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

>Osa06LNT0341900.1

GCTTACATATTCACAAAATGTATGTAGGTAATGCACTTGAAGGTTTGAGATGCTACAAACAAATGAAATCATTTAGTCCATTGAAGAGTGGCTTGTCAACATACTTACACCAAACTGACTGGATACAGCTGAACAACTAGATCAGTTATTCTGGGTTTCTAAGCGAACTTCTTGTCGAGGTGACGGTCTATGATTTCAGATACGGTTTCTAAGAAGATTACTTCACTTGACCCTGGGAGAACATGGCCCTCGGCTTCCTGGACGATGTCCTCAATCTCAGAGTCTCTATTCACAGTTTCCCTGCACAGTATACGCCCGATGTCATACGGTGTGAGGCCTCGTGCTGCACCTTTCTTTAAAAGCATGGTGCTGATGCACAGGACACGAGCACATCTTGCAGACAGCTCCCACCCATGGAACTTGAGAAGCTTGATGTCCTCTTCAGCGTCTAGTGATTTGATGTATGCAATGGTTTCATCACTGAATGGTTCACGAGCCTGGGGCCAGTACAGCCACTCAAAGGTACAATCTTCAAACTTCTCTGGCAAGCAGTAACCATGATCAATTGGAACCAACTTGTAATTGCCACCTTCTTCATCCTTGCACACTAAAATGTTCCCTGCATGACGATCAGCGTTTGCTAACCTAAGATCTAACACTGCTATTTTGTGGACCTCCTTCACTGGAAATGCTCGGGGACCCATATCCTCACAACTTCCATTGTTCTGAATGAACATCTGCAGTGATCCAATCTTGAAGCTCTTCCCCCTGTGTAAGCTCCGGACCAATGCTGTGGGAGGCACACCAGAGAACCCGATACGTTCTTCAGATTCATGATCACCAATTGGATGGTCAAGAATATAAGCAGCAACTTCCCTAAATGCACCTTCCCCTACAAGTGTCCCCCTCTTCATGCCTTCTCCATCAGTCGACACTGGAAGCCCTCTTGGGTTGTTTTTAGCCATAGGTTCCTCATCTCTGGGCTTAAACACTGCAATATTCTTCTCTCCTGATGCATCTTGCATGAAGTAAACACCCCCTGAACCTTCAGCTGACATCACTGGCAAGTATCCATTCTCAAGACCAGCTATGGCTGAGCTAATCATTCTCATCACTTCAAGTGATAGCTTCACCTTGTGGTTAACGATAATTGGTTCAACAAGAGCAGGCCTAGCACCAGCTGGTTTAGCAGGGTTCACAGCATGAGCTTCATTTTGAAGGTTCTCTTTCTCCTGCGGAGTGACAACTGTAACCACCGTGTCTTTATCAACTTGCTGTGTCCGTAACTTTGCTGGCTTGCGGATGAACAAATGGATCACAGCATCATCCTTCTTGCTAATATCAGCAATCAGCTGGTGGTCCTCAAGCTCCTTGCCATCACATTCAAGCTTGTGATCCTCACCAAGGTCCTCATCTCCCTCCACTGCCAGCTTACTCTTGAGATACTTGACATTGCGGCTCTGGTCCACCTGGAACTGAAACTTCTTTCCACTGGTAGTCTCGATGTTAATCAAGCGAAGATCAGCCAAGCGGATAACAAGGTGCAGAACATTTCCATCGGCAAGCCCATAATCCTTCACATGGCAGTTGTTCCTTGCCAGCTCGTGCCCATCAAGCACAAGCCTCTGCTTGTTAACCACGAACCCCTTGAACCGCTGAATGCGCAGCTTGACCGAGGCGATGGACTCCGAGCCGAGCACACTCATCGGCATCGGTGGGGCACCAGGCACAGCAAGAAAGATGATAATCGAATCCTGCAGCTGTGACCCGGACAAACAGTGGGGCGACCGGCTGCCGTCGAAGCAGATGGGCAGGAGAGCAAACTCTTCCACCATCGGGCTAATGGCAATGGCAGCAGACGACATCTTCACAGGAGGTCCTTAGGATGCCGAAGCTTCCTCAACTACTGCTACTATTTACACTAACCTAAAAATCAGATCCTTCACACTACGAATTAGAAGCCATGGAGAAGAAAGGGCAAGGGTTCCTTTCCTTCCTTAGAGGATGGAGGAAACCCTCTGCGATCGCGAGATAACCAGCGTGGTTACAATCCCATCTTGATCTCCAGGCACATCAAACCAGACATGGTTAGATGAGGGGGAGAAGTGACGAAATATCTCGCCTTTGCCCACCAGTGATTGAATCCCCCACACGGAATCAGAAGAGGGATTAATCAGGAAGGGCCCGAACCCCCTCCGATCCGGACGCCAACCGAGCCACAACCTCACCGATTCACCTCACTCCAATCAAACCCTGCAAGCACACCACCACACCACCACACAGATCAGAAAAACTCCCCACCAATCCAAATCCCAAGCCAACCGCCCCAAAAAAAAAAAGAAAAATAATCTCACAAGAATTCACAGGACAAATCAGCGGGGGATTCACCGCAAGAACCGACCAGAGGAGAGGAGGGGGGATACCCCGGAGAGGGGGGCGGGGCTAAATCCGGCGCGGCGCCTTGTTCTTCCTTGCTCCGAAGTTCACGCGAGATGGGGAAGCTTCGGTTTGGTTTTGGTTTGGGGAGAAAGAAATTCAGAGAGAGAG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.523699
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0341900.1 6 13602159 T C
Osa06LNT0341900.1 6 13603631 T C
Osa06LNT0341900.1 6 13603660 C T
Osa06LNT0341900.1 6 13603841 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
Osa06LNT0341900.1 osa-miR5789 Cleavage 4.5 19.364 1 21
Osa06LNT0341900.1 osa-miR5516b Cleavage 5.0 23.515 1 21
Osa06LNT0341900.1 osa-miR394 Cleavage 4.5 17.463 1 20
Osa06LNT0341900.1 osa-miR395f Translation 5.0 12.434 1 21
Osa06LNT0341900.1 osa-miR168a-5p Translation 4.0 17.882 1 21
Osa06LNT0341900.1 osa-miR528-5p Cleavage 3.5 8.649 1 21
Osa06LNT0341900.1 osa-miR1425-5p Cleavage 5.0 19.828 1 21
Osa06LNT0341900.1 osa-miR5490 Cleavage 5.0 15.382 1 21
Osa06LNT0341900.1 osa-miR5500 Cleavage 5.0 17.201 1 22
Osa06LNT0341900.1 osa-miR5516a Cleavage 5.0 23.515 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0341900.1 6 qGY6-1 Morphological trait Seed RZ667 RG424
Osa06LNT0341900.1 6 qLVBSL6-1 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0341900.1 6 qLVBTL6-1 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0341900.1 6 qSL6-1 Morphological trait Culm/leaf RZ667 RG424
Osa06LNT0341900.1 6 qTL6-1 Morphological trait Culm/leaf RZ667 RG424
Osa06LNT0341900.1 6 nan Physiological trait Eating quality RM253 RM162
Osa06LNT0341900.1 6 qHD-6-1 Physiological trait Flowering RG424 RZ667
Osa06LNT0341900.1 6 qPH2-6-1 Morphological trait Dwarf RG424 RZ667
Osa06LNT0341900.1 6 qTN2-6-1 Morphological trait Culm/leaf RG424 RZ667
Osa06LNT0341900.1 6 amy6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0341900.1 6 asv6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0341900.1 6 tgw6.1 Physiological trait Source activity RG264 RM3
Osa06LNT0341900.1 6 qSPN-6 Morphological trait Panicle/flower C235 G294
Osa06LNT0341900.1 6 qSFWd6 Resistance or Tolerance Other soil stress tolerance RG424 RZ667
Osa06LNT0341900.1 6 qPHw6-2 Resistance or Tolerance Other soil stress tolerance RG424 RZ667
Osa06LNT0341900.1 6 qSPN-6 Morphological trait Panicle/flower C235 G294
Osa06LNT0341900.1 6 gw-6 Morphological trait Seed C235 G294
Osa06LNT0341900.1 6 qLDLJ-6-1,2,3 Physiological trait Source activity RM217 RM3
Osa06LNT0341900.1 6 ph6 Morphological trait Dwarf RZ667 RG653
Osa06LNT0341900.1 6 gp6 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0341900.1 6 qRS6-1 Morphological trait Shoot/Seedling RZ667 RG424
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