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

>Osa09LNT0450900.1

GGCCAGCAGTTTGACAAGTTTTAGGAACTGTTACCTCGAAAGAAAAAAAAATTCAGACAAGTGCTCAAAATTAAGGTTCCTCACAGTTACCAGACAACTCTCACCATGACTGATTACGGAATTGAATTTTACCAGCCCATCATAAACATACAGTAAAAGCTAATGGCGTCGAATTTCACCAGTGCATCATAACCAATACAGTAAGCTCGCTAATGGTGAGTTATCTTATCTCCTCTCCCTCCTTTGCCTTAAGAGGAGGTGCTCTTATCTGATGCTGTTCCCATCCTCTGTTGTATCTCAAATAAAGCTTGGCCCACAAAATCGCATTCATCTTTTTTTGAATCCACGCCACAAAAAACTCTCCTCGTGAACAGGCGTGACTCCAAAAACATATGGTGTATGAGTTGCCACCACCTCGTGGAAGCAAACACATGTAGATCTCTATCCATGTTGTTCATCTCGTGTAAGATCAGGGAGATTAATGTTTCGTTGTTGATAGCATCTAATTGTTGAATCAGTATAATGCAGGGTCTTCTCGCTGTAGCTCTCAGGAACAGGTCAGACACCGCCTTTGACCCAGTATTTTTAAAATCCTTCAGCACTTGCATTGCATCAATGACTATGGAATCGAATGACTGTGTTGCTGCAAAGAGTTTGGTGACATCACTCTTACTGAGCGAGGTGTTCCCATACAGAATGGCATTTGTCACAACCCAGCGTGAATTTGGATCAATCGACTTGTTTGTTTCCAATAACTTTAGAAGAGACATTCCAACACCATCCCAATCCCCCTCTTTCTCATCATTTCCACAATAAAATCGTGTCCTGATTCTTGAGAGAATAGTCGGGCATATCAGGTTTATCCACCTCACAGATACTACCAGAATAGTAATACGATGCCCGAAAATCACCCAAGGATCATCAAGCAGCAATTTAAGCTGGATGCAAAACAAAATGTGTGTATGAGCTAAGAATCTAAAGTAGTGAAAGAACTAATCTTTCACGCGAAGTTACCATATCCACGTCATCAAAAAATTGTGAGCCATCCGATTTTCACTCTAAGCGTTATACTGGGTGGTTGTTATGTCAGTCATAACTGTTGAACCACATCTGTTGTGAGGGACCAACTCATCAAACCGGTCAAGGAAGATCAGAAGTGGACCATCACGTGATTCAGGTCTCTGTATGCAGGTGTTGATCTGTGAGACAGAGTCAGAAGGGAAGTCCTTGATGAGTGACGAAGCATCCACGCTCGCAACAGGAAGACCAAGGGTCCTTCCTATCCCTTCAACCACAGCTTTTTTATCACATGGACCATGTAAGAGAAATGTCATTTTGCCCTTTGTGGCCTCATGTGGGAGGTGAGTATAGTAACTCATGAAATTACCAATCATCTTACTGGCTCTGCCAACCACATTAGAAAGAGCGGGGTCATCCACCATTTTCATTTGCAGAGGAGTTGCAATGACTGGATGTAAGATTGGTGGGTACAGGGTCTCTCCAACAGTTTTCTCATCACTACCTTTCCAAATCATGATCTTGGTCCCTGAGGTAATTTGTCCTGTAGTCATAGGCAGAGTTCCTAGAACCTTGAAGATCCCTATCTTTTCTTTGTTCACTAACAAAGGGAATGACATCCCTGGATACATCACACCGATCAGCGGAGAACCAACCACCATCGTACTGCTGCAAGGGCGCAACTCTCTTCCAGATTGGCCATGAACTCGGTGGCGTCCTTCTTCTATCACCACCTTGACCTACCTCGGTGGAGATTGGGAGCGACGGGATGGCAAGAAGATGCGTGATGAGGATGGAGGCGCAGCGGTGGAGATAGAAGGTAGGAGTCTGCTCTTCTTCTCTGTGGGCGGAGCCTCCTCCTCTTCCTTGTCTGCCCCCTCTCCTCTAACCATGGCGCCGGGGTGCTCGTCGACGGCGTCTTCGTGTTCGGTGGCTCCCCAACGGCGCCGCTCATCCGTCAATGCTAGCTGATGCCTCGGTGAAGGGGACGGAGGAAGATTGGAGGAGGATGCAGGATGCAGCAGCATGCAGTACTGGAGATGGAGAGGAATCAAAGGATGAGGTGGTAGTGGTAGGCCTGATGGCTGCTGCTGGGT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.981237
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa09LNT0450900.1 9 22406863 A G
Osa09LNT0450900.1 9 22407554 A G
Osa09LNT0450900.1 9 22407575 A G
Osa09LNT0450900.1 9 22407827 A G
Osa09LNT0450900.1 9 22407892 A G
Osa09LNT0450900.1 9 22410402 C T
Osa09LNT0450900.1 9 22412017 A G
Osa09LNT0450900.1 9 22412520 T C
Osa09LNT0450900.1 9 22413309 G T
Osa09LNT0450900.1 9 22413720 C T
Osa09LNT0450900.1 9 22413739 T C
Osa09LNT0450900.1 9 22414014 T C
Osa09LNT0450900.1 9 22414295 T G
Osa09LNT0450900.1 9 22414296 A C
Osa09LNT0450900.1 9 22411503 T C
Osa09LNT0450900.1 9 22412832 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
Osa09LNT0450900.1 osa-miR5540 Cleavage 4.5 16.439 1 21
Osa09LNT0450900.1 osa-miR393b-3p Translation 4.5 20.223 1 21
Osa09LNT0450900.1 osa-miR2097-5p Translation 5.0 22.735 1 22
Osa09LNT0450900.1 osa-miR5152-5p Cleavage 4.5 24.345 1 21
Osa09LNT0450900.1 osa-miR528-3p Cleavage 5.0 21.272 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa09LNT0450900.1 9 Spk(t) Morphological trait Culm/leaf nan nan
Osa09LNT0450900.1 9 nan Morphological trait Root RG667 RZ404
Osa09LNT0450900.1 9 yldp9.1 Morphological trait Seed RM242 RM205
Osa09LNT0450900.1 9 nan Morphological trait Root RM215 RM205
Osa09LNT0450900.1 9 qTN-9-2 Morphological trait Culm/leaf RM215 RZ404
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