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

>Osa02LNT0152300.3

AAACTTTTATTATTCACTAATAACGCTCGCAAGGAATAGCACAAATGAAATGATACATAGCTCGCACAAAGTGTTGTCTTGCAGATTGCATCAAAGAAACATTCTGGATCCAGCAAGCATACTTTTACCCTATGTACTCTTGTGTAAAATATGGATCCTCTTTAGCTAATCAAATTCAACCTCAACGAGAAGGGAACATCCCCCTGAGAATCCACAGTAAGGACCTATGTGTGTAAAAAGGTACAAAATTTTCTATCTCAAACAAGGACAAAGCGATGACTAATTTCTGTGGGTTTTATCGTCGGATATGCCGATCTTAAAGCACGCCCAATGATTATACAAGTGGAGGAAAACGGCCTTCACATAGTTTCAGTAGGAGTCAGCAACCTTTACAAGCTGAATCAGTGTATCAGGTTGCTGTCCCGCTGATTCACTATTGGTCAGGAGTCAATAACTTGCTCAACTACAGCTTTTATGCTGATGATTCTTCGTTGTTCGTACCCCACTGTTCCTCGGTATCATTTCCGTTCACAAGGACAGCACCATCAGTCGAACCATCAGCTTCAACATCAACCTCAACAGCATCTTCTTGGCTCTCTTCTACTCCATTTTCCTCAATAGCCTCGTGAGTGTCATCTCCATTTTCATCTGGCAGCACCTCCTCTAGATGTATATGCATACTTTTGAAAGCTTCCACCAGAGTCTCATTGGGCCTCTCAGCATGGATAATGTACTCCTCAGCTGGTGGATAAATACCCCTTTTGGGCGCGACATTAGCTTCTACATTGAGAGCAATTTGCCAGTCTTCAAACAAGTTTGGGTACTCGTCAGGATCTGCCAATGATTCTGCTGCTTTGGGGTTTACCTTTTGGAGATCCTTTTTCCATAATGTTACAATCTCAGGGACTTTGCTCGGAAGATAAGATCTCGACATCAATGCTGCTTCTGGTATACGATTACTTTCGATTAACAACTGAAGGCATTCTTCAAGTTTTCCTAGCATGAAGAAACAAAGGAAAGCAACATTGTTCTTCCCTTGTTCTTTAGCCATAGATGTTAATTTTGTTAGCCCTTCAGCATCACCAAGGGATGAATACAGAAGTAATAAACCACTGAGGTCCATAGCATGTAGAAGACACTCCTCTGCCATATCAAGCTTTCCGGTTGACATAGCTAACTCTCCTAACTGCCTCCACTTGGACTCACTTTGTGCCTCAATGGCAATTGCCTTTGCAACTTCAAGCCGACCAAGCTGCACGGCCAAGTCAAATCTGTAATTAGAGTCTGTTGCTATCTCAAGGGCTTCTTCCAACATGCCCTGTGATTCCAAGAAACGTGCCACACTGTCATGTTGTTCTTTTGGTATAGATGGTAAAAGAGCGTTTGCACGATCGAAGTCTCCACGCATTACAAGTGTTTTATACTCAATCATGGTAAGGAGTAAAGTATACCCCACAACATTAAATTGCTTGTCAATAAGATAGACACGGCTTTGGTTAGCAAGATATCCCAGTAAATACATTTGCCGATCCAAGTGAAATAAGGTTGTGACCTCTCCTCCTACACAGTAATTAAGCCGTGACGAAGAATTGTTGTAGATAAAACAATCACCAACCCATAGGCCAGTTCGGATGCGTTCATTGATCTCATGAAGTAGTTCAAAGGCATCTTCCACACCTTCCTCGCCAACTGAACCCCCTCCATCCAAATGAGAAGAAACTACATCCCTATTGTACTTCAAAATGTAGAATGAGGTGTCACTTGCAATTGTCACTAAATCACCACTATCGGCCCAATAGAGATTTTTCACATTGACATCAATTCTGCGTATCATCCTGCCCTCTGCCCAGTCATGGAAGCAAATAAAATCATTTGTACACATAGCCAGCAATACTCCACCAAATATACGTTCTGCAGAAAATGGTGGTCTTATACTCTTTCTCTCCTGGAAATTTTTACTGTATATCTTTATCCTCGACGTGCTTTCTCTGACAGCATATTCTCCATCAACTGACCAAACAAATTCAAGTGCAGACCCGAATGATCTATTTCTCCATGCTAATGCAGTGTAGATTATGTATTCTCCATCTCCACATACAACAACAAATCTCCCATTCGGATTGTGCCTTAAGCTTTGTGGATAAAGATCACAGGTTCCCAACTCCTTCACAGCTAAGGGTAAGCGCTCACCATCTGCAATCTCATTGTCTGCACCAATAGTCTTGATATTAACAGTTTGGATTTCATTATGTTTTGACCATATGATTTTTCCACTGCTGTCCATGCTAGCAACAGGAACTTCACGACCAATTTTTATCATTATTGTCCCTTCATCATAT

Coding Potentia
Explanation CPC Score
noncoding -1.1445
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0152300.3 2 6132430 T G
Osa02LNT0152300.3 2 6121209 G A
Osa02LNT0152300.3 2 6132016 A T
Osa02LNT0152300.3 2 6123629 A G
Osa02LNT0152300.3 2 6136851 C A
Osa02LNT0152300.3 2 6119192 T C
Osa02LNT0152300.3 2 6119753 T G
Osa02LNT0152300.3 2 6120003 A T
Osa02LNT0152300.3 2 6120631 G C
Osa02LNT0152300.3 2 6121117 T G
Osa02LNT0152300.3 2 6121416 C T
Osa02LNT0152300.3 2 6122911 C T
Osa02LNT0152300.3 2 6123043 A C
Osa02LNT0152300.3 2 6123204 G A
Osa02LNT0152300.3 2 6123635 A T
Osa02LNT0152300.3 2 6124065 T C
Osa02LNT0152300.3 2 6124147 A G
Osa02LNT0152300.3 2 6124343 A T
Osa02LNT0152300.3 2 6125004 A G
Osa02LNT0152300.3 2 6125125 T C
Osa02LNT0152300.3 2 6125200 A G
Osa02LNT0152300.3 2 6125752 T A
Osa02LNT0152300.3 2 6125893 A C
Osa02LNT0152300.3 2 6126270 A G
Osa02LNT0152300.3 2 6127402 A G
Osa02LNT0152300.3 2 6127448 C G
Osa02LNT0152300.3 2 6127648 T C
Osa02LNT0152300.3 2 6127940 C T
Osa02LNT0152300.3 2 6128892 C G
Osa02LNT0152300.3 2 6128909 A C
Osa02LNT0152300.3 2 6129014 A G
Osa02LNT0152300.3 2 6129467 T C
Osa02LNT0152300.3 2 6129599 G T
Osa02LNT0152300.3 2 6129803 G A
Osa02LNT0152300.3 2 6129891 A G
Osa02LNT0152300.3 2 6130701 A C
Osa02LNT0152300.3 2 6131153 A G
Osa02LNT0152300.3 2 6131184 A G
Osa02LNT0152300.3 2 6131275 A G
Osa02LNT0152300.3 2 6131465 A G
Osa02LNT0152300.3 2 6132526 C T
Osa02LNT0152300.3 2 6133316 G A
Osa02LNT0152300.3 2 6134556 A T
Osa02LNT0152300.3 2 6134868 C A
Osa02LNT0152300.3 2 6135138 A G
Osa02LNT0152300.3 2 6135227 A C
Osa02LNT0152300.3 2 6135237 G T
Osa02LNT0152300.3 2 6135564 A C
Osa02LNT0152300.3 2 6136497 T G
Osa02LNT0152300.3 2 6133188 G C
Osa02LNT0152300.3 2 6123703 G A
Osa02LNT0152300.3 2 6135116 A G
Osa02LNT0152300.3 2 6122863 G C
Osa02LNT0152300.3 2 6126867 T C
Osa02LNT0152300.3 2 6136426 A T
Osa02LNT0152300.3 2 6133939 A C
Osa02LNT0152300.3 2 6121195 A G
Osa02LNT0152300.3 2 6121109 A T
Osa02LNT0152300.3 2 6119346 T G
Osa02LNT0152300.3 2 6119553 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
Osa02LNT0152300.3 osa-miR5541 Translation 5.0 19.21 1 21
Osa02LNT0152300.3 osa-miR5812 Cleavage 5.0 17.529 1 24
Osa02LNT0152300.3 osa-miR530-3p Cleavage 4.5 15.076 1 21
Osa02LNT0152300.3 osa-miR2099-3p Cleavage 4.5 17.692 1 20
Osa02LNT0152300.3 osa-miR2931 Translation 5.0 19.235 1 20
Osa02LNT0152300.3 osa-miR164c Translation 4.5 12.519 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0152300.3 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0152300.3 2 qEML-2 Morphological trait Seed R2344 R712
Osa02LNT0152300.3 2 tms5 Physiological trait Sterility nan nan
Osa02LNT0152300.3 2 nan Resistance or Tolerance Drought tolerance RG83 RG171
Osa02LNT0152300.3 2 qLER-2 Morphological trait Culm/leaf R2344 R712
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