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

>Osa07LNT0387700.1

TGAACAAGGTAAACTACGAAACCAAAGTCAGCTAATCCATCAGCGTCGCTGGGGAATTTGAATGACGCATGCAGAATTGAGTCCACCAGTCTAGAGTAACCGACATAAACAACACTTTGGATGTATTCATAGTTTAATAAATTATCTACGAACTATATACATAACATACATATTGAACCCTTAAGGTCAGTTTGTCTAGTAGGAGGTTTTGCTGTCTAACCGTGTAAACATCAGGCCTATGCGATGCAGCTAAACTATTATCAAGCTACAAGTGATGATCCTCCAGACTTAAAAGTGTACACTGTTCTGTAACTACATGACACATTTGGTACGACAATGCAACGAAACCTCTTCTGCAGTGAAAAAATAATCACGGGGTCCTGATAATTTTAATTGCTTCCCCTCCACTTCTCATGTCACTCATTAAAGCAATTTGATGCAGAAGTTGGGCAATCCTCTTATCCTTCTCCTGCGAGAGCAGCACGAGCAGGTCCCTCTCCCTCCTGTCCCGCCGGCGCGCGTAGAGCAGCGCTCCCACCACAACGGCCGCGCCCGCCGCCGACCACACGGCGGGCCTCACCGCGGGGCACCCGCACGTCCCGTGCACCATCAGCCCCTCCCGCACGGCCCCGACCCCGGCCGCCCACGCTCGCCTCGCCGCCGCGCGGCACCTCCCCCACCCCCACAGCCACTCCCCATCACCAAATTCATCATCATCATCATCATCATCCTCCTCGCCGTCGTCTTCCTCCCCTTCCTTCGCCGCAGCCTCCTCCGCCTCCCCCTCGACGCCGAGCCCCTCGTGGAGGCGCGGGGGGAAGACGTCGCAGTCGTCGAGGCCGCCGTCGTCCACGGCGGCAGCGCCCACGGCGACGACGGTGGCGGTGGGCGTCACGAGCTCCCAGGCGTCGGTGACGGCGGGGCCAGGCGGGGAGGAAGACGGCATCGAGCCGAGGGATGACGAGGAGAGCGAGAGGGTCAGCGTCTTGGGCTTGAGGAGGAGGTGCGGGTTAGGGGAGGGGAGGAGCAGCGGGTGGAGCGCCGAGTACGGCGATGCCGGCGCGGAGAACGGCGGGGACTGCGGCGCCGACGGCGGCGGCGGCAGCGCTGGCCTCTCGTCCATGGCTGCGGTTGCCGCGGCTCACCGGCGGATTCCGCTTCGATTTGCAGATGGTTTGTTTGGATCTGGATGATCTTTCATGTGGCGCTCGAGATCGATGACGACTGCTGCTGGTTTTCACTCCACCTGTACTGAATGGTCCGAGTTGAAAGGACAGCGATGTGTTTAATCCCAATTCAATTGAAATCTCTAGCATGCATTCAAATCTTATACATATTTCACACGAATTGCAGATTATTAAGAAAGAATTTGATAATTTTTTGAATAAGACGAGTGATCAAACGTTGTAAGAAAAACTTAAAATCCCTTATATTATGGGACGGAGGGAGTATTAATTTGGAATTTCAGATTAATTTGGTTTGTGTTTACATTTAGTCGCGACTAAAATCTTTTTTTTAAGCGTGTTTTCTCGATATCGATATTTTGAGTCTGTTTGACACAGCTCTAGCTCCACCCCTTCTGGAGTTTCCACCTCCACAGCTCAACCAAAACTGGATGGAAGTGGAGCTGGGTAGAGGAAGTGGACCCTGGATGAACTGGATGGAAGTGGACCCTGGGGTACCAAACAAGCCCTTTATTTCAACAAATCTACTAGTAGTACAACTTTCAGGTTAAAGTTTGAATCTAATTTAGTTGAGGTGGGCCATCAATTTTGCTTATAATCAAAATTTAAACTTGATTTGGTTGGGGTGCGCCAGGCCCGGGCGGTAGTGCAACGCCTGGGCGACACGCGAGGGCCCCAGTGGCAAGCCACTGTGGTGGACCCTCCCCCACAAAAAATAAATTTAATATCGAAGTGAACACATGGCCCACATATCAGATATTAAACTGATAAGAACAGATACTACACTTGATCTTAGCCAAAAGGCCGAGAAAGGTAT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.665542
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa07LNT0387700.1 7 24240626 A C
Osa07LNT0387700.1 7 24243455 A G
Osa07LNT0387700.1 7 24243519 T C
Osa07LNT0387700.1 7 24243592 A G
Osa07LNT0387700.1 7 24243755 A G
Osa07LNT0387700.1 7 24243766 T C
Osa07LNT0387700.1 7 24243512 T G
Osa07LNT0387700.1 7 24241278 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
Osa07LNT0387700.1 osa-miR408-3p Cleavage 4.5 14.718 1 21
Osa07LNT0387700.1 osa-miR2120 Cleavage 5.0 12.951 1 24
Osa07LNT0387700.1 osa-miR5072 Cleavage 4.5 16.737 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa07LNT0387700.1 7 grb7-2 Morphological trait Seed RM505 RM336
Osa07LNT0387700.1 7 qCDS-7 Physiological trait Source activity R2394 R2677
Osa07LNT0387700.1 7 qLCC-7 Physiological trait Source activity R2394 R2677
Osa07LNT0387700.1 7 nan Others Others RZ395 RZ264
Osa07LNT0387700.1 7 Ph7a Morphological trait Dwarf RG650 C285
Osa07LNT0387700.1 7 nan Resistance or Tolerance Other soil stress tolerance C451 R1245
Osa07LNT0387700.1 7 qLVG7-2 Resistance or Tolerance Cold tolerance RM336 RM118
Osa07LNT0387700.1 7 Ra7a Others Others RG650 C285
Osa07LNT0387700.1 7 QRl7 Morphological trait Culm/leaf CDO497 CDO385
Osa07LNT0387700.1 7 qSDS-7-2 Physiological trait Germination/dormancy RM320 RM234
Osa07LNT0387700.1 7 qPH7-2 Morphological trait Dwarf RZ626 RG650
Osa07LNT0387700.1 7 qCIVG7-2 Resistance or Tolerance Cold tolerance RM336 RM118
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