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

>Osa06LNT0326200.2

GGCTCAAATGATTGTGAATTATTAAATTTCATAGCTCGGTTAAAAAAAAAACTATACAAACTCGACAGATACGATACACATTGAACTTACATCTATAACTAGCCTATAAAGTCGCACATTCGCACCTCTATAACCATTTTCCACATCGCCATAAATAACTCGATTTCACGACGAATTATCGGAATCGATTGATCCATGAGTGTAATCGTCACCATGTCATTGTTGTAGTGTTCATAAATATACAAATTTGGGCAAAACAACTGTCGCAACTGTTCTACGTTTTACATCTGAAAGAAGAATAAATAATGTGGGCAAAATATGTTGTCTACATACATGTTTTAAGTACATTTGACACTTCTTCTCACTTGGTATATATACTAGACTATGAAAAAATCGTGTAATTATTGTGAGTAGTCCAGTCATTGATGACATCCAACGTTTCTAACTGTTCGTAGCAATGGGTTTCTTACCAAAAGGTGACAAGTTTGTTTCATCGGTTGATTTGCAAACTAAGTGCGAAGTTTAGACGTCATTGGCACCACCTGCAGTTAGCATCTTCAGCTTCGAAATAAATTGTGGAGGGTCATCTATGCTAGAAGATCCCAGGACAATTTCGCGCTTCAGTTTCATAGTAAGCTTGTGCACCGTCCGCAGTTCCGATCTAGTGGCTCCACCAATCATGAAGACAAAAATTCGGTTGCCTAGCCTCTTGAAGTCATTAGATCCATGTCTCAAGACCGAGGAGTCACTTGATTGACTATCATCAGAGTTTCGAGACTTAGCCCAGGTTGGTGTCCGCCGCGATCTCCTGGACATGGGTTGTGCTTGTGCTGGTTTAGTCGCGGCTGCACTTTGTGTAGATCCTTGTTCAGTGGAACTGGGTTCACTCATGGATGGGTATTCATTCAAAGGTAATGCACCTTTGCTCAGTTTCTCAATCAACTCCTCTATAAGTGGGAAAAAACGTGATAATGCCCAGGTTTCATCGCCATCCTGCCGTTCTGTCCTCGCAGCATTTTTTTTCTTTTGTGCATCAAATTTGAGAGAGAAGCCGCCAGGCCGTGATGCCTTTTTTGTATCTGAACCAACCAAGTATCTTAAACTATTTATGGCATCCATCTCATCATGTGGCAGTTTTGCTAGCTGCATCAACTTTTCCCCTTTGTCACCTTCAAACTTCTCTGGATATACAATTGCATATATAATAAGCAACCTCAATTTGTTTTCTGGGCTCATATCCTGCTTTGACCTGAGGATACTGATCACCTCCTTGGCTGCTGCATCTCCAAAAACTAGATCCTGCTCCACCTGCCCAATGTCACGGAGACCATACTCTCTGATAAACTTGTTGATTTTTCCAGCAATCTCTATATGGAGGGTCAATTTCTCAACTTGTTCACCGTATTGTGGCAAAGCTTGAACGATCTTCTGCAGATCCTTTGTAGAAATTTCACCACCATCTCTTGAATGAAGTTGAGCTGCTTTATTCTTTGAAACAAAGTTATTCATCTTATCATACAACCTCTCACTAGCATCAGCTATGTGAATGTGGCGAAGCTCAACCCAGAGAGGATCATGATCCTCCAATAAAGCCTCCTTTCTCTCAGGTTCTGATCCCGCTTTCGACACCTCATATATGTATTTTTGGCCATCCATTTCAAGTAGATCATGGCACATTGCATCATAGGTCCATTCATGAATAACAGGTGCTATCTGATCTATAGGCCTGTCGACAATGAGCAGTTCACATGTCTCCTTCTGGGGAAATTCAGGTATTGTTGATTTATATTTTGACACAATATCCCAAACAGCAGTCGCTAACCATTTTGGAACCATGTCAAATTTTGGTGTTGTCATTGGATCTGTGCCCTTTGGGGCACGATACCGCACACAAGGAAATTCCTTCAACGAAGCAAATGTGGTAGCAATGCGAGTAGCCATAGTGCTTATAGTGTCATTGAACTTTTTCGAGTTGTGCTGAGCACTATATAAATCAGTGAATGCCATGTCATGGTCAGTTGTGAATCCCTGCATGTCAATTGCAAAGAACTCCAAATTCATCTCTCTTAGTGCACCAATACGTGGTATCACACTGCTGTCGTTCTTTATGTAAGAGACCAGCTCCTTAGGAATCGGTGAACTAAAGAATATGTATGCCTTCCTGTACAGTGGACATCTCCCAGACATGTCAGATAGAAGCATTATGACATTTTCTTTCAGTGGCTGGAGGAAGTAGATTGCATCCATGGAAGGCATGGGCTCCCTTCGCTTGAAAAGATCTTCAACCAACGAGATTCCTGCATCGGTAATTTCTGCCATCTTGCAGGCATAAGCCATGATCCTCACCGTAAATTTGTCCATGATAAGAACCTTCCATGAGCTTTTGGTCTCCTTATCTTTGTCCGGCTGCAGCAAGTCCTTGAGTATACGATCCCGGCAGATGTTGCGGAAGATCTTGGGGTCGTCGCACGGGGCGCCGAAGTCCGACCCCGACATCGACATCCCGCCGCCGACCGGAGTTGATCCCCTCTACCTCCACTCCTCTCCTCCCTCTCCCTCTCCCTCAAAC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.747538
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0326200.2 6 1900914 C T
Osa06LNT0326200.2 6 1902918 C T
Osa06LNT0326200.2 6 1903456 A G
Osa06LNT0326200.2 6 1903702 A G
Osa06LNT0326200.2 6 1905386 T C
Osa06LNT0326200.2 6 1906974 A T
Osa06LNT0326200.2 6 1908203 A T
Osa06LNT0326200.2 6 1908783 G A
Osa06LNT0326200.2 6 1905471 A G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa06LNT0326200.2 DTM_#DNAt_MULE_japo_Os0243 Chr6 - 1904372 1905147 775
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa06LNT0326200.2 osa-miR5534b Cleavage 3.5 24.375 1 21
Osa06LNT0326200.2 osa-miR159a.1 Cleavage 4.5 15.128 1 21
Osa06LNT0326200.2 osa-miR159b Cleavage 4.5 15.128 1 21
Osa06LNT0326200.2 osa-miR810a Translation 4.5 24.99 1 21
Osa06LNT0326200.2 osa-miR812a Translation 5.0 12.71 1 22
Osa06LNT0326200.2 osa-miR812b Translation 5.0 12.71 1 22
Osa06LNT0326200.2 osa-miR812c Translation 5.0 12.71 1 22
Osa06LNT0326200.2 osa-miR812d Translation 5.0 12.71 1 22
Osa06LNT0326200.2 osa-miR812e Translation 5.0 12.71 1 22
Osa06LNT0326200.2 osa-miR1429-3p Cleavage 4.5 12.229 1 21
Osa06LNT0326200.2 osa-miR1852 Cleavage 5.0 13.86 1 21
Osa06LNT0326200.2 osa-miR1854-5p Cleavage 4.0 15.283 1 21
Osa06LNT0326200.2 osa-miR1861b Cleavage 5.0 18.079 1 22
Osa06LNT0326200.2 osa-miR1861d Cleavage 4.0 18.079 1 22
Osa06LNT0326200.2 osa-miR1861f Cleavage 5.0 18.079 1 22
Osa06LNT0326200.2 osa-miR1861h Cleavage 3.5 18.079 1 22
Osa06LNT0326200.2 osa-miR1861i Cleavage 5.0 18.079 1 22
Osa06LNT0326200.2 osa-miR1861j Cleavage 3.5 18.079 1 22
Osa06LNT0326200.2 osa-miR1861l Cleavage 5.0 18.079 1 22
Osa06LNT0326200.2 osa-miR1862e Translation 4.0 15.179 1 24
Osa06LNT0326200.2 osa-miR827 Translation 4.5 16.101 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0326200.2 6 qAC-6 Physiological trait Eating quality R2869 R1962
Osa06LNT0326200.2 6 alk6-1 Physiological trait Eating quality RM190 RM253
Osa06LNT0326200.2 6 hr6 Physiological trait Eating quality RM190 RM253
Osa06LNT0326200.2 6 ac6 Physiological trait Eating quality RM190 RM587
Osa06LNT0326200.2 6 qAC-6 Physiological trait Eating quality RM190 RM510
Osa06LNT0326200.2 6 qGC-6 Physiological trait Eating quality RM190 RM510
Osa06LNT0326200.2 6 nan Resistance or Tolerance Drought tolerance RM170 RM204
Osa06LNT0326200.2 6 nan Morphological trait Shoot/Seedling OSR19 RM225
Osa06LNT0326200.2 6 Hd3b Physiological trait Flowering nan nan
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