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

>Osa04LNT0255900.2

AGGTGGAAGCATTAATTTTTCATATACCTTAACACAATGTACTTTTACCTATATGTTACTCCATACTACATATACTGCTTTTAGAAATGTTTGTAAATGTTTCAGAACTGTGATTTCATTTCATGTTATCATCAGAATACCCGCCCTGCTTACATTTGACAAGGGTGACAGTAGAGATATGAAGAGACTCAAGTGAAGTTCAGAAAACAGTTTTCAGGCATACGCTACAACGTGTCCAATCGGAAACTGATCAACAGATTCATTTGGCGTTGCCAGCAATCTCTCCCCATGTCACGTATCTCGCCGCAATTGAAGCCCTCAATACCTTGTATGGAAGAAACCTGTATTTTGTGGGCATAGTAACAGATGCCAAACATGGCCATTTTTCTCCAGCAAAAACTTTGTACATTTGCAAGTACAGTCCACTGCCAGGCCAATGTAGAGTAGGCCTATTTTCTTCTAGACCATTTGTTGTGGTTTTCTTCAGTTAGTAGGGCAACTGGCAGGGGATTTCTCCAGCACAGATTGCTCACGTTTCCATTGGAGGTGATAACCAGGGATCTGCCTTGGACTCACCCCTTTCTGGATGGGTGGTGAGTTCCATGACTGTAGAGGCCTCCCGATCGGTTGAACAGATGCCAGAAAACCTGGAGGTGCTTCGGCTTTGCGCATTACTGTTAGAACTCTTGAGAAAAATGATGACCCACTCAATGATACTGCCTTCTCAACAGATTCCTTGTCAGTGAAAGTAACAAATGCAGCCCCTTTAGGGTGCCCAGAAATTGCATCTGTCAATATATTTATCTTAAGCACAGTGCCGCACTTCATAAAATGCCCTGACAATGCTTCCTTTGTTGCTGCAAAATGTACATTTGTCACGAGAACAGTTCTGGAGTCAGCATCCTCATCTAGATTAGCATGGGGACCTGATGATAGGAAACCTTGCTTCACATTGTTTATCTGTGCCTGCTTGGAACGAAGCTTGAGCACATCCAGTTCCACTTGTTTGAGCTTTAGTTTCACATCCAGCATTTCATTTTTCATAGGCTTGTTACAGCAATTTCCACCATCTTCATGTACAGAAGATCCTGTCTTAGATTGCGCTGGGCTGCTAACTTGCTGACTTTGCAAAACTTCAGTCTCTAAATTTCTCCGTGTAGCTAGTTGACCCAATTTGCTAGATCCTGGTACTTGTCCTTTTGTTGATTTACTCACATGGCATGCTGACTCAGAGACTGCTGTTACTGAGCTCTTCACTTCAGATATGAATTCATTCTGACTTTGTAGTGGAACACTTCTTGCTGGCAAATTTGGACTGGACTTTTGGCGAATAACATCTCTAACTTGAAGCTGATTACGCTCAATATCACCAAAATTTATCCGACCAATCAACCTGCTTCTATTGGACTTCTCTGTGTGCTCATGTGCTTGTACTGTGTTGACATCTTGATAGCTTCTGGGAAATCTTCTGGAATTTGCTATATCAAATAAATCTCCTTCTGTACTTGAGTTCATACGGCATCTTAGCTCATGCTCAGTGACCATTAACTTCGCCTTCTTATGTAGTCCATTTTGAACATGCATGTCATCATCTTCTGTAGCACAAATACGATCCTTTATGGCAGGCTTTCCTAGCCTATCCCAAACATTGCCACGTTTTTTAATAGATTCTGGATCTAGCACATCATCACTTCTTACAGCCAAAGGAAACCGTCTTGCAGAAGCATTTCTTCCAATGCACACTTCATGGCGGAGTTCATCTTGTGGCAATGCTTGTGCTGTCCTTACAGCTACACCAGACTTCAGTGTGGAGAAATTTCTGCCACTTGATGATCTCTGATCTTTCTTCTGATGTTGGCCCTCCCAATAACATTGATCGTCAACCAACTTTTCAGGAGTAACAGTAACCGTCGAGCTAATGTGGCGTCGGGCCACATTTTGTCCTTCAGTTGAGTCATGCTTCTGAAGAGTATGATGCTCTTGAGGTGATGAGATATCTGAATTGACCTGATCAATATTGGATGAGTTCGTTGAGTCCAAAAATATGAGCAATTTTTACTTGAAGTCCTTCAGTGTTCATGTTAGTTTAGAACTTCAGATATATGATGAAAAAGTTGAACGCTGTATGGACACAAACATTCAAAAAGTTGGTATTAATTGGTCGGTTACGGGTACCAGAACAAAACTGGACAGAATACTTCAAATACAATCTAAATTCAGTTTGTTAATTTCTTAGCGCTATTATTTTCAGTCCTTACCAGCCGGTAACCATTATTTGTATTTGAAATGATTTCCGGTAAATTCTGGTAACTGGCAGCAACCGATCCGGCCCAGGAAACCTGAAGATTTTTCTTGGTACTACGGTTCCGGATCTCATTTGTCAGACCATGCTGGATGCTAGAATTGTCAGCCAATGTTAAAGCCTTTTTACTGAGGTAACCCCAAAGCCATGAAACAAATTTTGCACTATCATCACCAAGGAAGGCCTCCAAGTCATCACGTGCTTGGTACTGGTGTTTCCCATTACAGACTAGAATGACAATGTATTCCGCGAGGATGTCGTCGGTGTAGCTGCCGAGGAAGCGGGGGAGCACGTCGGCGACGGCGGCGCGGAGGGCGTCGGCGTCCGGCGAGAGGCGGTCCATGCGGAAGGAGCGCTCCCCGGCGGCGAAGAGGCGCAGGCTCCGGCGCAGCAGCTGCTCCTCCGCCTCCGCCGCCGCCTCCCGCCCCATCGCCTCCGAATCTCCTGGTCGCGGGCGGCGGCGGCGGCGATAGGCGGCGCCTCTGCTGCTCAACGAGGGAGAGAGAGACGTGGCAGGT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.903368
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0255900.2 4 13821909 A T
Osa04LNT0255900.2 4 13822577 A G
Osa04LNT0255900.2 4 13822610 A G
Osa04LNT0255900.2 4 13824073 G A
Osa04LNT0255900.2 4 13824742 G A
Osa04LNT0255900.2 4 13824754 A G
Osa04LNT0255900.2 4 13824903 A G
Osa04LNT0255900.2 4 13825624 T C
Osa04LNT0255900.2 4 13825684 T C
Osa04LNT0255900.2 4 13826576 C T
Osa04LNT0255900.2 4 13827530 A G
Osa04LNT0255900.2 4 13827686 C T
Osa04LNT0255900.2 4 13827938 A G
Osa04LNT0255900.2 4 13828399 G A
Osa04LNT0255900.2 4 13828476 A C
Osa04LNT0255900.2 4 13829202 T C
Osa04LNT0255900.2 4 13829280 G A
Osa04LNT0255900.2 4 13822364 A G
Osa04LNT0255900.2 4 13829844 C G
Osa04LNT0255900.2 4 13822025 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
Osa04LNT0255900.2 osa-miR5802 Cleavage 3.5 16.531 1 24
Osa04LNT0255900.2 osa-miR5823 Cleavage 4.0 19.57 1 24
Osa04LNT0255900.2 osa-miR5837.2 Translation 5.0 10.247 1 21
Osa04LNT0255900.2 osa-miR6249a Cleavage 5.0 17.708 1 21
Osa04LNT0255900.2 osa-miR6249b Cleavage 5.0 17.708 1 21
Osa04LNT0255900.2 osa-miR166j-5p Translation 5.0 19.438 1 21
Osa04LNT0255900.2 osa-miR1428a-5p Cleavage 4.5 15.516 1 21
Osa04LNT0255900.2 osa-miR1854-5p Cleavage 4.0 16.429 1 21
Osa04LNT0255900.2 osa-miR1880 Cleavage 4.5 23.48 1 24
Osa04LNT0255900.2 osa-miR2874 Cleavage 5.0 16.853 1 24
Osa04LNT0255900.2 osa-miR5340 Cleavage 4.5 16.238 1 23
Osa04LNT0255900.2 osa-miR5340 Translation 5.0 16.712 1 23
Osa04LNT0255900.2 osa-miR5503 Cleavage 5.0 13.958 1 22
Osa04LNT0255900.2 osa-miR3979-5p Cleavage 4.5 24.053 1 20
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0255900.2 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0255900.2 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0255900.2 4 spp4-2 Morphological trait Panicle/flower RG449 CDO456
Osa04LNT0255900.2 4 nan Morphological trait Panicle/flower RG788 RZ69
Osa04LNT0255900.2 4 An8-glum Morphological trait Panicle/flower nan nan
Osa04LNT0255900.2 4 nan Morphological trait Root RZ69 RG449
Osa04LNT0255900.2 4 nan Morphological trait Root RZ69 RG449
Osa04LNT0255900.2 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
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