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

>Osa12LNT0128300.2

AAAAATTAAGCACCATTAATATTATAAAGCCAAGTTATACATTATTGTAGCGTCACACCGTCCATCGTTAATGGAATGGAAAATATTTCAGCCTTAATTGACGTCCATCGGCTAGGATAGCTCAGATGAGCACAGATGCCAGCAAAAAATGGCGGCGCTAGCTTACAGCATCTGGAGTAGCAGCAGCGTGGCCAGAAGAACGTACTCCCTGCTGCTGCTGAAGAGGGGAGGAGGAGCAAGTACTCCTACAACACAAGCATTGGTGGCAGAGCTACCTGCTGCACTCTTGGGCTCGGCAGCAGGGAGAGGTGGCTCAATGACGTCCGATGAGTTGAGCACCGGCATTGGTGCCAGAGCTGGCAGCATGCCACCAGTACTGCACTCCGCATCGAGTAGCTGCGCCAGGTCGCCAATTGGCACTTGCTTCATGGATGTAGACGTACCATCTCCTTGGCGTGTACAAGTATTCATTTTGTATCTTCTAACAGTCTTGGGGAAGTCAGTTATGAAGCCATCAACATGAACCAACTGAACATAGTTGTTGATCTCCACTGTTCCATCTGCGAAGAAATCCACCGGTGGTGATACATACTCATTGCGGAATACCTCCACATACACAGCTAACCCTGCAGACTGCACATCTTCCACAACCTTGCTTTTCCTAATAATAAAACCTTTGCTCTCGGCAAAAACAGATTCCCTGTCAACAATAACAGCATCTGCAAACTTCTTGATATCTGCTACGCAGGAATCAGAAACGTCCCCAACTTTTAACGGGAGCGAGTAGACAAGCTTGCATTGTGTTAACCTCTGCTTCAGTTTGACGAGAACAGCACTGTCTTTAGACTGAATCATAATCTCCTTGTTGTTCTTGGTAGTTGGGTCCATGTTGTCATAGCCAGCATTACTCAACGCAGTTGTTACAAGATCAACGACATCAAATCCTAATGATTTTGCCATAAATGCAGCATTCTTCATGATGATCATGATGCCGGATAAATCCTTGTCCTTTGCATATGTCAAAAAGTCGGATAACTTGAAAAACTTTCCTTGATTTGCGTACCTTGGGTTCCTTACAAAATCATGATATGGGTGGGTTATTTTCGGTCTCAAAGTGCTAATTTCTTCCCAAGTGAGGTTAAACGTGAATATTCCCGGTTTAGTCTGAATTTCTGGAACGACAGAAGCAAGTGAGCTAAACTTCGAGTTCTGAACATCTGTACTATCATACAGGTTAATGGAACTCATGCATATAGGAATTCCATCTTTGGTCATTTCGATGGAACAGTCAATGACATCTGCACCATCTCCAACTGCCTTCTCATAAGCAAGATCCGTACAGTCCGGGTAATCTCCACTAGCACCATTATGTGAGATAATTAATATATTCCCATGATCTGTTTTCCTGCTTGTGTTCAAATTAGTGAAACAGCCAATAGCCTCTGATGCAGTAAGTGGGTGATCCGTTAATACACCATCAACAGAGAAGCCACCATTGCTGACAAATGACAGATATTCCTCCAAAGGATCATAACTGTAGTTATAGGGAAAAATTCCATCGTTTGAAAAATCAGACGCATATATTTCTAAACCTGCATCGTGCGCATCTTTGACAATCTGTGTGGGAAGCTGAATATAGTTATCACTCGTCACTGGCCAGATATAGCTTTTGGGAACCATTATACCAGAAGCAATTGTCTTAATAAATGCCAGGTCACTCAGCATAGAGTCATATGTTTTGTTTGTAGAAAGATCGGAAACAGCTTTATCAAGAAAGCGGAATACTAGCTTCACTTTATGATCAATGCCTCCTGATAGAGTTTCCAGGAAACCTAGTTCAGGTGATGAGATGTACTTCACAAAGCCAAGCTTCTGTACTGAAAGAATGTAATTTGTCATGTTCAAACCATGCTCTGTGTAGAAAACATCATGCTCAACATTCAACCAAAGAGATGATGGCTCGATCGAGGACATGAAGCCGGTGACAGAAAAGATGCGGAAGTTGCAGAAATCAAATTTGTCGGTACGAGAAAAAAGTGCCTGTGTTAAAAAAACATTTGTCAGCAAAGACATGTTATAGTCCACAGGGAACCATCCGGTTTTCGGCACTCCATTGATTCTGTATGTCTGCTTCCCCCCTGGATAAACTTGGCTGATAGTGGTGCCATTCTGCATAAGTAAATCTCGGAGGCAAAAGCCAACACCGTCTTTCGTCAGTTGCACATCGCACCACAAGCTTGTGTCAGTCGAGGTAGCAGACAAGGCAAAACCAAAGGCGAATTGGCTGGAATCAGGAAACAATCCTGAAAAGCCACCTCTAGCAATAACAAGAGGAGCATTACCTGCACAACCAACAAATGCTTGTAGGAAATCACAAGGTAATTAGCTTGTGATTAGCAGGTTGAAAAAAGGACATGAACAATAAGCTAGAAGCAGGTGCCGAAAAATTTTAATTTCAGGCATGCTACTGCAAGTACAGATCGTGCTCATGGCCTTTCAGACATGGGACATAATTAACAGCATTCCCATCAAGATTTCCTGGAAAACCAACTCGCCGTCAAGGTTTTGAAGGTGGTTGACGCAAGCGGGAGCTCCGCAGCAACGGCGACAACTACGACGACTGAGAGTAGCAGGATCCAGCGGTAGGACAGCATTGTGGTGAGGGAACTGCTAATCCTGGAGAATTTTTTTCATCCAAGGCTCGGAGAAAGCATGC

Coding Potentia
Explanation CPC Score
noncoding -1.071
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa12LNT0128300.2 12 15896459 T C
Osa12LNT0128300.2 12 15894897 G C
Osa12LNT0128300.2 12 15895262 A G
Osa12LNT0128300.2 12 15895265 T A
Osa12LNT0128300.2 12 15895286 T C
Osa12LNT0128300.2 12 15895388 A G
Osa12LNT0128300.2 12 15895394 T A
Osa12LNT0128300.2 12 15895642 A C
Osa12LNT0128300.2 12 15896348 G A
Osa12LNT0128300.2 12 15896432 A G
Osa12LNT0128300.2 12 15896506 T A
Osa12LNT0128300.2 12 15896901 G A
Osa12LNT0128300.2 12 15897025 T C
Osa12LNT0128300.2 12 15897170 G A
Osa12LNT0128300.2 12 15897868 T G
Osa12LNT0128300.2 12 15897944 C G
Osa12LNT0128300.2 12 15898772 G A
Osa12LNT0128300.2 12 15897326 A G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa12LNT0128300.2 osa-miR5528 Translation 4.0 14.609 1 21
Osa12LNT0128300.2 osa-miR5528 Translation 5.0 16.639 1 21
Osa12LNT0128300.2 osa-miR5528 Translation 5.0 12.439 1 21
Osa12LNT0128300.2 osa-miR2868 Cleavage 3.5 16.329 1 20
Osa12LNT0128300.2 osa-miR3980a-3p Translation 4.0 17.432 1 21
Osa12LNT0128300.2 osa-miR3980b-3p Translation 4.0 17.432 1 21
Osa12LNT0128300.2 osa-miR5503 Cleavage 3.5 16.143 1 22
Osa12LNT0128300.2 osa-miR2106 Cleavage 5.0 16.561 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa12LNT0128300.2 12 qtl12.1 Resistance or Tolerance Drought tolerance RM7195 RM28166
Osa12LNT0128300.2 12 qtl12.1 Resistance or Tolerance Drought tolerance RM28048 RM511
Osa12LNT0128300.2 12 qtl12.1 Resistance or Tolerance Drought tolerance RM28048 RM28166
Osa12LNT0128300.2 12 qtl12.1 Resistance or Tolerance Drought tolerance RM7195 RM28166
Osa12LNT0128300.2 12 qtl12.1 Resistance or Tolerance Drought tolerance RM28048 RM511
Osa12LNT0128300.2 12 qtl12.1 Resistance or Tolerance Drought tolerance RM28048 RM28166
Osa12LNT0128300.2 12 qDLA-12-3 Resistance or Tolerance Blast resistance RG463 RZ816
Osa12LNT0128300.2 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG241
Osa12LNT0128300.2 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG241
Osa12LNT0128300.2 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG241
Osa12LNT0128300.2 12 nan Morphological trait Seed RG543 RG81
Osa12LNT0128300.2 12 qtl12.1 Resistance or Tolerance Drought tolerance RM7195 RM28166
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