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

>Osa04LNT0249700.2

CCTCGTGATAAAAAAGTTAAAATATGCTTTCTTTGCACGTCTTCTTTCAACATTGTACAACGGCGCATAAAAACTATACAAAGTCTATTTAAAGTACACATGTACATCACATATCTTACACAATATCGAGCACACAAGACTTGCTAACCACAAACTTTTCCAAAATCATGTACGTAAGATCATTCCTTGTGTTGCATAACTGGAATCGCAGTCTCAACATTCATAACACAAGCAATCCTCTTCCTTTCAACTCGCCCCAATGGCTAGCCCAGTAAGGATCCTGAAACAAATTCTCATTGTTGACCATGAGATGTCCCAGTAGATGAGTACCACTTCTCAACCATGCTGTTCTTCCCAAAATTCGTATTGGTTTGAAACTGTTGCGGATCATAGGTCCAACGGAGGTGTTTCCTTGTGCAGCAGGTCATGTGCAATGTAGTCCCAAGGAAGAGATACTGACATCAAGCAACATTTTAGAGGCAGAAGCTCATCATCAAAGCGTTTGTTGGTAGATGCAGCCTCGTAGGCATGCTTTGCTAGTTTTGATGCAGTAGATGCTGCACTATGGACAAGGGCCCGAAAGCTATTTCCTGGATCTTTCTTTGATCTCTCATGGCTCTGATCTGCTATTCCAGAAACAGCTACTTCAACTTCTCCACGTCCTTCAGGGCCCCTCATATAAAGTTTATCAAGTTTAGTGCGGTCATGCCCGAGTGAGAATAAGCTCTCAAATTTTGATCATCATAAGCTTCTCGAACGTTTTGGTAGCTGACGTAGCCTGAAAAGAGAGTTCTCTTTGGTGGTTTTTCTTGTTTGCTCCCAGTGTTTACCCCAGATAGCACATTTGAGCTAGGATTTTTCGATTCAGTGTTTTCAGGAAATGCTGCCCCATCATGTGCATTGAGAATAACACAGTAGCAATGTTCAGGGTCTGATAAAACAACTGCATCAAAGGTATCATCGAAGTCATCAATTGAGAAACAAATATTGGGGTATGCAGGTACCGTTTCTACTGCCTTCCTTCGATCAAGATGAAAATTTACGCGGCTCGGGGATGCATACACAGTTTTTGTGACCTTATAAACTGGTGATAATGGTTTGCTTTTCTCTGCACGGTTGCAAAGATCCATGATACTGCATATTGCAACTGTAACAGAGTATGACGTGTGAGCAATTAAATTCAAATAGAATGAACGTTCCCAATTGACATCAGCTAAATTTATATTGGTGATCTTTTCAAGCTTAGGAGCCCATCTTCGCACAAAAAAGGGAGGTGGATTTTCCATGTTATCACTGGACCTGTACCCGTTCAATTTCATATTATTAACAAAGAAGACAAGGTCATCCTCTTCCCTCCCCTTTGAAACCCTACCATGCACGAAGAAAAGATCAAGTATTTCATGCCAGAATTTATCATCCATTTCCACGTCTGATGCATCAGCTTCAGCATCAATAACTGTCCAGCCGATCAAATCTGAATGTTTTTTCACCATACTCAGCAGTTTGTTCCTTGAGGACGAGGCCCCGGAGCCGCTCTCTACGGCGACCTCGACATCTCCGGAGGAGGACGGCTGGTGCGGAGGAGGACCAGCCATCGAGAGAGCGGAGAGGAAGAAGGAACGGGAGAGAAGGGCGGCGGCGATCGGCGGTGGATGGCCGGATGCGGCCGCCGCCGGCGACTCTCGGTGGCGTTTGGGTGTTGAATGGGTTTATTAC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.802248
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0249700.2 4 5656497 T C
Osa04LNT0249700.2 4 5657628 T C
Osa04LNT0249700.2 4 5655948 A G
Osa04LNT0249700.2 4 5656302 G A
Osa04LNT0249700.2 4 5656415 G A
Osa04LNT0249700.2 4 5656752 A G
Osa04LNT0249700.2 4 5657370 A G
Osa04LNT0249700.2 4 5657416 A G
Osa04LNT0249700.2 4 5658406 A T
Osa04LNT0249700.2 4 5659301 A G
Osa04LNT0249700.2 4 5659518 A T
Osa04LNT0249700.2 4 5660033 C T
Osa04LNT0249700.2 4 5660700 T G
Osa04LNT0249700.2 4 5661053 T C
Osa04LNT0249700.2 4 5661531 G A
Osa04LNT0249700.2 4 5661733 A G
Osa04LNT0249700.2 4 5665597 T C
Osa04LNT0249700.2 4 5665938 A C
Osa04LNT0249700.2 4 5666290 G A
Osa04LNT0249700.2 4 5666431 T C
Osa04LNT0249700.2 4 5656118 C G
Osa04LNT0249700.2 4 5664752 C T
Osa04LNT0249700.2 4 5662754 G A
Osa04LNT0249700.2 4 5662970 T A
Osa04LNT0249700.2 4 5663097 T G
Osa04LNT0249700.2 4 5663268 A C
Osa04LNT0249700.2 4 5663396 G A
Osa04LNT0249700.2 4 5663735 A C
Osa04LNT0249700.2 4 5663171 T C
Osa04LNT0249700.2 4 5662486 G C
Osa04LNT0249700.2 4 5662583 A G
Osa04LNT0249700.2 4 5662707 G A
Osa04LNT0249700.2 4 5658982 G T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa04LNT0249700.2 DTM_#DNAt_MULE_japo_Os0053 Chr4 - 5662443 5663751 1308
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0249700.2 osa-miR5834 Translation 4.5 11.567 1 21
Osa04LNT0249700.2 osa-miR6256 Translation 5.0 17.396 1 22
Osa04LNT0249700.2 osa-miR171i-5p Cleavage 4.5 15.135 1 21
Osa04LNT0249700.2 osa-miR530-3p Cleavage 4.5 10.606 1 21
Osa04LNT0249700.2 osa-miR1426 Translation 4.0 15.038 1 21
Osa04LNT0249700.2 osa-miR444b.2 Translation 3.5 12.238 1 21
Osa04LNT0249700.2 osa-miR444c.2 Translation 3.5 12.238 1 21
Osa04LNT0249700.2 osa-miR1853-3p Cleavage 3.5 11.627 1 22
Osa04LNT0249700.2 osa-miR395x Translation 5.0 17.468 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0249700.2 4 qCTS4-1 Resistance or Tolerance Cold tolerance RM335 RM261
Osa04LNT0249700.2 4 qSNP-4a Morphological trait Panicle/flower RM401 RM335
Osa04LNT0249700.2 4 spp4-2 Morphological trait Panicle/flower RG449 CDO456
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