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

>Osa06LNT0343800.2

CAACATGACCATAATATGCTCATTGTAATCTGGGTTGAGACCCCACACACCAGCATGTCAGCCCTACATTGAATTATTTTACACTTAGCATAACATATAAGAATATTCTAATCTACAACAGAGAGACTACCCCAACTTCCCGATAGTGGGTCAATAGAAACAAGACAATTTCCCCACAGGACAGACCTATGCAAAATATATATATATTTGATGTCTTAATTTCCCTACAGACAACAATAGGAAATGTTTTGCATTACAAATTTTCTCGTAGCAAGAAGTCATAAAATGATGAAGCCAGAAGACTTCACGATATTACTTAGAGAAAGTTAAGTGTCTTGAGACGTGGATTGTATAGTCTTCATCAGCAACTTTCAACAATCCTGAACCATCTGAATCCCACCGTGGCACCATGACAGCATAAATAGGATTTAACTTACAAATTATACATGTTTTCAGGCTTGGATGATGTATAGATCTTGCCTTAATATGTAGTAGCATCCCATGGAACTTCCTGGTTCCATGATAAATTGCTCACGGAACTGACCTACCCGCTTGCTTGGAATATCGATGGAGAGTTCCTCCAAGCTTGGCATCCCTTCAGCTTGCAACCCTTCACCACATATTAGAAATTGGTTTCCCACAATGAACGATCCAGACACACGTATAGCTATTCCTGTTTCTCCGTGAGCACGACAGTGTAGCTTCTCAACAACATGAACAATTTTCTCTCGAGGACAATCACCTTTTAACTTCTTTCGTATATTTGATAAAGTATCAAATATGTCACTTTGGCCAACATACACATTCCCTGAGAAACTGAAAGTTGATTCTTCCATGTAGAATGTCTTCATATAATGCCAAATCCCATCAGTGCCGTTAAAGAGGAGGTAGTAATGTACGGCAAGCATCTCTGCTATTTGCTTTAATCTTTCTGTTGGATCAACAATACTTTTGACATAAGCTACCAAGTCCACGGTAGTGTTTTCATACCTCTTGATGAATGGGTGTGACAAAAGCTGCTCACACGAAGGCCTTGCATCAGCGTCTTTTTGCAAGCAGTCATTGATGAACGAACAAAACTCAGATGAATAAGAATCTTTTGGTGGTGTTGGTGATGGATCATCCAGAATCTGCAGCATGAGGTTGGCTGGGCCTTCATTCACATTATATGGAAATTTACCAGTAGCACACTCCAATATTGCTAGTCCAAGACTCCAAATATCAGCAGCATAAGAGTAGTTCTCGTTACGAATTCTCTCAGGTGACATATATGTGACTGTGCCTACAAAGGTAGCACACATGGCCATCGTATTATCCAAACCAGCACTCACTCCAAAATCTGTTATCTTTGCCTCACCCTTGAGATTTACCAGCAAATTTGCTGGCTTTATATCTCTATGCACTAGATGTCTTACTTCATGCAAGTAGCGCAAACCGAGCAATACTTTCTGCAGCATATGTGCAAGAACTGGTTCTGGTATTGATTTCTTAATCTTTATAACATTAGCTAAGGACCCACCATCCATGTATTCAAGGGCGATGCTTATTTGTCCAGAATCAGGCATGTAGAATGCACCCTGGAATTCAACTAAACCAATATAACAACATGCTTCACATAATGTTCTCATCTCATTCAGAATTTGTTGTCTCTTCTCCTTCTCAAATATATTTATCTTCTTCAAGGCCAAAATTCGATGAACTGGTATAAAAACAGCTCTCTGCACAACACTGCTTGCACCATTACCAATGGGGCCAAATATGTGCATATCATGAGAGGCACATCGGTATGCCTTTTCACCAGAATCTGACTCCTCTGGCCCAGTGCTTCGTTTATGAAAGCCATGCTCATTGATGTTATACTCACCCAATGATCTACTCAACAAATTCACAGTTCCACCATCAGAAACCACGTAGGAGTCGCAGGTGTCCTCCGGGAGAGGCACCCTGCTACTGACGCCGCCCTTGTCCGGGTCGTCGAACAGCAGGGGCTGCAGCTTCTTCTTCAGCTCCTCGAGCCCCGCCATCGGGAGGCCGCAGACGGACCCCCGCCAACGGGTCGGGCTCGGGCTCACACACCGGGCAGAGGCAGCCCCCAAAAGGAAGGGAGAGCAGCACGGCCGGATCCGAGGAAGAGGGGGAGGGGCACGAGCGGCTGGAGATAGGGCGGACCTGCGGCTCCGGCTCCGGCTGCGGCGACGGAGGGTT

Coding Potentia
Explanation CPC Score
noncoding -1.21572
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0343800.2 6 15812087 C T
Osa06LNT0343800.2 6 15812331 G T
Osa06LNT0343800.2 6 15812366 T C
Osa06LNT0343800.2 6 15812489 A T
Osa06LNT0343800.2 6 15813296 A T
Osa06LNT0343800.2 6 15813433 G A
Osa06LNT0343800.2 6 15814957 C A
Osa06LNT0343800.2 6 15815334 C A
Osa06LNT0343800.2 6 15815976 A C
Osa06LNT0343800.2 6 15816224 G A
Osa06LNT0343800.2 6 15817009 A G
Osa06LNT0343800.2 6 15818059 G A
Osa06LNT0343800.2 6 15819062 G A
Osa06LNT0343800.2 6 15819295 T C
Osa06LNT0343800.2 6 15819500 T A
Osa06LNT0343800.2 6 15815942 A G
Osa06LNT0343800.2 6 15821749 G C
Osa06LNT0343800.2 6 15815475 C G
Osa06LNT0343800.2 6 15817241 T C
Osa06LNT0343800.2 6 15814403 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
Osa06LNT0343800.2 osa-miR5537 Translation 4.0 12.082 1 22
Osa06LNT0343800.2 osa-miR5828 Cleavage 5.0 12.811 1 21
Osa06LNT0343800.2 osa-miR5144-5p Cleavage 5.0 14.184 1 21
Osa06LNT0343800.2 osa-miR5492 Translation 4.5 7.228 1 21
Osa06LNT0343800.2 osa-miR5507 Cleavage 4.0 14.701 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0343800.2 6 amy6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0343800.2 6 asv6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0343800.2 6 tgw6.1 Physiological trait Source activity RG264 RM3
Osa06LNT0343800.2 6 qSPN-6 Morphological trait Panicle/flower C235 G294
Osa06LNT0343800.2 6 qPHw6-2 Resistance or Tolerance Other soil stress tolerance RG424 RZ667
Osa06LNT0343800.2 6 qSPN-6 Morphological trait Panicle/flower C235 G294
Osa06LNT0343800.2 6 qSFWd6 Resistance or Tolerance Other soil stress tolerance RG424 RZ667
Osa06LNT0343800.2 6 gw-6 Morphological trait Seed C235 G294
Osa06LNT0343800.2 6 qLDLJ-6-1,2,3 Physiological trait Source activity RM217 RM3
Osa06LNT0343800.2 6 ph6 Morphological trait Dwarf RZ667 RG653
Osa06LNT0343800.2 6 gp6 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0343800.2 6 qTL6-1 Morphological trait Culm/leaf RZ667 RG424
Osa06LNT0343800.2 6 qRS6-1 Morphological trait Shoot/Seedling RZ667 RG424
Osa06LNT0343800.2 6 qGY6-1 Morphological trait Seed RZ667 RG424
Osa06LNT0343800.2 6 qSL6-1 Morphological trait Culm/leaf RZ667 RG424
Osa06LNT0343800.2 6 qLVBSL6-1 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0343800.2 6 qLVBTL6-1 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0343800.2 6 qHD-6-1 Physiological trait Flowering RG424 RZ667
Osa06LNT0343800.2 6 nan Physiological trait Eating quality RM253 RM162
Osa06LNT0343800.2 6 qPH2-6-1 Morphological trait Dwarf RG424 RZ667
Osa06LNT0343800.2 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