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

>Osa12LNT0126100.4

GCGTGCCCTCCCCGCTCCCGTCTCGCCCTCCCCTCCCTCTCCCTCTCCCGCCGAAGCCGCCGAGCGCCACCTCCGCCTCCCCCTCGCGCCGCCGCCTCCACCTCCGTTGCCGTCGCGTCGCCGCCGCCTCCGCCTCTACCTCCCCCTCGCGCCGCCAGCTCCGCCTCTGCCTCCTCTTCCTTCCCCTCTGCCTCGCGTGGCCGTCGCCGAGTGCGCCACCTCTGGCTCACGCCGCCGCTGCCGTCGTCGCTGTAGAGGAGGCGGATCCGACCTCCATGTGTTTGGGGGACGCGGATCTGACTGACGCAACGTCGTCATCCGCTGTCGTCGCCATCGCCGAGCGTCACCGCTGCATCCTCCGCCACACCTCCGTCCTTCACCGCCAAAGACCGCTATGAGCGGTCGACCTGGGGTGGAGGCGTGGAGCCGGCCGCCATCGCCGCAACTTCATGGCATAGGGGACGGTTGTCCGTCGATTTGAGGAGTGAGAGGCGGCAACAGCAATAAAGAGGGGAGAGGCCTGCCGGCGGCTGTATGGTGGAGAAGCGCCGCCGCAGCCCGCATCCCCTCCTCTCGCCCCTCCCTCTCCCACCCGGGCGATTCGCAAGCCGCCGCTGCCACCGCTCTCGACCGCCATCGCTGCCGTCTCATGGGCTCCAGGAACCGCCGGCGGGGGTGATCTTGACCTCGACCTCAGCCTTGGCTGCTTCAATGTGGGGATAAGTGGAGCTCCGTCCTGGAAGGGTGGAGGCGGGAGATGCTCTGACCATCGGCGGCTGGCATCAGCATCAGATCCAGGCTGCGGTGGCGCGGATCGAACGTAGAGGCGTGATCTGATGACGGTGGTGGAGTTGCAACCAAGGTCGATGGGGATGTCGAGGGCGTTGCTGATGAAGAAGCACCCCAGTTAATGATATGGCTCGCTTCTCTGGCTCGAGGGCGTTGCGGATGAAGAAGCCCCATGCTCTGGCTCAGGCTCCGCTACGGGGTTACCATACCGTAGATTATATTGTCAAGATGCACAGGACATAATGAATAAGTTCAGCACGCCGCAGACACGTCGTGGTCAATTCCTCATCGGAAGTATTGCTTGGTGCTTGTGTATTTTTTCCGCATAGAAATAAGATGGGATGGATTTTTTTTCTCCACAGATTATTTTATATGTTTCTAAGAATAGGAATATGAAGTGGAAAATATGGCATGTGTTCTGTATGCTAATAATCTAATAGAGTGGATCAGGTTGGTTCGAGTTTGTTTGCAAGGCAAACCAACATTACCTACATAGATGGCACCGTGATAATCATGGAATTGTTTCTTCTCCTTTTTACATGATCCTGTAAATGAAAGGAAGGTACTACTGATTTATTGGATGATCTTTCGTGACTTGCGGCTAAAATGATGGTGTAGTTTTAATCTCTGTATTCCCGTTTCATATCATAGAAAAAAAGAACTAATGTGGTTAAAAGGTGAGATATTGTATTTTTGTTGAATGTTTATAATCTCTAATAGGTTTATTTTTCTGGTTTTGAGGCTTGTGGGCCTAATATACCTTGAGACAGTGGCCCATGGCTGATAACCGGAAATGAGTCATGACTTACTGCTGGGACTTATCGAAGATCCTGTTTTGAGATAAATATGATTTCATTTCAGGTGGAAGTTCTGTTATTCTAAAGGAATCAGCATCTGCCTTCTAGAGGTGAAAAATGTATAGTCCTAATTACTAAGGCATTGTTTGATGTCTGCCCTTCTAGAGGTGGAATGTACAATCCTGGTTGCTAGGGCATAGGATGATGTTTCTTTTATTTGGCTTGTCCTGTGTTTATCTGGTTAAATGTCAAGAAATGTGCCATGTGCTATTGTCTCCCATGAAACATTGAAAGAAGAAGGGTTTATAAGGCGGCCCTATACATTAGGTCTTTAGATGTAGTATCCTTTCTTTGACAAGCTCTGATGGCCTACAAAAACCGGCTCTCACACCATTAGGTAATGTTATGTTTCCATTAATTTTACTGGGATATTGCATTACTTGGGATAATCACATGCATTTCCATGGCAATTTAAGGTCTAGCAAGAAAATAGTTTACTAAACGGACCAAGATAGAATTTCAAGTCTTACGAGTAAAAGTTGGGATGATCTGGTTTAATGCTATAATTTGTATGTACCAAATAATTCCGTAGACATCCTGAATACCTAAGTACTTTAAACATTTTCGTATGAAGAGTTGTTAGGTCTGCTAGCAGCAGTACGCTATTACTTCAAGTTAATCACTGCATGAATTTCTGTTTATGGGAATCTTGAGATTTACAATACATTTGAATGCTTACATTATATGTAGCTAAATAAACCCAACTAATGGAGGGTCAGTTCATTTATTTATCATGCAAGATTGTTAGTTTAACTATGTCAGATTTGCATAGGGTTCAGGGTTTAGGGACCTCATTAATAACCTCTACCACCATCTGAACCTAAAGATTTTGCATGCTCTGGTTGCAGCTTCAACCATTCCTTGGGTTTGCTTCTTATAATTGATGTATAATTTATTTTTGATTTGGTATTATTTTCTATAGTGACAACCTGTACTAATTACAGATCTAATATTGTGCCTCAACCTCACATGTTGAATATGTTGGCTTACGTCAGTTAGACCTCTACGTAGAAAGCATCAATGGTTGTGAGGCCTACTGATTTCTCTCTCACTCTAAGTCCGAGAAAAATATTGTCGTGTTGATGCTACTTCCAAATTTGAGCATACTAAGATGCACTGATGAACATGGTACTGTTACATTACTCTAAGATGTGATTTCAGGCTCATGGTTCTTCGTATGGTATAAGTTGCAGGTATTGAAGTGCTGGGCTGGAAATTCTCACAAATGCTAGGACACCCAGCAGCACTGCCACAACAAGTCAGCAATCAAAGTCTCCATGCGCATGTGCATGCTGCTGAATGAGTGCAAGGATATTTTTGAGGCTTTGTACAAATTATTTATGATCTACGCACCTACTTGAAGCCACATGTTGAAATTAATATATTGATGTTGTATCATCACAGAGGCGGTCTTTCTTAGTCTTCAATATTTTCTTAGAGCTAAACGGTTATATTTTTTTTGGTGTCTACTTAGCAACAATGCCATCTCTTCAGTTATTGCAACTGACAGAGCATGGACACAACCTTTTGTCTTTGAGAAGTTGTTTCTGGTGTATTACTTGCGGGTGGAACTTTAGCGTATGCTCAGTCAGCTCGGCGCCAAAAATGTCAGGAAGAATATTCTCATAGTGATGCAAATACATAGACCACGAGTAATCAGATCATTTGTCAAAATGGTGTTGATGGTAAATTGGTAAAATCAAGGAAAAAGAAAGATGGCTCCTCCCATTGAATTCAAGTGTTGAAATATGTGATTCAAGTATTCTGATTGAATACTTAAATTCAAGTATTCAAAGGTCTTACCAACATGTTATCTGAAAGAGCACTGAATCTAAACCATAGAACTTTATCATTTGAAGGTTGTTCAAGTTACTATGAGACCTGCCAAGCAATCTGCGCTGGTGCTACAAGATTGCATATCCACATGTTTATGTAGTTCACATTTGTTTCCCAAGTGGTGAAGATATTCAAATCTATATGTCGTTACTACACAGAATTGTTCAAGTCAGTAGTGTAAAACTAGCTAATTATATTCAACCAGCTTCAATTTTCTTACC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.180296
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa12LNT0126100.4 12 12835667 G T
Osa12LNT0126100.4 12 12836516 C T
Osa12LNT0126100.4 12 12836639 T C
Osa12LNT0126100.4 12 12834567 A G
Osa12LNT0126100.4 12 12834623 T C
Osa12LNT0126100.4 12 12834859 C G
Osa12LNT0126100.4 12 12835616 C G
Osa12LNT0126100.4 12 12836285 C T
Osa12LNT0126100.4 12 12837475 G T
Osa12LNT0126100.4 12 12837577 T G
Osa12LNT0126100.4 12 12837684 T C
Osa12LNT0126100.4 12 12838086 T G
Osa12LNT0126100.4 12 12838199 C T
Osa12LNT0126100.4 12 12838399 A G
Osa12LNT0126100.4 12 12838698 T C
Osa12LNT0126100.4 12 12839011 A G
Osa12LNT0126100.4 12 12834077 A G
Osa12LNT0126100.4 12 12835468 T 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
Osa12LNT0126100.4 osa-miR5807 Translation 4.5 10.088 1 24
Osa12LNT0126100.4 osa-miR5812 Cleavage 4.5 16.556 1 24
Osa12LNT0126100.4 osa-miR5821 Translation 5.0 22.059 1 21
Osa12LNT0126100.4 osa-miR399k Cleavage 4.5 15.936 1 21
Osa12LNT0126100.4 osa-miR528-5p Translation 4.0 11.589 1 21
Osa12LNT0126100.4 osa-miR528-5p Translation 4.5 10.459 1 21
Osa12LNT0126100.4 osa-miR1426 Translation 5.0 13.644 1 21
Osa12LNT0126100.4 osa-miR1855 Cleavage 5.0 18.443 1 21
Osa12LNT0126100.4 osa-miR1861n Cleavage 4.0 16.073 1 22
Osa12LNT0126100.4 osa-miR1866-3p Translation 5.0 19.047 1 22
Osa12LNT0126100.4 osa-miR1874-3p Cleavage 4.5 15.279 1 24
Osa12LNT0126100.4 osa-miR2093-5p Cleavage 4.0 13.278 1 20
Osa12LNT0126100.4 osa-miR2122 Cleavage 4.0 21.591 1 22
Osa12LNT0126100.4 osa-miR2920 Cleavage 4.5 10.986 1 23
Osa12LNT0126100.4 osa-miR5490 Translation 4.0 13.556 1 21
Osa12LNT0126100.4 osa-miR5490 Cleavage 5.0 12.302 1 21
Osa12LNT0126100.4 osa-miR1851 Translation 5.0 18.09 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa12LNT0126100.4 12 nan Physiological trait Eating quality RM247 RM179
Osa12LNT0126100.4 12 qtl12.1 Resistance or Tolerance Drought tolerance RM7195 RM28166
Osa12LNT0126100.4 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG241
Osa12LNT0126100.4 12 qtl12.1 Resistance or Tolerance Drought tolerance RM7195 RM28166
Osa12LNT0126100.4 12 qDLA-12-3 Resistance or Tolerance Blast resistance RG463 RZ816
Osa12LNT0126100.4 12 qtl12.1 Resistance or Tolerance Drought tolerance RM7195 RM28166
Osa12LNT0126100.4 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG241
Osa12LNT0126100.4 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG241
Osa12LNT0126100.4 12 nan Morphological trait Seed RG543 RG81
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