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

>Osa06LNT0334400.2

CAAGATCAAACTTGTACAACGTAACATTCAATATGTGGGCCATTTTTGGCTGAGTTTTTAGGCCTCCATGAAGACCTACTCCTACATGACAGCATGAATTTACAAGACAACACTCCACGCAGCACGGGCGTAGGAAAAAGTCACTTTCTGCTGGTTGTAGCTATCCTCCCTATTAAGCACCCAAATTATATGCTGGTAAAAACAAAAAACACAGCAAAAACTAGGAATTGAAACCTAGCATCCCCATTGTTCTCCCATTATTGGAGCATTACAAAATAAAACTCCGTACAGCTTGTGATTCGACTGTAATGGGAATCAAAATTCAAACTAGTATGAGTATCTCTTCCAATGGAACGAGCAATCTTCTGCCCTGCGCCTCCAAAATCACGGATCCCTGCAGCTGAATAATCATGATGACCGATGTCCAGGTTTTAAATCTCCAGAGAATTTATACGATGTGATGTCGCCAGATGTTCCTTGTGAAGCCTAGTTCACAGTCTTGGTCAGTAGCAGGTGAACCAGTACGAGGAAGCCAAGCCCAAGCAAGAAAGTTTGCCCCTTCATATTTTCAACTAGCTCCCACCAGTTTCCAGCTGAAAAGGAACTCTGTTCCTTCGTGGCTTCCTCTACTGCAAATTCTTCTAACAGGGCACGTTGACGTTCATTAACCATTGAGGGAAAATGTATTCGAAATCGGACATGTTGGTCCCCAAGATACCCAGCCTGGTTGGGCAATCCTTTACCCCTTAAAACTATAACCTGCCCTGGTTGAACTCCTTTGGGTATCTTAACTTCTGCTGTGCCATCTAAAGTCGGCACTTCAACTTTTCCACCAAGCATTGCCTGTGTGAAGCTAATCTTTTTGTCTACATGGATATCAGCACCATCACGAACAAACACTGGATCACTTGCTACTTGAAGCTTAATGTACAAACTTCCAGGTAGGGTTCCACGTCCACCACTATGTCCAGCCTCTGGTACATGAATTGTATCGCCAGAATCAACCCCTGCTGGAATGGTCACATTTACATATTTCATGCCATCTACCACCCCTGAACCTTTGCATGTCAGGCAGTAATCCTTAATTACTTTCCCAAAGCCTCTGCAAGAAGTACAAATGGATGTGAATGGGTTAATGGAAACTCTTCCTGCACCTCTACATGAAGGGCAAACATACATCTTTGCATTGGCCAAGTACCCTCTCCCATCACATGAGTCGCAAAGATTTTTTGCACTGAAGGAGACTTGCTTCATGCATCCTTTAACAGCATCTCTAAAGGAAAGATTCACCTCTACCTCAATATCGTTGGCATGTGCATCTACATCATGCTCAAAAACCTCGGAGAATATTTTGTAAAATTTACTGGAAAAAGGACCATTGTTTTGTCTGTAGAATTCTGCAAAGGGATTATGACCCTGCTTGTGGAATCCTGAAAATGGATCTTGATAGGCCCCATCAAAATCCATCCCACTCTTTGAGGAATTTGTCTCAGACCCTCTATAAAATAGCATATCATACTGCTCTCTCTTCGAAGGGTCGCGCAATGTTTGCCTCGTATGCATCTCTTATTTCCTGAAATGTCCTTTTTGCAGCAGTATTCCCCCTGTTTGTGTCTGGATGGTACCTTTTTGCAAGTGAATGAAAAGCCCTCTTGATTTCTTCCTGCGAAGCATCTTTAGGAACACCAAGAATCTTGTAATAGTCCTTCTCTGGTGAACTGTGTTGACCTGTAGCATGAAAAGACCTGCTCAATGTAAATGATGTCAACATGAACCGTCCATAGCATTTATCACCAATATAGATGCCACTGGAGCTGCAAGGCGTGGAATGCCGAATCCATTTGCTCCCCTGCGCAGCCACCTCGCCGGAGCGTAGCGCGAGAGACCTCGACGCGAGCCGGAGCCACCCCAGCCGTCCCATCCACGGCGGCGGCGGCGCACGCGGCGAACGGGCGGCTGGTCTTGCCCGTGGCCCGTGGAGCCTCGTGGAAGAAGCGCGAGGGGCAGAGGTCCCGAGCGCGAGAGAGTGGGAGGACGAGGAGGAGGAGGAGGATCGCGGAAGAAGCGGAGGGTTCGAGAAGATTCCAGAAGCAGCTCGAGCTGCCTCGACTAGTCGCCTCGGGAGAGAGGGG

Coding Potentia
Explanation CPC Score
noncoding -1.16728
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0334400.2 6 6036987 A G
Osa06LNT0334400.2 6 6042958 A G
Osa06LNT0334400.2 6 6036790 A G
Osa06LNT0334400.2 6 6037201 A G
Osa06LNT0334400.2 6 6037578 C T
Osa06LNT0334400.2 6 6038391 A G
Osa06LNT0334400.2 6 6039484 C T
Osa06LNT0334400.2 6 6039684 G C
Osa06LNT0334400.2 6 6041676 T G
Osa06LNT0334400.2 6 6041856 G A
Osa06LNT0334400.2 6 6042372 C T
Osa06LNT0334400.2 6 6042969 A C
Osa06LNT0334400.2 6 6044146 A C
Osa06LNT0334400.2 6 6044719 T C
Osa06LNT0334400.2 6 6044815 T C
Osa06LNT0334400.2 6 6045131 G C
Osa06LNT0334400.2 6 6046254 G A
Osa06LNT0334400.2 6 6043121 C T
Osa06LNT0334400.2 6 6042943 A G
Osa06LNT0334400.2 6 6038036 T C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa06LNT0334400.2 osa-miR5791 Translation 4.5 18.58 1 21
Osa06LNT0334400.2 osa-miR168a-5p Cleavage 5.0 21.675 1 21
Osa06LNT0334400.2 osa-miR169b Cleavage 4.5 16.41 1 21
Osa06LNT0334400.2 osa-miR169c Cleavage 4.5 16.41 1 21
Osa06LNT0334400.2 osa-miR169f.1 Cleavage 5.0 16.41 1 21
Osa06LNT0334400.2 osa-miR169h Cleavage 5.0 16.41 1 21
Osa06LNT0334400.2 osa-miR169j Cleavage 5.0 16.41 1 21
Osa06LNT0334400.2 osa-miR169m Cleavage 5.0 16.41 1 21
Osa06LNT0334400.2 osa-miR169n Cleavage 4.5 16.41 1 21
Osa06LNT0334400.2 osa-miR414 Translation 4.5 18.176 1 21
Osa06LNT0334400.2 osa-miR419 Cleavage 4.5 15.528 1 21
Osa06LNT0334400.2 osa-miR1847.2 Cleavage 5.0 17.279 1 24
Osa06LNT0334400.2 osa-miR1883a Translation 5.0 21.571 1 24
Osa06LNT0334400.2 osa-miR1883b Translation 5.0 21.571 1 24
Osa06LNT0334400.2 osa-miR2872 Cleavage 4.5 19.509 1 21
Osa06LNT0334400.2 osa-miR5077 Cleavage 5.0 24.725 1 19
Osa06LNT0334400.2 osa-miR169a Cleavage 4.5 16.41 1 21
Osa06LNT0334400.2 osa-miR169g Cleavage 5.0 16.41 1 21
Osa06LNT0334400.2 osa-miR169i-5p.1 Cleavage 5.0 16.41 1 21
Osa06LNT0334400.2 osa-miR169o Cleavage 4.5 16.41 1 21
Osa06LNT0334400.2 osa-miR1869 Translation 5.0 14.004 1 24
Osa06LNT0334400.2 osa-miR169e Cleavage 5.0 16.41 1 21
Osa06LNT0334400.2 osa-miR169k Cleavage 5.0 16.41 1 21
Osa06LNT0334400.2 osa-miR169l Cleavage 5.0 16.41 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0334400.2 6 nan Physiological trait Eating quality RM253 RM162
Osa06LNT0334400.2 6 amy6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0334400.2 6 asv6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0334400.2 6 AsTol Resistance or Tolerance Other soil stress tolerance RZ516 RG213
Osa06LNT0334400.2 6 tns6 Morphological trait Panicle/flower RG138 RG64
Osa06LNT0334400.2 6 sd6 Morphological trait Panicle/flower RG138 RG64
Osa06LNT0334400.2 6 qRCRJ-6 Physiological trait Source activity RM217 RM402
Osa06LNT0334400.2 6 sd6 Morphological trait Seed RG138 RG64
Osa06LNT0334400.2 6 tns6 Morphological trait Seed RG138 RG64
Osa06LNT0334400.2 6 qLDLJ-6-1,2,3 Physiological trait Source activity RM217 RM3
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