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

>Osa06LNT0340300.1

TACACGGAGGCAGCGACTGCATGCAGTGATGCAGATGCCCATAAACTCGAGCTTATAGGTGATTTTCAGGGGGACTTTTTGGGCAAGACAATGGTCTTTGCTACTTAAGGAAGAAGATGGCCAAAAAGTGAGAGAAGGTTGCTTGATTCTAGAGAAGAGAGTTTCTGGCTTTTTCGCAATGAAGGGATGGAACTTAAGGAAAAGATTGGGAGATTAATGCTCTCTGGTTTTCTTGTGTGGTATGGTTGAAACTTTGTATTAACTTTTTAAGAATTTCTGTTGCTAGAGCCTAAGTACTCGGGTCTAGTTGCTTGTGATGGTGTTAAACCTTGTGTAAGGGTGTGAGTTTATGTACTCTTGTAAGTTTCGTTGGGGCTGTGTACATCCTTTTTTGGGTGTAGAGGCCGGTTTAATCCATTATCTAAAAAAATGTAAAGGATGCACTATATGGCACTCTGAAGTAAGGTTTCCTGAGTATGGTCTTTTGGTGAACAAAAGATGGGAGATGGATTTTTATCGCT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.181388
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0340300.1 6 11774206 G A
Osa06LNT0340300.1 6 11774211 A G
Osa06LNT0340300.1 6 11776159 C A
Osa06LNT0340300.1 6 11776709 G A
Osa06LNT0340300.1 6 11777723 T C
Osa06LNT0340300.1 6 11778006 A G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa06LNT0340300.1 DTM_#DNAt_MULE_japo_Os0131 Chr6 + 11778169 11778524 19
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa06LNT0340300.1 osa-miR166a-5p Cleavage 5.0 23.087 1 21
Osa06LNT0340300.1 osa-miR166c-5p Cleavage 5.0 23.087 1 20
Osa06LNT0340300.1 osa-miR166d-5p Cleavage 5.0 23.087 1 21
Osa06LNT0340300.1 osa-miR166e-5p Cleavage 5.0 23.087 1 21
Osa06LNT0340300.1 osa-miR167c-3p Translation 5.0 19.359 1 23
Osa06LNT0340300.1 osa-miR166l-5p Cleavage 4.0 23.087 1 21
Osa06LNT0340300.1 osa-miR444a-3p.2 Cleavage 4.5 16.669 1 21
Osa06LNT0340300.1 osa-miR444d.2 Cleavage 4.5 16.669 1 21
Osa06LNT0340300.1 osa-miR444e Cleavage 4.5 16.669 1 21
Osa06LNT0340300.1 osa-miR444f Cleavage 5.0 16.669 1 21
Osa06LNT0340300.1 osa-miR2877 Translation 4.5 15.128 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0340300.1 6 qLDLJ-6-1,2,3 Physiological trait Source activity RM217 RM3
Osa06LNT0340300.1 6 qNFGP-6 Physiological trait Source activity RM136 RG456
Osa06LNT0340300.1 6 qSF-6 Physiological trait Source activity RM136 RG456
Osa06LNT0340300.1 6 gp6 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0340300.1 6 qRS6-1 Morphological trait Shoot/Seedling RZ667 RG424
Osa06LNT0340300.1 6 qGY6-1 Morphological trait Seed RZ667 RG424
Osa06LNT0340300.1 6 qLVBSL6-1 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0340300.1 6 qLVBTL6-1 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0340300.1 6 qSL6-1 Morphological trait Culm/leaf RZ667 RG424
Osa06LNT0340300.1 6 qTL6-1 Morphological trait Culm/leaf RZ667 RG424
Osa06LNT0340300.1 6 nan Physiological trait Eating quality RM253 RM162
Osa06LNT0340300.1 6 qHD-6-1 Physiological trait Flowering RG424 RZ667
Osa06LNT0340300.1 6 qPH2-6-1 Morphological trait Dwarf RG424 RZ667
Osa06LNT0340300.1 6 qTN2-6-1 Morphological trait Culm/leaf RG424 RZ667
Osa06LNT0340300.1 6 amy6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0340300.1 6 asv6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0340300.1 6 tgw6.1 Physiological trait Source activity RG264 RM3
Osa06LNT0340300.1 6 qSPN-6 Morphological trait Panicle/flower C235 G294
Osa06LNT0340300.1 6 qPHw6-2 Resistance or Tolerance Other soil stress tolerance RG424 RZ667
Osa06LNT0340300.1 6 qSFWd6 Resistance or Tolerance Other soil stress tolerance RG424 RZ667
Osa06LNT0340300.1 6 qSPN-6 Morphological trait Panicle/flower C235 G294
Osa06LNT0340300.1 6 ph6 Morphological trait Dwarf RZ667 RG653
Osa06LNT0340300.1 6 gw-6 Morphological trait Seed C235 G294
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