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

>Osa09LNT0446000.2

TCATTCACTAGCATCCAGAACACTTAATCTAACAGTAGAGGGAACTTTCCCTGCGATGTATTTCTGGATAGCCGAGAGAGCTTTAGGCACTTCCTTGAGAATACCAGGACTCTGTTCAGAACGATTAGCCAAGCCAAGGTTCGTGTTCAGAGTAAGGTGCTCAAGAGATGCTGCGTTCTCAAGAATATGACATGTTAGCTCAACCATGCTCTTCGCGGAGCAGAAACCGTTGATCGTCACACTCTTGAGGTACTCATATCGGTGCTCCGGAATCTGCCTCATAAGTGAGGAACTTCCAAATATCGATTCCTGTTCTGCTTGTTGCTGAGATATAGCCAAGAAGAAAGTCTCCAATAAAGGAGAAGCAGCAAGAAAGGAAACTAGAGAGAGATAATCATAAGCTGGCGAATTGGTCAATCCAATGAGAGAAATACTCAAGTACTTCAGGTAGGGGAATTTGGTAGGTAGCATTGGTGTGTTGAACACCTCACGGAGCGAACCTATGGAAAGAGTTTCAACATTTGGCATCATGGATGGAAGAGTGGCACGGGCATAACGGACAATGCGTGAGCTGCGCATATTTAGTTTCTTCACTTGCAACCACTCTCCAAGTGAAAGTTTTACCTTGTTTCCAGTAAAGTAAAAACTGGATACATTTGGAGCTTTGTTCTCTATAACTCGCACCCTGCTGCATTCTGAAACCGTAATATAGCTGAGCTGCTGCAGTGTGCAAGGTATCTTCAGGCTAACTATCTCATCGCAATGCCTGAGTTCCATCCCCTCGAGAGCCAACGAATTCAAAAGAAGGCACCCTAAATCATCCTCCGTGATACGCACAAAAGACAAACATAGCCTTTTAAGGCTTCTCCATGAACCAGGTTCGATTGTGGGACAGAAGGCGCAATGGCCAAGATCAAGAATCCGAATAGAATCTGCCATCCCATCAGATAGAAGTGAGCATGGGAAATTGTACTTTTGAGCAGTTCCATACAGCGTAAGAGTGAGTTCTTCGATCGCTGGTGTAATAGCAAATTGAAGCCAACGATCAACATGGTCACAGACATCTAGCTCATACGGGACTTCAAGCTTGAATGTCTTCACACAAGTGCCCGAGTGTCTTTTAAGAATGTGGTCAACTTTGCTGATGAAATCTGTCTCACAAACATGTTCATCCAATCCCAGCGTATCCTTGTTAAAGGTGAGGTTTGGATAACATAACCAGGAATTTAGAAAGGCACGAGACACACATGCAACACGAGCCGCATCTCGCATTGGCATCAGGCAATGTATACGGCGCCAGATGTCCTTTGAAAGCAACATCCCTGAATTTTTCATTCTTTTAGCACCCTGAGAATCATCATCTTGTTGGGAGGGTGAGAATTTCCTTTTACCCAATTTAGCAATTGATCTATCGCAGTCTCCCCAAAGTGTGTATCTCCTGCACTCCAAAGTATCCAACTGAACAGCAATACATTGGAGCAGACGAATCAGTGAAAAATCACATCCTTCTTTCCCAATCCCTAAATTCCCCACTCCTCTCCTCACCCTCACAATTCGGTAAACCCAAGTCACAAGTTTCAGCTCTGGTTGCCATGTTCAGTTAAGTGCCCCATGCTATGATAGGCTGCATCACTCTTTCACCAACGAATCAACTATCTCATGTTGTTATAAAAAAAAAAACTATCTCCGTCTCATAAAAAACCAATCCTATTGGATATGACACATTTTATTACTATGAATCTGGACATATAGAATATATCACATCCCATCTAGATTCGGTTTTTATGGGACGGGAGGGAGTACATCTCATACAATCCCCCCCCCCCCCCAATCATGAGAAAATAAATTGTAGATTAAAATTTGTTCAGAAAGACGCCAGTTTGGATACCTAGCCTACTCAAACAAAAACAATGAGGAACACTTAATCTTGTTACCAACCAATGCACTAGGTTTAACCCCCTGATGAAAAGAAAACAGGTTTTTTTTTAAAGAAATCCTACAAAGAAACATACTAGCCCGGATAGAAACACCATCACGGGCATGGCCGCTTTGTTGCAAAAGAACAATCTGAACAAGTTATATAAGCCGGAGGAGGAGGCCGAGGGAGCTTAGCTTACAGCGGTGTCGGTTTCGCCGGCGGCGACGGCGCTGCCGCCTCCGCCGGGTGGGCATGACCCGGTTCATCTCGAGCGTTATCCCCATGGCCGGCGGCGGCGACACCCGGAATCGAATCAACTCCGCGCGGTCGCCGTCGCTCCTACTCTCCTTCTCCGCTGTTCTACTTCGATCTAATCTATCGATCTCTCTTGCTATTTATTGGCAAATCCTGCGACGAGGAGGGAGGAGGAGGAGATCGTGTTGGCGCCGAACATCAGGAGTCCAGGATGGCCCAGGGGATTATCA

Coding Potentia
Explanation CPC Score
noncoding -1.19404
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa09LNT0446000.2 9 19461143 T C
Osa09LNT0446000.2 9 19462048 T C
Osa09LNT0446000.2 9 19462685 A C
Osa09LNT0446000.2 9 19460880 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
Osa09LNT0446000.2 osa-miR5788 Translation 4.0 15.969 1 21
Osa09LNT0446000.2 osa-miR5796 Translation 4.5 16.399 1 21
Osa09LNT0446000.2 osa-miR7694-3p Cleavage 4.5 15.724 1 22
Osa09LNT0446000.2 osa-miR164c Translation 5.0 19.776 1 21
Osa09LNT0446000.2 osa-miR426 Cleavage 4.5 22.243 1 21
Osa09LNT0446000.2 osa-miR395w Cleavage 5.0 14.272 1 22
Osa09LNT0446000.2 osa-miR1442 Translation 3.5 17.913 1 20
Osa09LNT0446000.2 osa-miR1852 Cleavage 3.0 18.843 1 21
Osa09LNT0446000.2 osa-miR1865-5p Cleavage 3.0 20.923 1 24
Osa09LNT0446000.2 osa-miR1873 Translation 4.5 12.646 1 24
Osa09LNT0446000.2 osa-miR2122 Translation 4.5 9.816 1 22
Osa09LNT0446000.2 osa-miR5082 Cleavage 3.5 17.909 1 24
Osa09LNT0446000.2 osa-miR5145 Cleavage 4.5 17.904 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa09LNT0446000.2 9 nan Resistance or Tolerance Other soil stress tolerance R2638 C1263
Osa09LNT0446000.2 9 cisc(t) Resistance or Tolerance Cold tolerance nan nan
Osa09LNT0446000.2 9 qGL9 Morphological trait Seed RM257 RM242
Osa09LNT0446000.2 9 Symptoms Resistance or Tolerance Other disease resistance RZ228 RG667
Osa09LNT0446000.2 9 mrl9a Resistance or Tolerance Drought tolerance RM201 RM410
Osa09LNT0446000.2 9 qCCAI-9 Physiological trait Source activity RM257 RM201
Osa09LNT0446000.2 9 Ta1 Morphological trait Culm/leaf RZ228 RG667
Osa09LNT0446000.2 9 Ta Morphological trait Culm/leaf RZ228 RG667
Osa09LNT0446000.2 9 Ta Morphological trait Culm/leaf RZ228 RG667
Osa09LNT0446000.2 9 ta9 Morphological trait Culm/leaf RZ228 RZ12
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