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

>Osa12LNT0117800.2

TTTCACACATATATATTTTTGCCCTTTTTTTTGGCACCATCATACAGAAACTATTTGTCATATAATGCATACATTTTCACTTAATTTTTGTTCCGCTAATCAAACAGTTTCTGCAATTGATCTAATTTTGCTCTCGTCCTTCTGGTCATGTAGCTACATTGTTCTCCCTGACACAAATGGAAGAACAGCTTCCGTGCTAACTTAAAATGGATTCTCTTCAATGTTGGAGACTTGATCGAAGCAATGATCTGAATTTTCTGAATTCTGACATACATACAGCCTACGGATTTAATCTTTCTTGAGGAGATCGTAGAACACTTCAGGCTTCTTGTAGTGCTTCTTGCACGCCTCCTGCATTGCAAATGCTATGTGGAGCAGAGTCGCCTCGGACCACGGCCTGCCGATGAACTGGAGGCCGATGGGCAGCCCGGCTTTGTCATACCCAACCATGACGGTGATGGCCGGCAAACCAAGGAAGTTTCCTGCAATTGAGTACCGGACCAACGCGGCTCCATTTATGTAGTCCAGTTCTCCGCTTTTTAGCGCGTCGTCTTGCAGCTTGTAGGCAGTCACACCGGTCATTGGTGAGACGATCACGTCTGCCGTCTTGAATATCTCCTTGTGGAAGTACATCTGACGATTCCGGAGCCGTTGCGAATTCAGGTAGGCTCTACTGCTGAAGGAACCATACACGCCAAGTGCGACCCTTACATCCCAACCGATTTCAGATCTCTTCAGCTTGTCAAGATATTTAGCAAGTGATGCAGTGCATTCTGAACCAATTGTCACATAGTGCGCAAGGCGCATCTCTTCGATCTCCGGTATGGTTACATCCAGAGTCTCCCAACCATAGTGCGCATGCAGCATCTGAAGAGATTTGTCGCAGCAGCTTCTGATGTCCTCTGAACTGTCATTGAACCACTTTGCATATTTTGCAAGCTTGATGTTCTTGATGGAGAGTGAAGACTTCAGCAAGGGCAGATTCAACTCAGGCCGCAAGTAGGATGGCTGAGACTGATCAACAATTGCTGAGTATGCGACGGCGGCGTCCTCGACCGTCCCAGCGAGGATCCCGGGCATCCCGACCGTCCAGTTCAGCGGCAGAACTCCGGCGTTCGACAGCCGCCCCGCCGTCGGCTTGAACCCGACCACGCCGCACAGCGCCGCCGGCATTCGCACGGACCCTCCGCCGTCGACGCCGAGGGCGACGGGGCAGAGGCCGGCGCAGACGGCGGCGGCGGAGCCGCTGGACGAGCCGCCGGAGACGCGGCCGGGGTTGTGGGGGTTCCTGGTGGAGCCGTGGTGCGGGTTGATGCCGCTGGTCCCCGCGCCGAGCTCGTGCATGTTGGTCTTGCCGGCGAGCACCGCGCCGCACGCGCGCAGCTGCGCCACCACCGCCGCGTCCGCCGCGCACGCCCGCGCCCGCCCCAGCCACCGCGTCCCGCCTGTGGTTGGGTAGGGCAAACAGTCGATCTCGTCCTTGACAGCGACCAGTATCCCGTCCATGGCAGACAGAGGTGTCCCTTGCTAGCCATAATAACTCTGGAAGAACACTGATTGATCTGCAAACCAATCGTATGCAAAGTTAACAGCTAACTAATCGGTGAGACGGCCAGGCAATGAATGCTTGTCTTCTTAGCCGTCTTTACAGTTGGATCAAAACATCAAATACAGCCAGCTCCAAGCCTCCCCTGTCAGGCTGTCACTGTTCCCTTAATCTCTTCCATCATAATCTCCCTGTAAATGTAAATGATCTGAACCATACCATAATGTGACATATGTGATGCTAATTACCAACATTAACATATCTCCATTGATAATGTCGTTGCCCTTTTTCTTGTTCAGAGAACAATAAATGTAACCAGCTCCAGCAGCATTAATTTCTGCAGCTCCCTTTCCTTTCTGTCTTCCTGTCTTCCTTCCATTGTGGATCAACCATTGTGATGTTTTTTTTTTCAAGATGTCAAAACAGAAGAAAAAAAACTGAAGAAATTGTTTGGAGTGTTGCTTGTGTATGTAGCTGTAGTTGTACTGCCTCCTGGTTGTTACCAAGTGGGTACAAAAAAGTTTGGTTGGCTGGCTAGAGGTCAAGACAGAAAGGTGGTGGTGAGTTGGTTTGAGAGGGACAAGTTCAGGCCATTCCTGTGTGCTGCTGCTTCTGCTGATGATAATTGCAACTTCCATGCATTGCTCTTGCTTCAGATACTGTTACTGCCAACTGTAACTTACATGTCAGTGTAAAAGAATGTTCTTTTTTTTTACCTCTCTGGTATCTCAGGGTGGATTCTTCAGCCTGCCTGATGATGTCTTCAGGGCTGTAGCTGATGAAGAAGGCCATGTTGAGGCCTGGGCCTGAGCACTCCTTCACTGCAGCCAAGAACCTCTTTGCAACCTGAACAGGAGTGACCTCCCCTGAGCTGTACGCCCTGTTGAAATCCCTGATCGTCCAGCGTTTCGGGCTCGACGGCGGCGAGCCGGCGAGGGTCGATTCGAGGCTCGCAGGGAGGCAGCTGACGGCTTCCTGGACACGCTCCGGCGGCGACAGGTCCGGCTTCGTCAGGCACACATTCTGCTCTGGAATGTCTTCCCAGCTGTGTGTGGAAGTGAACAGTGGAGGCTCTGGGATTTCAGCATCTTGGACAAGCTTGTTGATGAGATTATCCTTCTTGAGGATGTAAAGCACCATTGAGCCGATGATCGGCATCTCAAGAATCCACACGAAGATCTTCACCAGCAGCCCTGCTACCCGAGGAGCTTTGACGTTAGGGCTGATGTAGAACTCGTCGCTGTCCGGGCCGAGATTGACCTCGGCGGCCGGCTTGTACACCTTGGCGGCCATGGATGGCAACTTGGGAAGCAAAGGAGACTCTCCTCTGCACAACGACTGCTGCTAAGCTCCTCC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.829098
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa12LNT0117800.2 12 3503460 T G
Osa12LNT0117800.2 12 3503425 T G
Osa12LNT0117800.2 12 3503508 C A
Osa12LNT0117800.2 12 3504134 C A
Osa12LNT0117800.2 12 3504768 A C
Osa12LNT0117800.2 12 3505408 A T
Osa12LNT0117800.2 12 3506618 A C
Osa12LNT0117800.2 12 3507029 T C
Osa12LNT0117800.2 12 3507771 T G
Osa12LNT0117800.2 12 3506574 T C
Osa12LNT0117800.2 12 3505571 A T
Osa12LNT0117800.2 12 3505600 C 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
Osa12LNT0117800.2 osa-miR5532 Cleavage 5.0 14.669 1 22
Osa12LNT0117800.2 osa-miR5538 Translation 5.0 14.765 1 22
Osa12LNT0117800.2 osa-miR5807 Cleavage 4.0 22.424 1 24
Osa12LNT0117800.2 osa-miR7693-5p Cleavage 4.5 24.029 1 24
Osa12LNT0117800.2 osa-miR417 Cleavage 5.0 21.779 1 21
Osa12LNT0117800.2 osa-miR169r-3p Cleavage 4.5 21.643 1 21
Osa12LNT0117800.2 osa-miR169r-3p Cleavage 5.0 16.712 1 21
Osa12LNT0117800.2 osa-miR1851 Translation 5.0 20.188 1 21
Osa12LNT0117800.2 osa-miR2928 Cleavage 4.0 12.284 1 20
Osa12LNT0117800.2 osa-miR2928 Translation 4.5 20.725 1 20
Osa12LNT0117800.2 osa-miR5515 Translation 4.5 13.25 1 21
Osa12LNT0117800.2 osa-miR160a-3p Cleavage 4.0 21.948 1 21
Osa12LNT0117800.2 osa-miR160b-3p Cleavage 4.0 21.948 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa12LNT0117800.2 12 nan Physiological trait Eating quality RM247 RM179
Osa12LNT0117800.2 12 Pi-4(t) Resistance or Tolerance Blast resistance nan nan
Osa12LNT0117800.2 12 gy12 Morphological trait Seed RG869 RG98
Osa12LNT0117800.2 12 nan Physiological trait Eating quality RM20 RM101
Osa12LNT0117800.2 12 qDLA-12-3 Resistance or Tolerance Blast resistance RG463 RZ816
Osa12LNT0117800.2 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG241
Osa12LNT0117800.2 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG241
Osa12LNT0117800.2 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG241
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