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

>Osa09LNT0447900.1

AAATGATTCCAAAAAAAATGCATAAACAAACATAGAATAAAATTGAAAATTTAAATATGATTTTGATGATGTTCTCAATTAATCTATCAACGGCATTCTGATTAAACATAGTATGCCAAAATAAACATGTTTATATATCAACTCATTCCAACATTATGCAAACTAAACAAACACCAACGATCTTGGGGATCTGATCAGTATTGTTTCTCTATATTTCCCCCATTTTGGAGAATTAAAAAAAACTTCACAAAATGGTTAAATTAAGCAAACTGCTAGATATATATAGGAGATCAAAGCCCTAGGGGTTTATTTTCACCAGAGACTAAGTCAATACCCGAACCACCACATCAGCTTGAGCCAAGCCTAGCGCAAGGTTCGTTCTTGACTTGATCCCTCTGCAACTCACCCCATTTAATTTGCTCATCTATGCAAATATACTCCACACACTATATATAACTTAATTTTATTTTTATCCTCGCTCGCATATCGCCTCTCGAAAACTCTACCTGATCAACGATTGAGTTGCATCCATCAGCCAGTTTCGGTCGGCCATCGCCCGCCGCGGAAGTCCTCTCAGTCTTCTAACCTTCAAAAGTTAGACATTTGAGATGGCATCCGATTCGACTCAAAAATGGTCGAGTCGGAATCCACGTCAAATGTCCACTTATCTATGGTGAGATGATGCTGGCCTGCAGTGCCGACTTGATCTTCTGGATGGTGCAGGAGAGGAGGTTGCTGACGGTGTCGACGGACTCCACGGTGAGCTTCGCCGTCGGCAGGTTGTTGACGAGTATCTGGAACGCCACCGTCACCAGCGACCCGGTGTTGTTGCTACCGCCACCGCCACCGGCGGCGGAGTTCGGCGAGGCGCCGCTGCCGACCTCTGCCGGAGACGGCGAGGCGCCATTGTTGTGGCCGTCGGGGAGGATGGCGAAGCCGGAGGGGAGGAGGGAGACGTAGGCGGAGTCGCCGCCGTTCATGACGACGTGCATCGACTGCACGTCCACCGGAGCGTAGACGACGAGGGAGCCCGATGAGTCGGTGCACGTCTCCTGGAGGATCAGCATGTTGTTCTGGTTCCCGCTTGTGGCATTTGGACGGAGGAGGGAGACGGCATTGCCGTGGTGCTGGCCCTTGGCGATGTGGTCCATCTCCTGCATGGCCTCGCCGTTGGCAAGGATGTCCCAGTCGCCGCGCCGCTGCTCGTCGCGGAGGTAGTCGAACACGCGCTGCGGCAGCGTGCCGGGGAGCCGCACCGACGTGGTGGCGCTCAGCACGACGCCCGGCGGCTCCCCCGGCGCGCCCACGCTGTGCCGCGCCATCATCCGCACCTTGTCCTCCCCGTCCCCGCCGCCGCCACCGCCGCCGCCCCCACCCTCGCCGCGCCACTCGTCCAGGCGCCGCCACTTCTGCGCCGCCGACGCGCACACCCCCGCGCAGAAGTTGTCCGTCATCCGCTGCGCCAGCTTCAGCATGCTCCTCCTCCCCACCGGCGTTATCGCAGCGTGGTCGCGGGCGGGGAGGGAGTTGGAGCAGAGGATGGCGAGATACTGGCACTGTCGCTGGAGCGAGGCGAGCCAGCGGCGGGCGCCGAGGGCCTGGCCGGAGCGGAGCAGCGGCCGGTAGAGCTGGTGCGCCGCCGTCTCGTCGTACTCCGCGTGAACCACCCACGTGACCTTGGAGTAGCCATTGTTCATGTCCTGCACGATGCAGCCGGTGGGGAGGAGGCGGCAGCCCATGTACGACGACGACGACGACCCGCCGCCGCCGTTCTGGTCGGGGCGGAGGACGGCGTCGACCGAGACGTCGACCACCGCCCAGAGGCCCTCGGCGTGCTGCTTGCAGAAACGCAGGAACACCACCTCCCGTATCGGCACCAGCGGCGACAGCACCTGCAGCTCCGCGTGCATCAGTTGAATTGACCCGCTGCGCGTGCCGCCCATGCCGCTGGAGATGATGTCCGTGGTGCTCGCTCTCGCCACCACGCACGGGAACATCTCCGACCACCGTGGCGCGTCCATGAGGCTGTCGACGAGGTCGACGCTGCTGATGATGGCGATGCCGGACTCGCGCGTCGCCTCGGAGACGTAGCCGGCGGGGCACTGGCCGACCACCCTGGCGAACGCGCGGTGGTACTCGTCGTAGTTGAGCGTCTCGAACCCGCCGTCGAGGCTGGGGAGCCAGAGCGGCTCGTCCATCTGCGCCACCTTGACGAGCTCGTCCATGGCCGCGAGGGCGAGCTCCAGGAGCACGGCGCGGTCGATGGCGCCGCCGTCGGCCGCCGCGGCGTGCATGGCGCCGTCGAGGCCGCCAATGCCCGCGGGTAGGCGCATGGCGGCGGAGCCCACGGGCCCCCCCGTCAGGCCGGAGGAGCCGCCCATCAGGTCGGGGATGGACTGCATCGCCGCCGAGGCCCCGAGCGCGCCGAGCCCGAACCCGCCGTTGCTGCCGACGCCGAGCTCGAGGCCGGAGCACGCCTGCAGCGACGGCGGGCCCGGGGAGGAGATGCTCGAGATTGGCCGGCCGAGGAACTTGCCGGCGAGCGCGCAGACGCGGTCGAGCTCGTCCTTGAGCCGCGCGTTCTCGATGCGCAGGTGCTGCTCCTCCAGCGACACCTCGCCGAGCACCGCCGCGCCGCCGCAGCTCGCGCACATCGGGTTCCTCATCGCCTCCCGGATCGTCATGTTCTCCGCCCTCAGCTTGTCGTTCTCCTGCCGCAGCAGCGCGTTCTCATGCCGCTCGATCTGCGTCTTCATCTGGGTGCGGCGATTCTGGAACCAGAACTTGACCTGGCGGCTCTCGAGGTTGAGCCGCCGGCTGAGCTCCATCCGTTGCTTCTCGTCAGGATGTGGACACTCCTTGAACACGGCTTCGAGTTCTTGGATTTGCTGCGGGGTGTGGCGGTGATAACGCTTCTTCTTCTTGCGCGGGTTGCTGTTGTCCGGGTCGAGTTCGTCGCCGGAGGCGCCGTCCAGGTTGTCGCTGCCGGAGCGGCTGTCGTTCTCTTCCTCCCGGCCGCGTCCCAGCGAGTCGCCGTCGCCGCCGCTGCCGCTCCCGCCGTTGCCCATCATGGCAAGCGACCGGTTCACGTCGCCGAGCTGGCTACCGTCCATAGTTTGCAGGCCGAGAGAGAGGCCGGGAGCGGCGAACCCGCCGCCGGGCTTGGGGACGGGCGGCGTAGGGAGGAGGCGGGAGTTGTGTACTCCGCCGCCGCCGCCGCCGCCGCCGGCGTCGTAGGAGAAGACGCCGGAGCCGGCGCCATCGAACATGCCACCGAAGCTCATCACGCGAGCTCACTACAAATGACAAAACAAACACCAGTTTTTCTTCTTCTTCTTCTTCCTCCGGCCAAAATCACTCCACCGTGATCCTACCAACTCCGGCGGATCCCCTCAGATCCCAACAATTCAATAATTTTTATGAGCCTCGGGGAGAGGATTTGGCACGCATTAAAACGGCTGGAGGGCCGCATCAGCAGCGCGGCTATACATGGCATGGCGGCAGCAAATATGGAAGCGAATTATTGCAGCGTCGCGGACATGGAAGGCAACAAGCCGGACACGCCGGAGGCGCGAGCCAAGAAACAACAGCTCATCCGCCGGAGAAGACAACTTTACACACACACACCCCAAGCTCGGTCGCCGCCGGCGTCCGTCCTCGCCGATCCTTGCTTAAACCAAGAAAGCTACTACTACTACCACTTCCGCCGCACCGTGCGACAGGAGAAGGAGAAGCTAGTAGTAGTAGCTAGCATGAGAGAAGAAGCGAAGAGAGGAGAGGAGTTGAGGAGGAGGAAGGATGGGAGATGATGAGAGGAGGAGGAGGCGAGAGGGTGGCTGGAG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.0582022
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa09LNT0447900.1 9 20570201 G A
Osa09LNT0447900.1 9 20569828 A G
Osa09LNT0447900.1 9 20571801 T C
Osa09LNT0447900.1 9 20572426 A C
Osa09LNT0447900.1 9 20569274 A C
Osa09LNT0447900.1 9 20568458 T 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
Osa09LNT0447900.1 osa-miR5819 Translation 4.5 18.61 1 21
Osa09LNT0447900.1 osa-miR1850.1 Cleavage 5.0 20.46 1 21
Osa09LNT0447900.1 osa-miR1862d Cleavage 5.0 13.816 1 24
Osa09LNT0447900.1 osa-miR1862e Cleavage 3.5 14.077 1 24
Osa09LNT0447900.1 osa-miR2118a Translation 5.0 3.271 1 22
Osa09LNT0447900.1 osa-miR2927 Cleavage 4.5 23.713 1 23
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa09LNT0447900.1 9 gy9 Morphological trait Seed RM242 RM215
Osa09LNT0447900.1 9 qMXN-9 Morphological trait Root RM201 OSR29
Osa09LNT0447900.1 9 nan Morphological trait Root RM160 RM3808
Osa09LNT0447900.1 9 Symptoms Resistance or Tolerance Other disease resistance RZ228 RG667
Osa09LNT0447900.1 9 mrl9a Resistance or Tolerance Drought tolerance RM201 RM410
Osa09LNT0447900.1 9 Ta1 Morphological trait Culm/leaf RZ228 RG667
Osa09LNT0447900.1 9 qCCAI-9 Physiological trait Source activity RM257 RM201
Osa09LNT0447900.1 9 nan Resistance or Tolerance Other soil stress tolerance R2638 C1263
Osa09LNT0447900.1 9 nan Resistance or Tolerance Drought tolerance RZ12 RM201
Osa09LNT0447900.1 9 Ta Morphological trait Culm/leaf RZ228 RG667
Osa09LNT0447900.1 9 Ta Morphological trait Culm/leaf RZ228 RG667
Osa09LNT0447900.1 9 nan Resistance or Tolerance Drought tolerance RZ12 RG667
Osa09LNT0447900.1 9 yldp9.1 Morphological trait Seed RM242 RM205
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