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

>Osa04LNT0254100.2

GGCCGCGAAGACATCGCTTCTCCTCCTCGCACGCTCATCCTCCTCCCCGCATGTACTGAAGCCGCATCCTCGCAGGAGCTCCTCCCCGCTGCCGCCGCTCCACTGAAAACTCGCCGAAGCCGCCGCCACTGCCACTACCTCCGTCGGATCCTGCTTCTTCCCCCATCGCCGCAGCCGTCCTCCTCGCTCGCTCCTCCTCCTCCCCGTGTGATTTAAGCCGCATCCTCGCCGGAGCTCCTCCACGCTGCCGCCGCTCCGCCGCATCCTAACCGGAGCAGCCGCCGCCGAATCCTACTTCTTCATCACCGCCGTGGCCGGAGCCGATCTCGGCCCCTTCCGCCGCCACCGACACCGCCGTGCACTCCACCGCTGGCCAGCACCGAGGTCGGCCCTCTTCCCCATCTGCCACTTCATCATCAGATCACCAATGTTTGCCCCATTGTTGAAAGCCTATAGTACGAGTAAGTCCCTCAAATCCTGTTTCTTTTCTTAATCTTCTCCGTACGTGTGGAAATTTTGATCTCTATGTCTGATGATCTTTGTTCTTGAGCCTTGGCTATGTTGGATAAATATTCAAGAAACCTAGATAGTGACTGCTGATACGATTCCTGTTATGTCCTGTCTGATGCTGAATCACGAGGGATTCTCCAAGAGGACGGGAAGCTGTCAAACAGCACCAGGCAGTCAAGTTGTAGAGATGGTGAAAAGTATGGAGAAGCTGCAGTCAAGTTGCTTGCTGCTAAGTTAGGACTAACAGGATCAATGGGTGCTTGCTGATAAAAGAATGCATATAAATAACAAATGGTGGAGGCGGATAAGGAGGCTGGTCAAGTCTAGCCTCCTACAACTATGTCACTGCAGTACAACATCAAAAAAGGAGATTATGATATCTGAAAACTACAATCGTGAAATTTGAAAAATAAAGTGCATCAAGTTTGCCATGGAGATGGCAACTACCAACCCATAGTCATGCGGACATCAAGAAACATCATAGGAGCACCTCACCATCACATGGCTATGAGCAAGAGGGGTCTGCTAGACTGTTGTGAATTCCCAAAACAAAGCTGGATGCGCTAGACACCATCTGAAGTTGGTCCATGGCAACTCAATTTCTTCTAGCAAATACAGTATTATGAACAACAACTTTTCATGATTCTAACCTCCAATAATCTGAAGTTCCCAGTTTGATTATATAATCTAGGAACCAAATCATGAAGCTGGCGACATTGGTAAGAGGAAATGCTGTTGATCAATTTAATTTTGTATTACGCTACTGTAAGATGGCTTGATAGGAGTTTTGCAATACATACTGCACTACTGTAGGCACTGGCACAGTTTGAGAGCACAACATATAGAGTTTCCTTATTCAACACAAAGGCCATATCGTTTCATTCAACAAATGGGCTAATAATGCCATTACATTTGACGCATGCCACTACATTTCAGAACACAAATTCAGCCATTTGTTTCAGAACACTACATTCCTGAACAAAGCATACATATTTGTTTTGTGGTTTACAATGTGATGTTTATATCACAGGCTTTGTGTACTTGATGCTGGAAAACATTTATGACTTTATATATACTTCCTCAAACAATTTAAGATTCTCTTTCTTGATTTGTTTCTGCATGTAATGGTGAGTTTTCTGATTACTAATAACTGTCATATGGCTTCATTTATATTCGACCCTATGGCAATGTCGGAGCTAACCGGGTTTGATTATTTGTGATCACCTCAAGTGTTGCTGCTTAAGCCAAAGGAAGAGGAAAAACTTTTATATAAGCATTTCATTTCATATAGGTTCCCACATCTTTTCTAGGTACTATTGACACTCTAGAAAAGATTGGATGGCCTTCTAGGTAACATTGATACTCCTGTCCAAAAGGTGTTTGACGAATTTGGAAGGCCTTCGCTGATTGCTAAATATTTGGAAGGCCTTCGTTGTTTGCTGAAGATAGACCAAACCTGTTTACTTAAACAAGAAATAGATGGTTGTGGGGGAACATTCATCTTTACATTCTTTAGCTTTCCCTAATTTTTCAGTATCTTGTAGTACATGAAATTGCAATTCCTTTTACTTACTAGAAAGTAAATGTCATGCATTTGCAACTTTGTTATACAACAAATATATCAATAGGGGTTTGTGAGCAATGTTTTGAAAATTAGATTATATCATGTAAGGATTTCATATCTTTTTTTACCAAGACTATCTTACGAGTTTTTAGCCTGTATTTTGTGTTCAAATCTTGATGTTTTCATGCAGTCAATCTTGACAAGAATGCCACCATCCTTTTCTTTTTTGCCATGGATTTCATTGTTATGCTGTAATCTGGTGTGGAATATAGGAATGGCTACTTTGTACATTATGAATATACATGTACCTTTGTTGGCTAGAAAGTAGTGTGATTCAAC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.148655
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0254100.2 4 11255951 T C
Osa04LNT0254100.2 4 11256153 A C
Osa04LNT0254100.2 4 11256341 A G
Osa04LNT0254100.2 4 11257570 A G
Osa04LNT0254100.2 4 11258445 T G
Osa04LNT0254100.2 4 11258527 A G
Osa04LNT0254100.2 4 11259029 C A
Osa04LNT0254100.2 4 11259053 A T
Osa04LNT0254100.2 4 11259327 T C
Osa04LNT0254100.2 4 11259386 A G
Osa04LNT0254100.2 4 11257537 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
Osa04LNT0254100.2 osa-miR5532 Cleavage 4.0 12.439 1 22
Osa04LNT0254100.2 osa-miR5798 Cleavage 5.0 13.511 1 21
Osa04LNT0254100.2 osa-miR5828 Translation 4.5 12.525 1 21
Osa04LNT0254100.2 osa-miR5830 Cleavage 4.5 14.449 1 24
Osa04LNT0254100.2 osa-miR5835 Cleavage 5.0 12.85 1 24
Osa04LNT0254100.2 osa-miR5337b Translation 5.0 18.591 1 21
Osa04LNT0254100.2 osa-miR395f Cleavage 4.5 13.355 1 21
Osa04LNT0254100.2 osa-miR164c Cleavage 5.0 13.027 1 21
Osa04LNT0254100.2 osa-miR164c Translation 5.0 20.271 1 21
Osa04LNT0254100.2 osa-miR171i-5p Cleavage 4.5 9.628 1 21
Osa04LNT0254100.2 osa-miR418 Cleavage 5.0 13.945 1 21
Osa04LNT0254100.2 osa-miR1852 Translation 4.5 11.268 1 21
Osa04LNT0254100.2 osa-miR1879 Cleavage 4.5 14.508 1 24
Osa04LNT0254100.2 osa-miR5498 Cleavage 3.5 18.092 1 21
Osa04LNT0254100.2 osa-miR5509 Cleavage 5.0 14.144 1 21
Osa04LNT0254100.2 osa-miR5513 Translation 4.5 15.434 1 21
Osa04LNT0254100.2 osa-miR5518 Translation 5.0 11.284 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0254100.2 4 qCER4-1 Morphological trait Shoot/Seedling RG190 RZ69
Osa04LNT0254100.2 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0254100.2 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0254100.2 4 spp4-2 Morphological trait Panicle/flower RG449 CDO456
Osa04LNT0254100.2 4 An8-glum Morphological trait Panicle/flower nan nan
Osa04LNT0254100.2 4 qPEN-4 Morphological trait Panicle/flower RG190 RG908
Osa04LNT0254100.2 4 nan Morphological trait Root RM261 RZ69
Osa04LNT0254100.2 4 nan Morphological trait Root RM261 RZ69
Osa04LNT0254100.2 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0254100.2 4 qSNP-4a Morphological trait Panicle/flower RM401 RM335
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
Osa04LNT0254100.2 4 11259053 Blade-pubescence-at-vegetative 10.68865871 +