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

>Osa06LNT0345400.1

CAGTACTTAGTTCAATCACAAAACACATCACACTATAAATACATAGTTCATCACAAAACATAGTTCAATCACAAAACACATCAGTACATGGTTCATCACAAAACATATCTCATCCACTTGTGCAGCAGGAGTACACTAATTTGAAATGGAAACTTGAAATTAGATGTAACTTGAAAATTAAATTGACCAACATTTTCTTCAAACATCCATTGGCGCAATGCCATCCTCATTAGAACATTCCACTGTCTCTGTCTCTTGCTCTGTTCCATTAGCCAAGGACAACATGGCACAGAAGTTCTGCTCCAGGTTCTCCATGTCCTTCTCAGTAAGATAGACCCAACCACATTTCCACCTTTTCTTGATGCTGCAGTCCAATCTTTGGTGCAAATCAGAGCTTGCACAATTTCAGGGTCTAGACTGCTACGGAATGGATCAATAACACGGCCACCGACACTGAATGCAGATTCTGAAGCTATAGTTGATACTTGAATAGCCAGAACATCACGAGCAAGTCTAGTGAGAAACTGAGAATAGGAAACTCATGTTGCTTGAGTGACCACCAATGCAAAATATTAAATGTGGTTTTGTCTGATGTGTACCATTCCAATAGTGGCTGTTCCAAGTAAACTTCTAACTCACTCTTAGTGCCTATTCCAGGGGCAGTACTAGCACGCAAGTATTGTTGAACATCTGCATCAAGCTCATCATCGCTCTCCCCATCATAGTCTTTACTCACTAAAAGATTATTCTGCACATTTGTAGCTGCTGGACTCTTTGAACTTGCTTGACTAGATGCATAAGTATCAAATAGCTTATTAATAACAACCATGAAATCCGCCATGTGTTTTGGGGCTACCACACCATAAACCTTATCTGCATAATACTCAAGAAGTGTTCTCTTGAACCTAGGATCAAGCAAGCAAGCTTCAGAAAGAGCCATATTGGACTTCTCCCAATATTTATCATACTTAGGTTTCATTGACTTGCCCATAGTTGCTATGATTGTATTAGAACTACGGCACCATTCTTCTACTGCCATCTTAATTTGACAGAATTTTCTAAAAAAACAGATTTGCAGTTGGATAACTAATGCCAGAGAAGATCAAAGTAGAATCATAAAATCTCTTCAAGCATATGCACAATGACTTTGCCATAATCTAATCATCATCTTTTGGGGCACATTTATGATATTTGCTTCTATGACAAAGAAAGAGCCTATTAAAAGCATTTCTATAGTGAATAGCTTGCTTTAACATGATATATGTGGAATTCCACCTTGTTGGAACATCCAAAGACAGCCCACAAGTAGTGTCTAAACCATCACACTCAGAAGCACACTTCATGAATTCTGACCACTGCAGTGGGGAGTTCAAAATTGAAATTGTGTTTCTAATATTTGAAACACTAGATGAAATTTGCTTCAACCCATCTTGAGCAACAAGATTGAAAATATGATTCAAACATCTCACATGGAAAAAGATCCCCTCACAAACCAAGGGTTGTATATCATTCAGTTTTTCTACTAAACCCCTAGCACATACATCATTGGCAGATGCATTGTCCAAAGTAAGTGCAAGCAATTTCCTATCAAGGTTCCAATCCAGTACACTATCATAGAACTCTTTGCACAAGTTTTTCCCTGAGTGATGACCCTCTACATGCATAAACTTTATAATTCTCTTTTGCATGCACCACGTATCATCTATCCAATGCACAGTGATGCACATATAACCTTTATTTTGATTTGAGGTCCACATGTCCATGGTTGTACTAAAGCGGCATGCAAGAGTTTTAAAGTACTCATACATTTTCTTCTTCTCATCCAAAAACATATCCAATATATGTTTCCTAACAGTTATGCGACTTTTGATTGGAAAGGTAGGGTGCAATGACTTAATAAAATCCACAAAGTACTCATGCTCAACAATACTAAAGGGATATTCATGCATAATGATTGCCAAGTAAAATTTCTTCAAGCTAACAGCCTCATCATACTTGTAAGTCTCAACAGCAGTGCCGCTTTCACTCTTTTTTAGATTTAGAAGCTGCTGGCCACTTTTTATTTGGTGCTTCTTGTCTAAGTGACTCCAAAATATTGTTGTGCCCCTGTTGCTCTCACGACGAGTTGTATAGCTGCACTTCTTACACTTTGCCCAAAGCTCTACAATCTCTGTTCCATCATCTCCTACTACCTTTTTCTCATACTTGTCAAAGTGGCTCCAAACCTCTGAACTACACTTCTTTGCTTTCTTTGCTGGAGGGACATTTGCATCCTCGGTAGTTTCCTGTGTCAAATCAACTTCTACTCTTGCTGCTGCAACCACATTTGTGGTAGGATCTCCTACATTTGCAAGAGTTGGTTGTGATGCTCGCAAAGCTACAATGCCCGCATTGCATACACTTGCACTGCTGCTACTTGCATGTGATGATTCCATCACAAATCTGCTGCTGCTGGTTGCGCAGATGTTGCCGCTGGGCTGCTGGCTGCTACGAGGCGAGGAGTCGTCGGCGTTGGTGGCGGTGAGGAAGAGACTGCAGTGGGGCTTGAGGTGTCGTCGGGTCGTCGTCGGTGGTGGTGGCAGCGGTGAAACGGCGAGACGCGGCGGGACGGCGCTATGAGATGGCGGGGACCGAGCCAGCCGGCGGAGGTGCGAGATGGTGGCGGCGGCCGGTGGCGAAACGGCGAAGAGCGAGGGCGGCGCGAGATGGTGGGGGCGAGGACAGCAGGGGCCAGGTGACCAGCGGTGGGCGGTGGCGCGGGCGGTGGGCACGGGGGCGCGCCGCGATGCCGCGATCTGGACGCCGCAGCCGCCACTCCGGTGCTCCGCCTCCAACTCGCAAGTCGCGTCTCACTGTCTCTCTCCTCTAGGGTTAGCTAGTTAGGGTAGATGCCACTGCGATTTGGGTTGGGCTAGGAAGTTAGGGATGAATTATGGACTATTGAATCTATGGGCTTTTTGAACTTCGGAAATTCCGACAATTTTTCCAGAATGTTTCCGATCGTTTCCGGGTTCCGACGGAAACTGCTA

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.14112
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0345400.1 6 16992437 T C
Osa06LNT0345400.1 6 16992334 T C
Osa06LNT0345400.1 6 16992746 A G
Osa06LNT0345400.1 6 16993082 A C
Osa06LNT0345400.1 6 16994510 A C
Osa06LNT0345400.1 6 16994962 T C
Osa06LNT0345400.1 6 16995141 C T
Osa06LNT0345400.1 6 16995162 A G
Osa06LNT0345400.1 6 16995404 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
Osa06LNT0345400.1 osa-miR5544 Cleavage 4.5 19.948 1 22
Osa06LNT0345400.1 osa-miR5797 Translation 5.0 10.188 1 21
Osa06LNT0345400.1 osa-miR5821 Cleavage 4.5 13.516 1 21
Osa06LNT0345400.1 osa-miR1440b Cleavage 5.0 12.665 1 21
Osa06LNT0345400.1 osa-miR396e-3p Translation 5.0 15.494 1 24
Osa06LNT0345400.1 osa-miR528-3p Cleavage 5.0 17.681 1 21
Osa06LNT0345400.1 osa-miR1861g Cleavage 5.0 22.692 1 22
Osa06LNT0345400.1 osa-miR2864.2 Cleavage 4.5 15.069 1 21
Osa06LNT0345400.1 osa-miR5158 Translation 5.0 11.504 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0345400.1 6 amy6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0345400.1 6 asv6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0345400.1 6 tgw6.1 Physiological trait Source activity RG264 RM3
Osa06LNT0345400.1 6 qSFWd6 Resistance or Tolerance Other soil stress tolerance RG424 RZ667
Osa06LNT0345400.1 6 qPHw6-2 Resistance or Tolerance Other soil stress tolerance RG424 RZ667
Osa06LNT0345400.1 6 qSPN-6 Morphological trait Panicle/flower C235 G294
Osa06LNT0345400.1 6 ph6 Morphological trait Dwarf RZ667 RG653
Osa06LNT0345400.1 6 qSPN-6 Morphological trait Panicle/flower C235 G294
Osa06LNT0345400.1 6 gw-6 Morphological trait Seed C235 G294
Osa06LNT0345400.1 6 qLDLJ-6-1,2,3 Physiological trait Source activity RM217 RM3
Osa06LNT0345400.1 6 qLVBSL6-1 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0345400.1 6 gp6 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0345400.1 6 qRS6-1 Morphological trait Shoot/Seedling RZ667 RG424
Osa06LNT0345400.1 6 qGY6-1 Morphological trait Seed RZ667 RG424
Osa06LNT0345400.1 6 qLVBTL6-1 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0345400.1 6 qSL6-1 Morphological trait Culm/leaf RZ667 RG424
Osa06LNT0345400.1 6 qTL6-1 Morphological trait Culm/leaf RZ667 RG424
Osa06LNT0345400.1 6 nan Physiological trait Eating quality RM253 RM162
Osa06LNT0345400.1 6 qHD-6-1 Physiological trait Flowering RG424 RZ667
Osa06LNT0345400.1 6 qPH2-6-1 Morphological trait Dwarf RG424 RZ667
Osa06LNT0345400.1 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