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

>Osa06LNT0351400.2

CCCTGGTATCAGATAAGATTAGCATACATATATAGAGATATTGGATAGTGCATTGCAAGTTTACAGGTGATTATGTCTGACTATTTCAACTGGTATACCGTGACCAAGTTCTTTCCTCAGTTTGCATCATGGACAACTGCAGGAATGTGCTATTGTAAATCTGTAACACCTATAGCCCAGGAAAACAACAGGGGTGGCCATGCCAACACAGCGACACAGAAAAGAATCGTCAGAAGCAAACCACCAAAGGTGTTGTAGGTAAGCTATGGCAGCTGATCATCTTCAACGACCACCTGTTCATTCTTTGTGTTCGCCATTGACAGAACCGTTCTGCTCGCCGAGCTTATGGAACTCGGCTTCGATGACCTCGACGATCTTGGCATCCTCAGGATCTTGGTCAGGGATATTCACATGCAGGGAGCCCTGCTTGATGAGCTCCTGGTTCAATGCCTGCTCGTCAATGTAGTGGTAGAGCTCTTGGTGGAAAGGATGATCGAGAGAGAAGCAATTGTTGACGTCGTTCGACGAATTTTTAGATGATCCTGAGCCTTCCCGCTGACAGAAATGGGGAAGGGAGGAGTGGTCCATAATCTTTAGAAGCTCATCTCTCCCACAACCATGCAAAACGTGAACCTTCTTCCGTGTCCTCTCTTGCAAGAGAGGCTTCACAACCTTCCAACATGCCGAGAATATATATGGAGCATTAACTATATAATAGGTCTCTGCCTTTTCAGGGTAATTCAGATCGTCAACAGTAGATATTGCAGTCAAAATCTTCATTTGGTTGAGTGCTGACAATTTCAATCCAGTCATATCTAGAACCTTTATACAGGTGCTAATAGGCCGCCCAAACTTCTTTGATGCCATAGGCAAAACAATACGGTCACGGTACTCATTGATTTGAATATGAGATTGCACATAGTAATGAACCGAAGCTTTGTCATATGTACTCTGTCCAACACCAATGGCAAATACTGGGATGCCCTGGAAAAATAAAAGGACTCCTTTGAGTATCCTGATAATCCAACAAGCTGTGTCTCACGTATTGATCTATATAAATCTACAGGAATTATAGGTTTCTCCAGTATACTATCAATTTCATTTTGTATCCTCCAATTCAAGGAATCCACAAGCTAGCAAAAACAAAATATCTTTAAGTAATGAAGCAATCCAAGAATCATTTTTTGTTCATCATTCATCAAAT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.849121
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0351400.2 6 24142609 T G
Osa06LNT0351400.2 6 24144153 A C
Osa06LNT0351400.2 6 24144288 T C
Osa06LNT0351400.2 6 24144623 A G
Osa06LNT0351400.2 6 24144885 A C
Osa06LNT0351400.2 6 24144938 C T
Osa06LNT0351400.2 6 24145000 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
Osa06LNT0351400.2 osa-miR398a Translation 5.0 16.006 1 21
Osa06LNT0351400.2 osa-miR5160 Cleavage 5.0 10.429 1 22
Osa06LNT0351400.2 osa-miR5160 Translation 5.0 16.383 1 22
Osa06LNT0351400.2 osa-miR2275c Cleavage 4.0 9.501 1 23
Osa06LNT0351400.2 osa-miR5795 Cleavage 4.0 23.274 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0351400.2 6 RPLD4 Physiological trait Eating quality RG424 RG172
Osa06LNT0351400.2 6 nan Physiological trait Eating quality RM253 RM162
Osa06LNT0351400.2 6 amy6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0351400.2 6 asv6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0351400.2 6 tgw6.1 Physiological trait Source activity RG264 RM3
Osa06LNT0351400.2 6 prt6.1 Resistance or Tolerance Drought tolerance R2549 RG716
Osa06LNT0351400.2 6 nan Morphological trait Root RM4447 RM5509
Osa06LNT0351400.2 6 ph6 Morphological trait Dwarf RZ667 RG653
Osa06LNT0351400.2 6 qLDLJ-6-1,2,3 Physiological trait Source activity RM217 RM3
Osa06LNT0351400.2 6 gw6 Morphological trait Panicle/flower RG424 R2549
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