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

>Osa06LNT0336100.1

ATATGGTCTATTTCAACCAATATGAATGATCAATTTGAGATCAATGCTTCCAGAAAAAATGCATATGGACAGTTCAATGACTAACCTACAGAGTTAACTAGTTTACCAAAATTTTCTATGACAAGCATAAATCATGCTCTATTGCTCTTCCCCATGTTCTTCTTTCGTTTCTTCAAGTAGTGCCAAAACAACCATGATTGTGTGGCTAATTATGCAGAAAGTATCCCTTCCAAGCAGAAGTCATGGTTTAGGCCATTTTTTCGAAGCTACTTTGCAAAAATAAACAAGAACACCTAAAAGAAAATGTCTATTTCCTTTTCGCTCATCTCATATACATGATCCCGTGCCTCAGACAGAGCAACCTGTCCAAATTTAGTGAAGAAGTTGTTTGCAAGATTTAATGATGTGACTGCAAGATCTTCATTAGCTTTAAGTGCTTGTGCCAATGCAAATGCTCCATCATCTCTAATCTCATTAAAGCCCAGGTCAAGTGAAGTCAAAGATTCATTGATGATCTTGAAACTTCGAGCCAAGCAGATAGCACCATCATCTCCAAGTCCATTTGCCCTCAAATCCAATGTAGATAATGTTGTGTTGTACTTCAAACAATCAGCAACAAATTCTGCACCTGATACACCTATCTGGCACCAACCAAGTTTAAGGGTTTGGATTTTCCCATTGAACTTGAGAACATCACAAAGAGCCTTTACCCCCTCTGGCCCAATCGGATTATAGCTCAACTCCAATGTTGTCACCACTGAATTATCCTTCAGAGTTTCAGCTATTGCACTTACCCCTTTAGAGTGAATGTTATTACCACCCAAGTCTACAGTAGAAATTGTTTTATTCTGTTTCAGAGCATCTGCAACCTTTTCAGCTCCCTCATCACTTATATCGTTCATGTATAGACTGAGCCATAGTAAAGACTTTGTCCTTTTGATGAACTCAGCAACATGAAGAGAACCTTCAGAGGTAATGTTGTTGTTACCAATATCCAAAACAGTGATCTTCCCTTTGTGAGCAGACAACGCTGACATCAATGCACGTACTCCCTCATTCCCAAAACCATTGCCATGCAAATGAAGTTCCCTCAAAGTTTTGTTCCCTAGAATTCCTTTTGCTAGGCTGGATGCACCAAGAGGACCACCATAGTTGCCATTGACAAATAAGCTCCGTAGCACATTATTCTCAAGGAGTGCTTCTGCAATACTTGCAAAACCGCTGTATTCTATTGTGTTGTTGCTGAGTTGTAAAGTACGTATCGTCTTGTTCTTTTTCAACATATCCGAAATTGCTTTTGCCCCCTCGTCTCCAATATTTGTACTGTTCAATAGGAGCTTCTGGATACCTACATTCTCTACCAATATATCTTAGCTCCTTCGTCTCCAATGGCATTTCCAGATAAGTTGAGAGATTTTAAGGCTGTATTTATCTGAAGAATGCCATCAAAGGCTTCTATCCCCACAGCTGTTATCCCATTGCCAGAAAAGTCTACCTCTTCTGCACTCTTGTTATAGGCTAAGCTTTCTGCTAGAAAAAACAGACCCTCATCCCCAAATTGACGACCTGCCATGTTAACATTTTTCAGAGTCCTGATTTCCTTATAGAACTTATTTAAATTCTTCCTTGATTCCTTTTCAGCATTAAAGCTTGCAGATGTTGACAAATTGGAACCAGCGGCAAAGGACCACATGATCCCAGAAGGGGTAGATTCTCCAGAACTCTGGTCCTTTGTCTTCCCGGGAAGCAAATTCTGAACCACCCTCCATATGACAAAGCTCAGGGCGAGGACCGCCGCGGCCGGGACGACGTACGGCGAGACGCCCCTGACCGCCGCCGCCGCCGCCGCCGCCGGTGGTGCCTCCCCCTGCTCCACGCGGTACTCCCTCCGGCGCGCGCCCCCGCGGCCGACCCCCCCGGGGGGCCTGTCCGCGCTGCCGTCGAACAGCTCGCGCGCGGCGCGGGTCACGGCGAACGAGTAGGACGCGGGCGATGCGTGGCGGGACGAGGACGAGGAGGAGGGGAGGCGCCGATGCGGCGGCGTGGGGAGGGAGAGGTGGTGATGGTGGCGGCGGCGCGGGGCGGAGGGGAGGAGGACGAAGGGCTTGAGGAGGAGGGAGGACTCCATGGGAGGCGGGAGGGGTGGTGTCGAGATGGAGACGAGGAAGGGG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.839136
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0336100.1 6 7148762 A T
Osa06LNT0336100.1 6 7150333 A G
Osa06LNT0336100.1 6 7151534 C A
Osa06LNT0336100.1 6 7151927 C T
Osa06LNT0336100.1 6 7152208 T G
Osa06LNT0336100.1 6 7152342 T C
Osa06LNT0336100.1 6 7153014 A G
Osa06LNT0336100.1 6 7153266 A G
Osa06LNT0336100.1 6 7154014 G A
Osa06LNT0336100.1 6 7154341 A G
Osa06LNT0336100.1 6 7154393 T C
Osa06LNT0336100.1 6 7154456 T C
Osa06LNT0336100.1 6 7155006 G C
Osa06LNT0336100.1 6 7151267 G A
Osa06LNT0336100.1 6 7152949 C T
Osa06LNT0336100.1 6 7150429 T G
Osa06LNT0336100.1 6 7154163 C T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa06LNT0336100.1 osa-miR5833 Cleavage 3.5 13.197 1 21
Osa06LNT0336100.1 osa-miR5833 Translation 5.0 21.476 1 21
Osa06LNT0336100.1 osa-miR166j-5p Translation 5.0 10.72 1 21
Osa06LNT0336100.1 osa-miR530-5p Cleavage 4.5 14.562 1 20
Osa06LNT0336100.1 osa-miR2118a Cleavage 4.5 16.936 1 22
Osa06LNT0336100.1 osa-miR2868 Translation 4.5 10.759 1 20
Osa06LNT0336100.1 osa-miR2920 Cleavage 4.0 14.324 1 23
Osa06LNT0336100.1 osa-miR5509 Cleavage 4.0 9.692 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0336100.1 6 nan Physiological trait Eating quality RM253 RM162
Osa06LNT0336100.1 6 nan Morphological trait Panicle/flower RM276 RM121
Osa06LNT0336100.1 6 nan Physiological trait Source activity RM276 RM121
Osa06LNT0336100.1 6 qHD-6-1 Physiological trait Flowering RG424 RZ667
Osa06LNT0336100.1 6 qPH2-6-1 Morphological trait Dwarf RG424 RZ667
Osa06LNT0336100.1 6 qTN2-6-1 Morphological trait Culm/leaf RG424 RZ667
Osa06LNT0336100.1 6 spf6 Physiological trait Sterility RG213 RM557
Osa06LNT0336100.1 6 qGT-6 Physiological trait Eating quality RM276 RM121
Osa06LNT0336100.1 6 amy6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0336100.1 6 asv6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0336100.1 6 qPSP-6 Physiological trait Flowering R2171 RZ144
Osa06LNT0336100.1 6 qSFWd6 Resistance or Tolerance Other soil stress tolerance RG424 RZ667
Osa06LNT0336100.1 6 qPHw6-2 Resistance or Tolerance Other soil stress tolerance RG424 RZ667
Osa06LNT0336100.1 6 sd6 Morphological trait Panicle/flower RG138 RG64
Osa06LNT0336100.1 6 qLDLJ-6-1,2,3 Physiological trait Source activity RM217 RM3
Osa06LNT0336100.1 6 tns6 Morphological trait Panicle/flower RG138 RG64
Osa06LNT0336100.1 6 ph6 Morphological trait Dwarf RZ667 RG653
Osa06LNT0336100.1 6 sd6 Morphological trait Seed RG138 RG64
Osa06LNT0336100.1 6 tns6 Morphological trait Seed RG138 RG64
Osa06LNT0336100.1 6 qGY6-1 Morphological trait Seed RZ667 RG424
Osa06LNT0336100.1 6 S5 Physiological trait Sterility RG213 C235
Osa06LNT0336100.1 6 nan Resistance or Tolerance Blast resistance C1478 R2171
Osa06LNT0336100.1 6 gp6 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0336100.1 6 qRS6-1 Morphological trait Shoot/Seedling RZ667 RG424
Osa06LNT0336100.1 6 qLVBSL6-1 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0336100.1 6 qSL6-1 Morphological trait Culm/leaf RZ667 RG424
Osa06LNT0336100.1 6 qLVBTL6-1 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0336100.1 6 qTL6-1 Morphological trait Culm/leaf RZ667 RG424
Osa06LNT0336100.1 6 nan Resistance or Tolerance Lodging resistance C1478 R2171
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