resistance or Tolerance Drought tolerance RM349 RM1136
Osa04LNT0275600.1 4 gpp4 Morphological trait Seed RZ569 RZ565
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