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

>Osa11LNT0089000.4

TTGTAGTTACACGTGCGTTCTAATAAGAAACATTATTATATCTAGTATGCTTACCAAACCCCTAAACACGTCGGCAATCCTCAAAACACCTGAGCCTCTTGAATTGCATTCTCAGTTCTGGCAACCACCGTTCTGATACCATCTTTTCTTGTTCACCATTAAGATAGCAGCTGGCCACCCTTTCATATTCCTGTTGAGCACTATGTACAGGGTTTAGCAAAACACGATCATTCTCAACCAGATTTCTTCGCGTCTGATCAAGCTGAGGATCCAGTCACCAGTTTGGACAGATTTATTAACAGTTGGGAGTGGGTGCTGACTCATGGATATTTCAACAGTCTACTCTTGATAATTGCTGCCTCCTTTTGCCATCAAATGATACCCAGACGTTACTTCTTGCATCATCTGGTATCTTCAATTCAAGTCGTGCAGAAATCAGGAAGGATGACAAGTCTAAATGACAATGAGTGCGGGCAGATTGGAGTAAACAGCAAACATGGGGCATTTGGATGGACCATTGAGCCTCCAGCTGCACCAGAGTATGCTGTACTGCCAGTCGGTATAGCTACTATCACCCCCATCTCCTTCAACCTTTGTGATTAGATGGTTATGCTCGTAGCATTCAATTTTGGGCAGGTATGGATCAGAACCCTCATATATGCATTTTAAGGGTTATATAAACTCCAAGTGTAATGTTACCATGGATGACAGTTACCACTCCAAGTGCTGAGGAATCCTAGCACAAAACCTTGCATCTTGAATATAGAAGGTGTGCACAAAACCATAACCAGGAATCCTAGCAAATATATCATGAACAGCAGGCTCGATGAGAACATTCAAATGATCAAAAGCAAAGCAACTGTAATGCTATGCAGGATATCTGTCAATTGTTGAAACGATAACCTCTTTAAGATGCATCAATTGCAAGGGAAAGCCTGTTTCCTTTCCTCCCTTCTGACGCGGCCCAGTCAACCTCTTTCTTCCTGCACCAGCCTGGCCTAGTGTGTCGGCCTCTTCCTCCTCCCACGAGAGCGCCGTAGGTATAAAACCCCCCTTACATGTACAGCTTGAGACGAATTTCAGGCCTGCTGATCGATTATCAATTGATCTGCACATTTGGACTAGAACTCTGCATTGCAACAAGATTACCTGACCAAACTGATCCAATGTAAACCAGCTCACGGCCATCAAGAAAGAATGTCGACGGCAGCGGCATGCATGACAGGAGATACTTAACGATCTTCTCCACCGAGCAACAGCACAACCCAAGTCATATTAACATGTCGCATGAATCTGGCAAGGCTATTGAATGAAGAGCACCCTGAGTTAAATCATTAGCTTCCAGGTGTTGATGATCCATCAATATGACCTGTTTTTTTTTCTCTCCAGATAAGGGATACCGTTCCTTTCAGCAGATTTTTGTGATCCAAGCTGACAATTGCCTTTAGAATTGCTGGCATCAGATGTCCTAGGATCAACTGTTACCACTGAAGCTTCGATTTACCTTTCCTCAACAGATGTGGAGGCTCCATTGCTGGATGGTTTTCCATTAGTAATACCAGAAGCAACTGATAGAATATAGTCACTATCAAAGGATGCCCCAACTTTTCAAGACCATAAAATCTCAGCTGCTTTATAGTCAATGGCTCATTTTGTTCAGCGCTGAGACTCTGTTTTGTCCTTAAGTGGTCAGTAAACTACTCGACCGTCACTGAGGGTTCAGAACAGATTTTGGATATACTCCTTTGCTTCTAAAAATGTCAGTCATCCCATTTGTTTGGGGAACACATCTCAAGAAGGAAACCATGCCTCAAGGGGATTACTCTCTAATATATAGCTTGACTGAAGTTCTGTCCTGGTGCCATGCAGTTCACCTTGCTCAGTACTACTGTCGTGCTTGCTCAGTACTTTTGGATACACTTCTATGCCACATCCAGATTATGCCGTGCTGCTTCAATGTCTATGTAACATGTTTCCCTCTCCTTCACTGTTCCATCAGATTACAGAAGTGCTGTTTTTGCTACCTTCTGAGGAGAAACCTGGGCTGTTTGTGAGCTGGTCTGTTTGATCATTCTTCACAGGCTTACCATTCCCATTTAATGAGCCATTTTGTGTATCCACAGTCTCTCAGCACAAGTGACATGCTGCTTCCATCTCGAGACCATCACATATGTCCTACCATTCCCTTCCTGGCAATGAAGATAAATGGGCTTCTTCACACTATCAGACACAACTTCTGTCAATCGCTGAACCTGTTTGGCAGAGGGTGCAGTCCCAATCTCAACAGGTATATTCACCACCTCTATCTTTCCCAGTGAGACAGCTTCCTGAACTGCCAAAAGATATAAATCATCTTTAACATCTTCCTCCCAGAGATCAACTATAATTTTGAATCCCTTTGACAATAACCATTCTAGTTTCTCCCCGCTGAATTGTCCTCCCCTCCAAAATGCAACCTCAACAGTCTATCTCATCTGGCAGTCGAGCCCGATCCGCGAGCTGAAGAACGACGCCCACGCGGCGACGACACCATGCCGCGCGCCACCACCACCTCCCGAAGACACCATGAAGCGCAGGAAGGGAAGGAGAAGAACGCGGTGGCGGGTGGCGACGGGGAAGGGGACGGAGTTGGCCGCGACGGCGTCGACGAGTGAGGCCGTGACGCGGAGGGGATCGGGAGGCGGCGCGGCGCTTCCGCCTCAACTCCGAGCGCCTAAGCCACAGCCGCCGCCCCACCACGCTCGAGCGCTGGCCCTACTCGCCGCCGCCTCCACTCGGACTCGCCGTAGCAGCCGCCGCCTCGGCCGCGCCGCCACCGCCGGCAGCAACGCCGCCGCGGCGACTGAACGGGGAGAGGGGAATCGACACGTCACACGCCACACGCCTCTCC

Coding Potentia
Explanation CPC Score
noncoding -1.01471
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa11LNT0089000.4 11 4559389 T C
Osa11LNT0089000.4 11 4557952 G A
Osa11LNT0089000.4 11 4558326 G C
Osa11LNT0089000.4 11 4559077 A C
Osa11LNT0089000.4 11 4560273 A G
Osa11LNT0089000.4 11 4560517 T C
Osa11LNT0089000.4 11 4560656 A T
Osa11LNT0089000.4 11 4561765 T C
Osa11LNT0089000.4 11 4561917 A G
Osa11LNT0089000.4 11 4562605 T C
Osa11LNT0089000.4 11 4563170 A G
Osa11LNT0089000.4 11 4564541 C G
Osa11LNT0089000.4 11 4565013 T G
Osa11LNT0089000.4 11 4565769 A C
Osa11LNT0089000.4 11 4566629 A G
Osa11LNT0089000.4 11 4560132 A G
Osa11LNT0089000.4 11 4564443 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
Osa11LNT0089000.4 osa-miR5796 Translation 5.0 19.661 1 21
Osa11LNT0089000.4 osa-miR6255 Cleavage 4.5 20.346 1 22
Osa11LNT0089000.4 osa-miR818f Translation 5.0 11.842 1 21
Osa11LNT0089000.4 osa-miR167a-5p Translation 5.0 6.75 1 21
Osa11LNT0089000.4 osa-miR167a-5p Cleavage 5.0 15.442 1 21
Osa11LNT0089000.4 osa-miR167b Translation 5.0 6.75 1 21
Osa11LNT0089000.4 osa-miR167b Cleavage 5.0 15.442 1 21
Osa11LNT0089000.4 osa-miR167c-5p Translation 5.0 6.75 1 21
Osa11LNT0089000.4 osa-miR167c-5p Cleavage 5.0 15.442 1 21
Osa11LNT0089000.4 osa-miR319a-3p Translation 4.5 13.806 1 21
Osa11LNT0089000.4 osa-miR167d-5p Translation 5.0 6.75 1 21
Osa11LNT0089000.4 osa-miR167d-5p Cleavage 5.0 15.442 1 21
Osa11LNT0089000.4 osa-miR167e-5p Translation 5.0 6.75 1 21
Osa11LNT0089000.4 osa-miR167e-5p Cleavage 5.0 15.442 1 21
Osa11LNT0089000.4 osa-miR167f Translation 5.0 6.75 1 21
Osa11LNT0089000.4 osa-miR167f Cleavage 5.0 15.442 1 21
Osa11LNT0089000.4 osa-miR167g Translation 5.0 6.75 1 21
Osa11LNT0089000.4 osa-miR167g Cleavage 5.0 15.442 1 21
Osa11LNT0089000.4 osa-miR167h-5p Translation 5.0 6.75 1 21
Osa11LNT0089000.4 osa-miR167h-5p Cleavage 5.0 15.442 1 21
Osa11LNT0089000.4 osa-miR167i-5p Translation 5.0 6.75 1 21
Osa11LNT0089000.4 osa-miR167i-5p Cleavage 5.0 15.442 1 21
Osa11LNT0089000.4 osa-miR167j Translation 5.0 6.75 1 21
Osa11LNT0089000.4 osa-miR167j Cleavage 5.0 15.442 1 21
Osa11LNT0089000.4 osa-miR1872 Cleavage 4.5 16.463 1 24
Osa11LNT0089000.4 osa-miR2867-3p Translation 5.0 18.013 1 20
Osa11LNT0089000.4 osa-miR2874 Cleavage 4.5 18.101 1 24
Osa11LNT0089000.4 osa-miR5507 Translation 5.0 13.185 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa11LNT0089000.4 11 nan Morphological trait Seed RM332 RM229
Osa11LNT0089000.4 11 elr11-1 Physiological trait Eating quality RM1812 RM209
Osa11LNT0089000.4 11 qDLR11 Resistance or Tolerance Other soil stress tolerance RM2596 RM286
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