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

>Osa04LNT0257700.2

GGAGCGCAACCATTGCTGCTTTTCTGTTTACTTCCTTAAAAAAAGCAACTCAAAAACTGGAAATACAACCACCAGGACCGATTCTGCCGCCGTGATCTAGCTGCGTCCATCCCCACAGCCACACGACGTGTCTTTGAATTCGGCGCACGACGCGGACAGCGAGCTAGCCTCGGATGCCCTCACAACTGACTCCTCGCGATGGCTATCCACATAGATCGTGGGCTCACGCATACAGACTCAAAATGAAACACATGCAGATTAAGTAGCTTAGCACACAAGTTTATTGTTAACATGAATAACAGAAGCCAAAAGCATATTCAATACAAGTATACATGCAGATGGATTGCCACATTGGCTAGAAAGTTAACCATTAAGGTCTAGATGGGAGCAGGCCTCACGAAGAGAGACTCTATAATCTCCCTAAGAAGTGTGGCAAATGTGTAGGCATCATTCCTGTCATCGTAGAAGAGTACCATAGAAACGGTGAAGTTCACAACTCGCTGCACCATGGGCAGCAGTGTACCATGCTCAAGGCGGGTCTGGTTCGTGGTTCTCCATTCATCTTCGACCAGTGAATCAATCTTTGCAAAGGCGACCTCGCTTGTGACCCTATTCTCATTCATGTAACACTCTACGGAGCTCGCAACATCTCCCTTGTTCTTTCCACACTTAAATGCAGCAATATCATTCATAAAACGTCCAATCTTTGCGCATGCTATGACTGCATCATTACCACTAGCTGCCCACTCGAATGCTTCTGTCGTCACTGCATTACCCCAGCCAATCATAGCAGCCACACACACTAATTGCACGGCCGAGGATTTGGTGGACAAAACCACCTGATCTTTAAAGCTTGGCTTGTGTTTCTGGTAGGACCATTCAGCTTCTTGTAGGTAATAAGTAGACTGCCTTTGAAACTCTTGTTTGGTGTAAGTAACCTTGTATTTTTCGTTGTCGGACACTTGGTGCTCAAACTCCTCAAAGTTGATTAGCAATTTAATATAGAACTTTTTCAGGTACTCCGGCAAAATAGAAATAGCGCTTTTGTCCCATCTTTGTATGGCTGTGTTTAGCTGCCGGCATTCCTCAACGGTGGCATGAGCATCATACGTATCATCCATCACAGTATCCAGTGCAATTATTTTGGCAACAAACATTCTGGTGAATGCAAAGTCTTCTTCGTAGAACATCATGTAGGACCAAGCGTATGCCTCTATCGTACGATCCCTAATGTAACGTAGCTCCATATATCCATAAAGATCTTTCCACCATTCAGAAATTGCTTTGAGTTCCTCCAAGTGGATATGTTGCAGGAGGTTAAAATCTAGCTTCGCAAGTTCAAGAAGAAGTGGAATATTTCCCACCTCTCGTTCGTACTCCGACATGTAGCAAATAGTCTCAACTCTCTTGAAAGTCCTTGGCAGTGGTAGGCTAAGTGCACGCTTGACTTGCTCAGCTAATGGAGGGTTGAGAACACTGTCTTGACTCATCAATTCAAGGTGTTTTCGTGCAAATGAGATTGCTTCTTCAAGTTCTGGCTCGCCATGAATGAGGAGGTGTGCAGCGTTGTATAAACTTAGTAGCCCCTTTGGGTCATTCGCTATATCATTTCGAAACTTGCCATCATCTCCCTTAAATTTATTGAATGCATCTGGAGACACCCAAAACCCATGTTCCCTAAGCAAGCGAAACCGAAGAGCAATCTCATAGAGACTAGAGCTTCTGAATTCACTGCCATGGATGCTTGTTAGAGCATCTTCTATCTCCTCTTGGAAGAGGTGATCAATTCCGAGATGTTGGACGGAATCCACTAAGTTCATCCTCGCCGACATGTCGTGGCAGGTCCCAAATAGTGTCTGGATTTGCCCTCTCAGCTTCTCAGCCCTCTCCTGCATCCACCTCTCTGATCTAGAACGAGTCGGAGGCGTACGGGGAGACCGCTCGGTGAATGCGCCTCTCTTCCTCCCTTCTTGGCAACCATCGCCTCCCTTCCCGTCGGGCTGCCGGTGCCTCCCCTCTCACCGGATCTAGCGGAGGGGAGGGGGCCACCACCATTGCTGGGCCATCGCCTACTGGCTCTTGTGTCCTCTCCCGCGAGACAGAGAGAGAGAGGGGGGAGGGGGAGAGAGAGAGCGAGGTTGAGGAGGAGGAGGAGGAAGAG

Coding Potentia
Explanation CPC Score
noncoding -1.00946
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0257700.2 4 16350417 T A
Osa04LNT0257700.2 4 16350775 C G
Osa04LNT0257700.2 4 16351050 T C
Osa04LNT0257700.2 4 16351356 C T
Osa04LNT0257700.2 4 16351400 T C
Osa04LNT0257700.2 4 16351408 A T
Osa04LNT0257700.2 4 16352743 A G
Osa04LNT0257700.2 4 16352949 T C
Osa04LNT0257700.2 4 16353427 T A
Osa04LNT0257700.2 4 16353465 C T
Osa04LNT0257700.2 4 16353734 C T
Osa04LNT0257700.2 4 16353991 A C
Osa04LNT0257700.2 4 16354118 T G
Osa04LNT0257700.2 4 16354798 T C
Osa04LNT0257700.2 4 16354881 T C
Osa04LNT0257700.2 4 16356014 C A
Osa04LNT0257700.2 4 16356431 A G
Osa04LNT0257700.2 4 16356809 A G
Osa04LNT0257700.2 4 16356876 T C
Osa04LNT0257700.2 4 16356902 G A
Osa04LNT0257700.2 4 16350501 G A
Osa04LNT0257700.2 4 16351180 A T
Osa04LNT0257700.2 4 16356841 A G
Osa04LNT0257700.2 4 16351193 A 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
Osa04LNT0257700.2 osa-miR812r Translation 5.0 13.933 1 24
Osa04LNT0257700.2 osa-miR6253 Translation 4.5 22.594 1 22
Osa04LNT0257700.2 osa-miR7695-3p Translation 4.0 17.629 1 21
Osa04LNT0257700.2 osa-miR160c-3p Translation 4.0 21.069 1 21
Osa04LNT0257700.2 osa-miR396a-5p Translation 4.5 15.406 1 21
Osa04LNT0257700.2 osa-miR396b-5p Translation 4.5 15.406 1 21
Osa04LNT0257700.2 osa-miR396c-5p Translation 4.5 15.406 1 21
Osa04LNT0257700.2 osa-miR2275a Translation 5.0 19.539 1 22
Osa04LNT0257700.2 osa-miR2275a Cleavage 4.5 23.317 1 22
Osa04LNT0257700.2 osa-miR2275b Translation 5.0 19.539 1 22
Osa04LNT0257700.2 osa-miR2275b Cleavage 4.5 23.317 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0257700.2 4 nan Morphological trait Panicle/flower RG788 RZ69
Osa04LNT0257700.2 4 An8-glum Morphological trait Panicle/flower nan nan
Osa04LNT0257700.2 4 nan Morphological trait Root RZ69 RG449
Osa04LNT0257700.2 4 nan Morphological trait Root RZ69 RG449
Osa04LNT0257700.2 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0257700.2 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0257700.2 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0257700.2 4 spp4-2 Morphological trait Panicle/flower RG449 CDO456
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