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

>Osa12LNT0114000.1

CAGCGAGTCAATGCATCATCAGTCAGGACAAACACAGACATGAAAAATTGATGGAGTTCATCAACAATATTGTAATGCTAGCCACCTCAAGAATCTCAGTTATCTAAAAATAATTACATAACTGCGAAATGGCTATGAGTAATAACATTCAATCAATAGCTACACAACCTATTCTCTATAGGATGGATTTGATACAACGTCTGATCTCTATTGGATCTGATACAACTTATGATAGAACCCCCTACTCATTGGGTAGTCACACTCTTTGCCAGATTCCTTGGTTGATCAACATCAAATCCTCGAAGAACTGTCAGATGGTATGCGAGCAGCTGTAACGGAATTATGTTAATCACTGGCTGGAGACAGTCAGCGACCTCTGGAACTTCAATAACCCTGCAAGATCCACTAGGGCAAACTGCAGATGCGTCTCCCTTTGAGCACATCACTATCAGACGCCCCTTGCGAGAAAGGAGCTGCTGAATCACTGACTGTTGCTTGCTGAAGCACGCATCACGTGTAGCAATGACGATGATCGGAAGGTTTTCATCCACTAGTGCAAGTGGTCCATGCTTCATTTCACCAGCAAGCATGCCTTCGCTGTGCATCAGAGCAACCTCCTTAACTTTAAGAGCACCCTCTAAGGCAGTGGCATAGTTATAACCTCTGCCAAACACAAGGAGAGACTCTGAATCGATCAAGGAAGAGGAAAGTTCCTTCATCTCGGTATCAAGTTTTAAAACCTCGCTGACATTGCTTGGAAGATTGGAAAGACCACTGATGATAGCTTGACGTCTAACTTGGGTGGATATTTGATCAGATCCAACAGCCAAGGCCACCATCACCATGACTACTATTTGACTTGTATATGCCTTGGTACTAGCAACACCTATCTCACAACCAGCATTGATATGAACTCCACAATGTGTTCTTCTTGATAGTGTGCTTCCTACGGTATTTGTTATGCCAACACAAAGTGCTCCATTTTCTAGTGCATAATCAAGAGCAAGGAGGGTATCTGCTGTCTCCCCTGACTGGCTAACGAAAACTGCAGTGTCTTCCCTGTAGATGGGACCTTGTCTGTCCAGCAAGTCACTTGCAACCTCCATAGTCACAGGAATACCAGTTAATTCCTCCACAAAAGGTCTTGCAGCCAAGGCAGCATTGTAACTTGTACCACAGCCAATGAAAACTAACCTTCTACTGCGCCTAATAGTTTTGAGGTACTCCTTTTCCTTTAATCCTCCTAAAAGAACACCACTATCCTTCACTCTACCCCTCATGGTTGTTGTTAATGAATGTGGCTGTTCATGGATTTCCTTTTGCATGAAGTGGTCATAACTTCCTTTCTTTATCTGCTCAACTTCCATCTCAAGGACAGACAATGCTCGTTGCACAGAAGCTGGCTTCTCTTTCTCATGGTCAAACTTAAGGATAGACACACTGCCATCCTTAATATGAACAATTTCATCATCTTCGATAGCCAAATAATTCTTGGTATGCTCCACAATAGCAAATAAATCACTAGAGAAGAATAATTCTTTGGGCTTCCCGTTTGTTGTCAGAGCTTTGACATCATGAAATGGTTTCCCACTATTTTGGCCACTTAATTCATTGACACCGAGTATCAGTGTGCTGCCCCGTTTGCATGCAATCAATTCATTGGGGTAGTGTGGGCTTTTAAAGATAAGTGCGTAGGCTCCTTCAAGCTGCCTCATGACTTCCATAACAACTTGGCTAAATGTCACATCACCTTCTTCATCATGCGCCTTATCAAAAACAAACTTTGCCAACTTAGGGATGACTTCTGTGTCAGTATCAGACTCAAAGGTGAACCCGTGCCGGATTAGTGTCTCTTTCAGAACCTCGTAGTTTGTGATGATGCCATTGTGGACGACCAAGAACTCATCGCCGGCACCAGAAGATTGGGGGTGGCTGTTCCTTGGGGCAGGCACACCATGCGTGGCCCACCTGGTGTGGGCAATTCCAGCATGCACATTGAAGGCGGCGTCCAGGTTCACATCCTTCTCATCAACCTCGGAGTAGACGGATCGTACGAGGTTCTCGATCTTGCCCTCCTGGCGGAACACCAGCGGGGACGCCCCGGCATAGGCCGGCACCGCCGTAGAAGAAGAAGAAGAAGCGCAGGAGGGAACGTCGGCGTCGACGGCGATGCCGGAGGAGTCGTAGCCGCGGTACTCGAGGCGGCGGAGGCCATTGAAGAGGACCTCGAGGATGTAGCGGCGCTCCCGCGACACATTGTAGTTGAGGTACGCGAAGATCCCGCACATCGTGCGCCGCGCCGCGCTGGGCTGGGCTTCTAGAAGCTTCCAGAAGTTTCCGGGTTCGGGAGAGAGAGAGAGAGGGAGGACGCGGTTACGACGGCGGCGAGGAGTCGCCGGCCGAGGCGGAGGAAGAAGAGGAGAAAAAGGCCGCGTTTTTTTTTTTTTGATAGGAGAAG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.983216
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa12LNT0114000.1 12 1500426 C T
Osa12LNT0114000.1 12 1500609 T C
Osa12LNT0114000.1 12 1501970 A T
Osa12LNT0114000.1 12 1502438 A G
Osa12LNT0114000.1 12 1503714 T C
Osa12LNT0114000.1 12 1504474 T C
Osa12LNT0114000.1 12 1504852 C T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa12LNT0114000.1 osa-miR5807 Cleavage 4.0 17.366 1 24
Osa12LNT0114000.1 osa-miR169q Cleavage 4.5 19.621 1 21
Osa12LNT0114000.1 osa-miR171i-5p Cleavage 4.5 17.639 1 21
Osa12LNT0114000.1 osa-miR1850.3 Cleavage 5.0 14.311 1 22
Osa12LNT0114000.1 osa-miR2093-5p Translation 4.5 18.144 1 20
Osa12LNT0114000.1 osa-miR2870 Translation 3.5 16.365 1 21
Osa12LNT0114000.1 osa-miR3979-5p Translation 4.0 21.359 1 20
Osa12LNT0114000.1 osa-miR5505 Cleavage 3.0 16.026 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa12LNT0114000.1 12 gy12 Morphological trait Seed RG869 RG98
Osa12LNT0114000.1 12 nan Physiological trait Eating quality RM20 RM101
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