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

>Osa02LNT0163600.2

ATCCACACTTCCACAAAAAATGGTTGAGAATAAATTACATGTTCCAAGCAATTCCACGACTTCTGGATCAATAACACACACGGAGCTGGCAAAATGGAGCTGGAAAAATCTAGAAGTATCACACATTGACACACCACTACAATTATAGGATAGATGAAATGAATACATTGTGAAACAACAGTCATCACTTCTTCATTTTTCCATCTCTATCATTCAGTCAAGCATATTTGATCCCTTCTATAGATTTTTATAGACTTCTATTTTGTTATCCTCTCCTGCAGTAAGCTGTGTGCATCTTTACAAAGATCAGTGCTCTCAGGGTCACTTGCTTTCGTAAGACGCAATTGCATACGTCAATTAGAGAAATCTTCAAAAAATGAACCAAAACTCCCCGCGATTACCTTCCACAATTCCACCTTTTCTTCTCTACACAAGCCTGAAACAGAGTAAACATTTGTTTTCACATGGAAAAAATTCCATCAAGCAGTTGGCCATAATGAGAAAGAGCATCCAATCAAGCTATGTATCATTTTTGCACTGCACTAAATATCAGAGATTTGCAGCATTTTTCACTGCACTAAATATCAGTAATGTAAAATATTATTAAAAAGGAAGCTTAACATAAACTTGTTAGTTTTTCTTTGAATGAATAAACTTGTTAGTTCTTACGTACATACTACATACGAACGAAAATAAGGGAGGACCAGATGTGCATTCAGTGATGGTGGCATTCATGAACCTGAGCAGTTTAAAAATGAAGAAATATACATCGCTTCAGAAGCACCAGAAAATAAGATAGAATGAACCTGAGCAGTTTAAAAGTAAACATTGCACATGGTACAAAAGCAGAAATCAATTAATTTCCGGGAGATATAATGAGCATTGCACAAAGCAATGGTTGAAAGGCATTATAATCATACAGTCCATTTTGTCAGATATTTTTAATACATACACATATTTGTCTATACGATATATAATTCTAATCATGGAAGTGTATATTTCATCGTCGATAATTAACTCACTTTTCCTTAAACTAACTCTAGAAAATCCCAATAATTAAGAATCTAATCAGAATCTGCTTGCAAGTATTTGGGTTTTTCATTAACCAATCAACCAATCGCAGCAGAGGAAATTTAGGGGGAGAGGATAAACCAAGGCAATTTCCGACTTACCTTCTGCGCCTTACCACGATGCGAACAAATCGATTCGTCAACTACAGTACAACACTAACTACCTCATCCTGATGAAGGCATGAAACAGAGAAGAGAATCTGAATTTATTCAGACATTAAACATCTGATTTTTTTTTCATAAATTCACAAATAAACTGGTAAGTTGTTCCTTTAGAGTTTAGACAATACATTGAAAGTGCTTGCACATTACTAATGCATGGCATTTTACATATTCAGGTGTCATGAATAAAAATGTAAACCAAATTTGACTTTTTAAAGGGAAAAATTATCACTGCATTCCATGTGGTTCAATAGAGCACAATTCCACAATTGAAGTAAAATCTCATTATGTATATAACCTTTCGGTACACATCACAGAAAATGTATACAACGGAAAGTAAAAGAAGCTCTCAATATTGGCATCATGATTTAGATAATTAAATTCTTCTTTTAACTTGGATGTCAATTTGGATGTTGATCTCTTAAGAGAGCACACAACATGTCTATCAATTTAATTGGTTTCCTGGGTTATGTTGTTGACCAAGCAATGAAGTTCAAAAGAAATTATCTAAATTTTCAGATATAAACATCCCAATAATGACTTACCTTGTTGGCGAGCGGATCGCAGCCTGTGCGAGGCCAGTGCCGGGGTTGAGAAATCCGACCACCGGGACTTGGAATCTCGAACTCGCACGCGGCCAGAGGAAGGGGCTGGTGCCGGGATCAACCACGAAAACAGGGCGGCATCACTAAGGCCAGATCGGAGCAAGAGGGAGGAGCGCTAAAAATCAAATGGAAGACATCAAACCCAAATCGTGCTTATAACTTATTTAAACTGTATAACTACGAGAATCCAGTTTGTGAGTATTTTTTAAGCTCTGTTGAACACATGATAACATCATAATATTGTATTCACATCATCACAATACATGATCTATTTAAATTGAGAAAATAATTTACAGAACCAAAAGCTAGTCTGCACCTGAATTGCCAGCATCACTTGTTTCAATCCCACATAACAGAATGACCAGCACGCATGTTTATTGTACTATAAAAATTTACACCCTACTTATCAAAACCCAAGACATCATAACCTACTCTCATTCTTCAGTAAAATTAGCAACCAGAAATTAAATGGGCATCCCACAAAGGAATTTAACCTTCTCACATCACAAGAACATGCATATAATTTCATATACAAAAATTGCAAAATATTATATCCATGTGAATTAAATTCATTCTTCCAATATAGCAAGCAAGGTGTACACCTCAGAACAAGTAAAAATGAGTGTAACACATCAACAGAGGCGACTTATCACCATATTGGGTTCAGGAATGATCTCCTCTAGATGGTAGATTGTCTAACATTAGTCAATTGACGGGTGACTTCAGAGGGAATTCATCTGAAACAAAAGGCTGTTGGCTCTTGTTAAATTCTCCATTGTTGTTCTGATGGTATTTGCAGCCGCAACCAACTAAAATATTCCCTAATTGCTCCTTGAGCAAACAACTCCCAATCCAATCCACAGAACATTCAATCACGCTTGCGTCCTCACGGCCGAGGAGCTTGACCGGAGTTCTTGTCTTCGGCGACATTACCTGAGACGCCGGGAGCTCGTCGGGCCCGAGTATCCTCCAAGGCCACCATGACCCGTTCCGTCGCCGGGGATCATCGTGTGGGTGCGGTGACGGAACGGTGACGTAAATCCTGGATGACGACGGATGCGACGACGGTGATGGGGATTGGTTGAGGGCGAGCCGGCAGCGGGGATCGGTGGCGGCGAGACGACGGATGCGACGAAGGCGGAGCGGCGGCAGTCGAGGGTGGCGGCGACGACGGATGTGACGACGGCGGAGCAGCGGCAGTCGAGGGCGGCGGCGACGACGACGACGGATGCGACGATGGGTGACGGCGAAGTGGAGGCAGTCGCGGGCGGCGGCGACGGTGGTGGCGCGGGGATCGGTGGCGGCGAGACGACGGATGCGACGACGGCGGAGCTGCGGTAGTCGAGGGCGGCAACGACGGCGGTGGCGCCGCGTGAGAGGGAGAGATTAGGGTTGGGGAGGGGCGGGGACGCGTGAGAGCGAGAGAAAGGGGGCGGAGAGGATGGCGCGGTGGAGAGGTGGAGACGATGC

Coding Potentia
Explanation CPC Score
noncoding -1.23661
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0163600.2 2 16399458 C T
Osa02LNT0163600.2 2 16397842 A G
Osa02LNT0163600.2 2 16401314 A G
Osa02LNT0163600.2 2 16401453 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
Osa02LNT0163600.2 osa-miR414 Cleavage 4.5 17.581 1 21
Osa02LNT0163600.2 osa-miR417 Translation 5.0 11.523 1 21
Osa02LNT0163600.2 osa-miR1857-5p Cleavage 4.0 2.993 1 21
Osa02LNT0163600.2 osa-miR1858a Cleavage 4.0 11.369 1 21
Osa02LNT0163600.2 osa-miR1858b Cleavage 4.0 11.369 1 21
Osa02LNT0163600.2 osa-miR812f Cleavage 5.0 14.059 1 24
Osa02LNT0163600.2 osa-miR812g Translation 5.0 14.022 1 24
Osa02LNT0163600.2 osa-miR812h Translation 5.0 14.022 1 24
Osa02LNT0163600.2 osa-miR812i Translation 5.0 14.022 1 24
Osa02LNT0163600.2 osa-miR812j Translation 5.0 14.022 1 24
Osa02LNT0163600.2 osa-miR2866 Cleavage 5.0 14.271 1 20
Osa02LNT0163600.2 osa-miR5075 Cleavage 3.5 22.278 1 21
Osa02LNT0163600.2 osa-miR5075 Cleavage 4.5 16.147 1 21
Osa02LNT0163600.2 osa-miR5075 Translation 4.0 8.917 1 21
Osa02LNT0163600.2 osa-miR5144-5p Translation 3.5 10.343 1 21
Osa02LNT0163600.2 osa-miR5151 Cleavage 5.0 8.412 1 22
Osa02LNT0163600.2 osa-miR5490 Cleavage 3.5 15.327 1 21
Osa02LNT0163600.2 osa-miR5513 Translation 4.0 14.892 1 21
Osa02LNT0163600.2 osa-miR5811 Cleavage 4.5 15.028 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0163600.2 2 d50 Morphological trait Dwarf nan nan
Osa02LNT0163600.2 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0163600.2 2 np2.2 Morphological trait Culm/leaf RM324 RM262
Osa02LNT0163600.2 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0163600.2 2 nan Resistance or Tolerance Drought tolerance RG83 RG171
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