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

>Osa02LNT0152300.1

AAACTTTTATTATTCACTAATAACGCTCGCAAGGAATAGCACAAATGAAATGATACATAGCTCGCACAAAGTGTTGTCTTGCAGATTGCATCAAAGAAACATTCTGGATCCAGCAAGCATACTTTTACCCTATGTACTCTTGTGTAAAATATGGATCCTCTTTAGCTAATCAAATTCAACCTCAACGAGAAGGGAACATCCCCCTGAGAATCCACAGTAAGGACCTATGTGTGTAAAAAGGTACAAAATTTTCTATCTCAAACAAGGACAAAGCGATGACTAATTTCTGTGGGTTTTATCGTCGGATATGCCGATCTTAAAGCACGCCCAATGATTATACAAGTGGAGGAAAACGGCCTTCACATAGTTTCAGTAGGAGTCAGCAACCTTTACAAGCTGAATCAGTGTATCAGGTTGCTGTCCCGCTGATTCACTATTGGTCAGGAGTCAATACCCACTGTTCCTCGGTATCATTTCCGTTCACAAGGACAGTACCGTCAGTCGAACCATCAGCTTCAACATCAACCTCAACAGCATCTTCTTGGCTCTCTTCTACTCCATTTTCCTCGATAGCCTCGTGAGTGTCATCTCCATTTTCATCTGGCAGCACCTCCTCTTGATGTATACGCATATTTTTGAAAGCTTCCACCAGAGTCTCGTTAGGCCTCTCAGCATGGATAATGTACTCCTTAGCTGGTGCATAAATACCCCTTTTGGGCGCAACATTAGCTTCTACATTGAGAGCAATTTGCCAGTCTTCAAACAAGTTTGGGTACTCGTTGGGATCTGCCAATGATTCTGCCGCTTTGGGGTTTACCTTTTGGAGATCCTTTTTCCATAATGTTACAATCTCAGGGACTTTGCTCGGAAGATAAGATCTCGACATCAATGCTGCTTCTGGTATACGATTACTTTCGATTAACAATTGAAGACATTCTTCCAGTTTTCCAAGCATGAAGAAACAAAGGAAAGCAACATTGTTCTTCCCTTGTTCTTTAGCCATAGATGTTAATTTTGTTAGCCCTTCAGCATCACCAAGGGATGAATACAGAAGTAATAAACCACTGAGATCCATAGCATGTAGAAGACACTCCTCTGCCATATCAAGCTTTCCGGTTGACATAGCTAACTCTCCTAACTGCCTCCACTTGGACTCACTTTGTGCCTCAATGGCAATTGCCTTTGCAACTTCAAGCCGACCAAGCTGCACGGCCAAGTCAAATCTGTAATTAGAGTCTGTTGCTATCTCAAGGGCTTCTTCCAACATGCCCCGTGATTCCAAGAAACGTGCCACACTGTCATGTTGTTCTTTTGGTATAGATGGTAAAAGAGCGTTTGCACGATCGAAGTCTCCACGCATTACAAGTGTTTTATACTCAATCATAGTAAGGAGTAAAGTATACCCCACAACATTAAATTGCTTGTCAATAAGGTAGACACGGCTTTGGTTAGCAAGATATCCCAGTAAATACATTTGCCGATCCAAGTGAAATAAGGTTGTGACCTCTCCTCCTACACAGTAATTAAGTCGTGACGAAGAATTGTTGTAGATAAAACAATCGCCAACCCATAGGCCAGTTCGGATGCGTTCATTGATCTCATGAAGTAGTTCAAAGGCATCTTCCACACCTTCCTCGCCAACTGAACCCCCTCCATCCAAATGAGAAGAAACTACATCCCTATTGTACTTCAAAATGTAGAATGAGGTGTCACTTGCAATTGTCACTAAATCACCACTATCGGCCCAATAGAGATTTTTCACATTGACATCAATTCTGCGTATCATCCTGCCCTCTGCCCAGTCATGGAAGCAAATAAAATCATTTGTACACATAGCCAGCAATACTCCACCAAATATACGCTCTGCAGAAAATGGTGGTCTTATACTCTTTCTCTCCTGGAAATTTTTACTGTATATCTTTATCCTCGAGGTGCTTTCTCTGACAGCGTATTCTCCATCAAGTGACCAAACAAATTCAAGTGCAGACCCGAATGATCTATTTCTCCATGCCAATGCGGTGTAGATTATGTATTCTCCATCTCCACATACAACAACAAATCTTCCATTTGGATTGTGCCTTAAACTTTGTGGATAAAGATCACAGGTTCCCAACTCCTTCACAACCAAGGGTAAGCGCTCACCATCTGCAATCTCATTGTCTGCACCAATAGTCTTGATATTAACAGTTTGGATTTCATTATGTTTTGACCATATGATTTTTCCACTGCTGTCCATGCTAGCAACAGGAACTTCACGGCCAATTTTTATCATTATTGTCCCTTCATCATATCCGATCACAACCCTTCTTGAACCCTTCATGTATCCTAAAGCCCACACTCGCTCAAGGCCATAGTTAAGAGTGTTCTCAAGCCTGTAGGTAGTAGAGTGCCACAAGCGAACTGTCCCATCCTCAGAGCCAGTAAGTATTATAGGTAACTCCGGATGGAAACAAACAGCAGAGACATTATGTGCATGTCCTTCAAGCGTTTGAACACAGCTCTTCGTTTGATAGTCCCAAACCTTCGCGGTCTGATCATCAGAGCCTGTAATTAAGTATGGGCGATCACCACCAGTAAAGTAATCAACACAATTGACACCTTTTGAATGGCCATCTAATGTGAAATTAGGATCAGGGGAACCAAGACTCCATACCTTTACTGTGCGATCAAGTGAAGCACTAGCAAAAGTATTGGTATCTTTCGGGTTAAATGTGACTTGCATAACATAGTGAGAATGCCCCTCGAAGATTTGAGTGCACATCCAACCCTGATGTAATCCGTATGAGCTTCAAAAACCTTGACCTTATCCATCGTATTGTAATTGTACACACGTATGAACATATCGTCGGCACCAGCAACTACCCATTGTTTCCGTGTGATAAATTTAGATGACCGAACTGGTAACTCTGTGACTTCAAATGATTTCACCATCGTCTGCGTCTGGTAGTTCCAGATGCAAACGCTCCCTGAATACAGACTCGACAAAATCC

Coding Potentia
Explanation CPC Score
noncoding -1.13363
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0152300.1 2 6121209 G A
Osa02LNT0152300.1 2 6119192 T C
Osa02LNT0152300.1 2 6119346 T G
Osa02LNT0152300.1 2 6119553 T A
Osa02LNT0152300.1 2 6119753 T G
Osa02LNT0152300.1 2 6120003 A T
Osa02LNT0152300.1 2 6120631 G C
Osa02LNT0152300.1 2 6121117 T G
Osa02LNT0152300.1 2 6121109 A T
Osa02LNT0152300.1 2 6121416 C T
Osa02LNT0152300.1 2 6122911 C T
Osa02LNT0152300.1 2 6123043 A C
Osa02LNT0152300.1 2 6123204 G A
Osa02LNT0152300.1 2 6123629 A G
Osa02LNT0152300.1 2 6123635 A T
Osa02LNT0152300.1 2 6123703 G A
Osa02LNT0152300.1 2 6124065 T C
Osa02LNT0152300.1 2 6124147 A G
Osa02LNT0152300.1 2 6124343 A T
Osa02LNT0152300.1 2 6125004 A G
Osa02LNT0152300.1 2 6125125 T C
Osa02LNT0152300.1 2 6125200 A G
Osa02LNT0152300.1 2 6125752 T A
Osa02LNT0152300.1 2 6125893 A C
Osa02LNT0152300.1 2 6126270 A G
Osa02LNT0152300.1 2 6126867 T C
Osa02LNT0152300.1 2 6127402 A G
Osa02LNT0152300.1 2 6127448 C G
Osa02LNT0152300.1 2 6127648 T C
Osa02LNT0152300.1 2 6127940 C T
Osa02LNT0152300.1 2 6122863 G C
Osa02LNT0152300.1 2 6121195 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
Osa02LNT0152300.1 osa-miR5541 Translation 5.0 18.826 1 21
Osa02LNT0152300.1 osa-miR5812 Cleavage 5.0 19.079 1 24
Osa02LNT0152300.1 osa-miR5837.1 Translation 4.5 13.147 1 21
Osa02LNT0152300.1 osa-miR6255 Cleavage 3.5 11.198 1 22
Osa02LNT0152300.1 osa-miR164c Translation 4.5 14.323 1 21
Osa02LNT0152300.1 osa-miR530-3p Cleavage 4.5 15.028 1 21
Osa02LNT0152300.1 osa-miR1847.1 Translation 5.0 12.613 1 21
Osa02LNT0152300.1 osa-miR1850.1 Cleavage 3.5 18.249 1 21
Osa02LNT0152300.1 osa-miR2092-5p Cleavage 5.0 14.83 1 21
Osa02LNT0152300.1 osa-miR2099-3p Cleavage 4.5 18.855 1 20
Osa02LNT0152300.1 osa-miR2931 Translation 5.0 20.487 1 20
Osa02LNT0152300.1 osa-miR2871a-3p Cleavage 5.0 12.621 1 21
Osa02LNT0152300.1 osa-miR2871b Cleavage 5.0 12.621 1 21
Osa02LNT0152300.1 osa-miR1854-3p Cleavage 4.5 10.214 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0152300.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0152300.1 2 qEML-2 Morphological trait Seed R2344 R712
Osa02LNT0152300.1 2 tms5 Physiological trait Sterility nan nan
Osa02LNT0152300.1 2 nan Resistance or Tolerance Drought tolerance RG83 RG171
Osa02LNT0152300.1 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