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

>Osa06LNT0342800.2

GTGGAGTATAGGACAAAGCACATATTCGGCCATTCGGGTGTACGCGTATTACTGTCAGTGCCAAAAGCAAAACAGGGTCAGATTTACCAGACCACCGCATGTGAGCTCCTACACTTCTTTGCGGTTCCTTTTTGGGCAACAAGGCCTCTGGTATACTGGGCTACTGGCATCTCTCCCGTGGAAAGGCATTTGCAGAACCTTGGAATTTGGGAGCTTCATTCTCTTGCCTTTGACGCCTTGACCCAACATGAACCATCAGCAGTCCAACACTTCTCTGGTCCCAACTCCCAAGCGGTTACTAGGGCCAAACTATTGTTTCATTTCACCGGAGGGCATCTTCTCATCTTCTAGCTGCTGTGTGTAAATAATTACATCCCATAATGCTCCTTTTACCTGATCCGATTCTTGAAAAGAAATTTCACATCGCCAGTAGCTGATTGCCTCTTTGCAGTAATTTGCATTACAGCACCATCAGCTAGCATACGCTGAACAACCCTTGCTATATTTTTTGCATCATCTATACCGAGATGATGGCTTCCGACGATTGGCATTTGTAGCTCCCTCATCATTGTCATCATTCCGGTAGCCCTTCTGTTATAGAAGTTGAGATAGATATCCTTCAAATTGATCCACTCCATAAAGTAAGAAGGTAACTTAATTTTTGAAACCCTGCACTGTTCAGGTACCTTTGTCTTCAGATCCCAATTCCCACAAGTGATGAATGCTGCACTGTTGAGTGCTCCTCCTTGCTCCTTTTTCCAAAATTTGTGATGTTCGATCCAGTCTTCAAACTCTTGAAGTACTTCCATGAAAGGTATAGCAGTATCATGCCATACACGGTCAACTCCAAATTTCCCATATTTCCCTTCAATATATTCTCTTATTCTTTGCTCACTCATCGCAGTAGGGTGTACAAACCTACAAGCAACACACGAGGGGATAGAGATAGTAACTGATATTACTGAAAAGGCAAGAAAATACAGAAAGGATTAACATCACAAACGAATAAAACAATATGAAATATTGCATATACTAAGTTATACAATGTTACAGTGTCACATTTTTCTCACTTATTTAAAATATTTAGATGTCTATTCAAACTTACAGCATCACACAAGAAAGAAACAGCTGATATAATTTGTCTGACTGTAACAAATGCTACACTATCATGCGAGTATTATTCACACACCATGTATTGGGCTGTCCAGTGGGTCGCCTCTAAGCCCAATGCCCATGACACCAGCTAAAATGGCATGTCTTTAGAGGATATTTTCTGCATGTGTGGTATATATGGGCTGTTTGGATGGTTCCATAACAATATATTTGGCGTGTGGCATGCCGCACATTGTGTGGCCAAGAATTTGTTGGCCACAATTGTGACAAGTTGTGGCAAAAAATTCACTCTATGACAAGTGGACCAGCTAACAGAAAGTGTGGCATAACTCACTTGTGGCATGAACCAAACGCTAGCCTTAGTTGGTCAAACTTGGTTGCCACAAGTTTAGCAAAGGTTGGCACTCAACCAAACATGCATTGCCCATATTCATGATATTGATATCCTATGGTTTTTAGATTTTGCAAAGAACAAACAGCATGTAAATTCAGGACCTTGATTCTTTCTTTTAGAAAGTAGAAATTCAAAAGGATATTTTTGGGAGGAAATTAAGAACTTGAGTCATGCAGAACCATTGGATAAGAACAGAAAAGTAAAACCAGGAAAAATATTTTTGGTTCTGTTGTTTGTCCATGAATCCCTAGACACACTCTAGCTGCAGTATAGCTGTTGCAAAATTTCCAATTGTAGCGGTTTATGTGCATCCATCTAGTCATAAAATGTACTTCCTAAAAATTTAATTTGTATTCAGTTATATGCTTATATGTTTTAATTCACTCAATTATTACACATCTCAACCAGCATGGGCTCTCCTGTATGAAACAGAACAATATACTGAAATTTTAATTTTGCCATTCATTGCGAGTTTTAAGACTATATTATGTTTTCTACCATCCCTGTTCAGTCAACAGTAAACCTCTCCTTGCCCCTCTTCCGTTACTAAACCACTAAATCTCTCCTTTTTGGCATCCATGCTCAGTCAACACTGGTTACAACCAAATTTACTTTTAAGAATAATGCCGTTATGAAGTTAACTTAATAAAAAATCGAAAAAGAATACAAAAATCCTGAAAAAGATCATGGATTACCCTGAAACAAATCTTTCATAATTTCACAAATAAAAATACCCTAGAGAACTTTTTTAGGTTCACCGCATGAAAATTGAAATGATTGAGGCGCTTTCGAATAGTATAGTTACATCAAATTTTCCTCAAATATATATGTTGAAATAATGAAAAATTTTCAATATTCCTCAATTGTGTTGTAAAAAGTTCTTACAGGAATTTATGATTTCTCTTAAGTGCCCCTTTTTTGTTGAAAGCTTTGAAAACTATAAATTTGCATAAGTTTTCAAGAATTTTCTCCGTAAGAGATGGTCTTGTGGGAAGTTTGATGATCAACTAGCCTTGAGTAGAGTGACGGGAAAAGAGAAAAACACTCTAACAAACGAGTTGCAAAAGAGAGGCAGGATCCTTAGATGGTTGAGGGAAGTATAATATCGGTAAGTCAGAATGAGTGAACATATTTTCAAAAAAAAAAAATCGAAGTAAAAAAGACAACATATTCCACAAAAGGGATTCAAATATTGCATCTTAAATCTTAATCTCATAGTTCTTCGATTAAATTTCTCACTAATCTTGATAATAGTTCTTGGTGCTCAACTGAGTGAAATGAGAACCATACAAAGCTAAACCTTCTGTATTTAAACTAATAAAGAACTATATTACCACCAAAGAATATTCACAAGAAATTAGAGAAATAAAAGTTGCAAAACTCATCTATGTTTGGGGGCGAGTTTGGTAATCATTCAAATAGTCTTATGTATTGAGAAGAATATTTCAATAACTATTAATGTACAGATGGGCTATACCTGTGAAATGAATCGACGAACTCCATGCTTTGGGCATCAATCATTACAACTGGGAATTCAAGAATTTCAACCTTACCTTCCAAATCAAGGACCAAAAAGTAATCCAATTTCTGAGATTTCACTTTATCTGCAGCTGAATAATTCACTGGAAGGTCTGTTGGCAGATTGTGATTGAATTTCTCAAGATGCAAAGTATCATTCAACATGGTGCATTTCCCCTGGGTGTAGTACAGGCACGTGGGCTTCCATGGGCGCCTGGAGCTCGGCCGCGGCGGCGCCTCCATCACCGCCCCATCCCCGTCCGCAGAGGGAAGCGGAGAGGCCTGAGATAAGGCGGCGGCGATGGCGAAGCCTCGGTGGTGGGGGACGCGAGTCACGCGAGGGCGCAAGACGGAGGAGGGCGAAGAGAAGGGGCGCAGTAAGGAATGGATCAGGAAGGGGGAGGAGAACGCGGGGGGAGAAACCCTAGCGAGCGCCATCTAAGGCGAAGCTACCCTACAGTTCGCTATGGCCGC

Coding Potentia
Explanation CPC Score
noncoding -1.20771
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0342800.2 6 14421692 A G
Osa06LNT0342800.2 6 14420427 A G
Osa06LNT0342800.2 6 14419054 G C
Osa06LNT0342800.2 6 14419110 G C
Osa06LNT0342800.2 6 14419409 C T
Osa06LNT0342800.2 6 14420189 T C
Osa06LNT0342800.2 6 14422122 A G
Osa06LNT0342800.2 6 14422811 A G
Osa06LNT0342800.2 6 14423134 A T
Osa06LNT0342800.2 6 14423338 C T
Osa06LNT0342800.2 6 14423616 T C
Osa06LNT0342800.2 6 14423783 T C
Osa06LNT0342800.2 6 14423969 T G
Osa06LNT0342800.2 6 14425137 T A
Osa06LNT0342800.2 6 14425259 C A
Osa06LNT0342800.2 6 14425931 G C
Osa06LNT0342800.2 6 14426591 G C
Osa06LNT0342800.2 6 14427044 A C
Osa06LNT0342800.2 6 14427639 G A
Osa06LNT0342800.2 6 14428018 C T
Osa06LNT0342800.2 6 14428331 G C
Osa06LNT0342800.2 6 14428394 A C
Osa06LNT0342800.2 6 14428711 T G
Osa06LNT0342800.2 6 14421883 T C
Osa06LNT0342800.2 6 14423868 A C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa06LNT0342800.2 osa-miR5535 Cleavage 5.0 21.502 1 22
Osa06LNT0342800.2 osa-miR812v Translation 5.0 19.859 1 24
Osa06LNT0342800.2 osa-miR5830 Cleavage 4.5 10.579 1 24
Osa06LNT0342800.2 osa-miR6255 Cleavage 4.5 9.262 1 22
Osa06LNT0342800.2 osa-miR169r-5p Cleavage 5.0 20.698 1 21
Osa06LNT0342800.2 osa-miR1882a Cleavage 5.0 11.798 1 24
Osa06LNT0342800.2 osa-miR1882b Cleavage 5.0 11.798 1 24
Osa06LNT0342800.2 osa-miR1882c Cleavage 5.0 11.798 1 24
Osa06LNT0342800.2 osa-miR1882d Cleavage 5.0 11.798 1 24
Osa06LNT0342800.2 osa-miR1882e-5p Cleavage 5.0 11.798 1 24
Osa06LNT0342800.2 osa-miR1882f Cleavage 5.0 11.798 1 24
Osa06LNT0342800.2 osa-miR1882g Cleavage 5.0 11.798 1 24
Osa06LNT0342800.2 osa-miR1882h Cleavage 5.0 11.798 1 24
Osa06LNT0342800.2 osa-miR2101-3p Translation 4.0 16.932 1 22
Osa06LNT0342800.2 osa-miR2122 Cleavage 2.0 19.427 1 22
Osa06LNT0342800.2 osa-miR2871a-3p Cleavage 4.5 15.655 1 21
Osa06LNT0342800.2 osa-miR2871b Cleavage 4.5 15.655 1 21
Osa06LNT0342800.2 osa-miR5073 Cleavage 4.0 21.049 1 23
Osa06LNT0342800.2 osa-miR5081 Translation 5.0 13.992 1 22
Osa06LNT0342800.2 osa-miR5159 Translation 4.5 24.755 1 24
Osa06LNT0342800.2 osa-miR5495 Cleavage 4.5 12.864 1 21
Osa06LNT0342800.2 osa-miR5501 Cleavage 4.0 10.141 1 21
Osa06LNT0342800.2 osa-miR5504 Cleavage 4.5 3.298 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0342800.2 6 amy6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0342800.2 6 asv6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0342800.2 6 tgw6.1 Physiological trait Source activity RG264 RM3
Osa06LNT0342800.2 6 qSFWd6 Resistance or Tolerance Other soil stress tolerance RG424 RZ667
Osa06LNT0342800.2 6 qSPN-6 Morphological trait Panicle/flower C235 G294
Osa06LNT0342800.2 6 qPHw6-2 Resistance or Tolerance Other soil stress tolerance RG424 RZ667
Osa06LNT0342800.2 6 qSPN-6 Morphological trait Panicle/flower C235 G294
Osa06LNT0342800.2 6 ph6 Morphological trait Dwarf RZ667 RG653
Osa06LNT0342800.2 6 gw-6 Morphological trait Seed C235 G294
Osa06LNT0342800.2 6 qTL6-1 Morphological trait Culm/leaf RZ667 RG424
Osa06LNT0342800.2 6 gp6 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0342800.2 6 qGY6-1 Morphological trait Seed RZ667 RG424
Osa06LNT0342800.2 6 qLDLJ-6-1,2,3 Physiological trait Source activity RM217 RM3
Osa06LNT0342800.2 6 qRS6-1 Morphological trait Shoot/Seedling RZ667 RG424
Osa06LNT0342800.2 6 qLVBSL6-1 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0342800.2 6 qLVBTL6-1 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0342800.2 6 qSL6-1 Morphological trait Culm/leaf RZ667 RG424
Osa06LNT0342800.2 6 nan Physiological trait Eating quality RM253 RM162
Osa06LNT0342800.2 6 qPH2-6-1 Morphological trait Dwarf RG424 RZ667
Osa06LNT0342800.2 6 qHD-6-1 Physiological trait Flowering RG424 RZ667
Osa06LNT0342800.2 6 qTN2-6-1 Morphological trait Culm/leaf RG424 RZ667
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