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

>Osa02LNT0145200.1

CTTTCATGTTTGTATTTTGCGTGGCAAGAATTCTATCTGAACACAAACATTCGATTCAGGAATCCATTCATCTCGAACTTGTGTCAAAATGCGTTTCTATTTGACTACGCTCGCGTGGCATCACTAACGGGAGAATACATATAGCCACATTATTACAACTGAAACATAGCTACATTATTTCACGTATAAATACATGCACATTGTTGGTGCTGCTGCTCTGCTCGTGCTGAACTACTTGTCTGCGGCCAAGACGCGGCGACGGTACTCCCCAAGGGCCCAAATAGGGAAGATGTTTCTATACTCGGAGTAGCTGATCATGCAGTTTTTGTTGAAGACTCCAATGATCTCTTGCTGGGGAAATTCACCATCTTCCGATTGTAAGTTGATCAAAACCTTCGCTGCTCGATGCAAAGGAATTGGATCTCTCTCAGCCTGCCCTGCATCGATTAGGGCTAGCATGGCCCAACCAGTGTTCACCGCATGAGGTCGCTTCCCTTCGAGATTGGTATAAACCTGATCTTGGGATGACAAATAGCTTTCTCCCCAGCCTCCAGAAGGAAGCTCTTTTGACAACAAAAAGTCACATGCCTTTCTGATTGCAGGACTGTTTTTGAATGTCCTACCAGCAGCAACTAATCCCTTTACACCAAACCATGTGCCATAGGTAAAACAAACAGCCCAAGAACCATACCATGAACCATCGCTTTTTTGAATACCCTCAATAAAGCTAGCAGCTTTGCTTATACAGTTGTCTATTTCACTCTTGCGGTGTCCAGGGTAGAGCTTTTTAAATGCTGTCAGGGCCTGAATTGCTGCTGAAGTGCATTCCACATAAGGATAATCAATCACAATGTCCCCAAAGGTCTCAGCAGGATTGATAAGCTCCAGCCAGGCATAAGACCTTGTGAGTTCATATGTTGCAAATCCACCATTATCATTCTGTCAAGAGTACAAGGATCTGTAAGGTAAGGTTCCTCCCAAAGGAACATGCATGTGATATATTTAAAACACCAATTAAAATACACAAGAGAATGGGGGAGCTATTGGCAACAAAACTTTGTGGAGCACTGGAACTTCAAAACATTTTTTTTTTGAAGAAATGATTATATGTCGTACTTCAACAAATCTAGTTTGCCATAGTTCTATGTATCTTTAGAGAATAGTTGAGTGGAGAACCCATCAAACCTGAATGCCCGGTACAACAAAGTAAGGCTGCATGCATTAGTAACTCTTCCTTCAGCCATTAAACTGCTATATTAGAGACACTTTATAGCCATGACAAATTAGACGTCTTATGATAATTGATAAGCACAAAATTATAATGTGACGGATGCCTTTTCATACATAAGGGTACTTGCAGATTCAATTGTTAAACAGGAGTCCATTTACCACATCCCAAATTTTAATTATCAACTGAAAAGCAGATCTCCAATATTCTAAGTTTCTAATGCATATTAATCAGGGTTGAGAAGCAAAAAAAATCGTTTCGGTATCCTACAGAAATACGAGGTGCTTAAAAAAGGGACAAGACAAACATCTTCTCTGTCCTTGTTCTGAATGCAAAAGGAGCACTTGAATATAGGCATACACTATATGATGCTTACTGAACTGCTGCTCCAAAGCTTCATTTTTTTTATATATTATTCATGTTACATATGAAATGTTAAAATGACATGAGAGGTTTACAATCACCCTTAAATATGAAGACTGATTAAAACTTACCATGTATGACATCAAACAATTGACAGAATCATACAGTCTATTAACTTCCACTGCTTCGCCAACAATATCTGGAGAAATCTTCGATAGCAATAATGCCGCCTTAAGTCCTTCTGCAGTGCAATCTGATATAGGCCAACCATGATCAGCAGTAGAAAAGGGCCATGCACCTTTAGATATGTGGCGGTACCACTGACTAAGATCTCCAGGGCAGTCATCGATAACCTGCGTTTTCTTTATGTAGCCATGTGCTAGTTTAAGAGTAGGACCAAATTCTTCAATGAGGCCAGTAGCCACTATAGCTTGAACTGTGAAAGCTGTGTCCCACAGCTGGCTTCCATTATAACCCTGCATTTTCATGCCATCTTCTGCAATCCATAGGTAATCGTGGACTCTTGGAATGTGGAGTTTGAATGCCTCTGAGTTTGGATCTTCAATCCAGCAAGCAAGCATATTTAATACCTTGTTTACTGGACCAATGCAAATATATCGGGTGTTCTCATCTTCATAATGAATATGCTGCATGACAGTGTCCAAAGCTTTCTCCCTCAATTTGTTCCCAGGCCAACGCAACATAGCTGGTTCAACAAATTTGTGGAGAGTGGCCCATAATACATCCTGCACGAATGGATGTGGATAGTACAGATCTTCCTTAGCACATAGATTGCGAGCCTTGTCCCAATCAACTTCATTGTAGGGTACTTCGTAGAGTTCCTTTCTTAATTCCAATATAATTGGTGTAACTGGGCCCACAAACCTCTTTCCATAAATGTAACACATAGGCAAATAAACCATCCGGCAATGACACCACATTCGCCCTGGATGAATCGGCAGGAAATATGGCAACAACCATATTTCTGGTGGCACTGGGTTGTTGCCAGACCAGTCAAATACACCAAGCACCGAAAGCCAAAACTTGCCCCATGATGTAATATAAGTTGCTCCCCCATGGTCTAAAATCCATTTTCGTCCTTTCTCCATAGCTCCATCGCCGCTATCTGGCCCCTCCCCAAGCAATCTCAAAGAAACATATGTCAACGCTGAGCCAAACATGGTGCTGTGGCCCTCAATGTGCAAACCCCATCCTCCATCTTCATTCTGATGATTGTAGAGATACCGCCGTATCTCCTTCTGATGTTCAGATGACAAAGCAGTGTTCAGCGCTCCGCTCACATATAATGTTATAATCAAGCCTGGCATAAGGAACATGGGACCACCATAATCCCCAGGCCAGTGTCCATCATGTGCTTGAAAAGTAGAATAACGAGCAATTGCCCTTTTTAGAGAGGATAATACAGCTTCGCCTGTAACAGCTTCATGCTCCTCTAGCTTGATAGCTGGAATGTCCAGCTTAAGAGGATTTGCTTTAGCAAACTGCATGCGCATGAGGAGGTCGGAGCTGTGCTTGAGCTCGTGGCGGCGGGCGGCGGGGTCGAACTCCCAGACCTGGCGCCCCACGTGGCCGTTCTTCGTGCGCAGCCACGGGTCCCCCCCGCCCTCCGCC

Coding Potentia
Explanation CPC Score
noncoding -1.29308
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0145200.1 2 2128540 G C
Osa02LNT0145200.1 2 2128596 G A
Osa02LNT0145200.1 2 2128803 T G
Osa02LNT0145200.1 2 2129716 T C
Osa02LNT0145200.1 2 2129929 T G
Osa02LNT0145200.1 2 2131349 T A
Osa02LNT0145200.1 2 2133284 C G
Osa02LNT0145200.1 2 2133773 T C
Osa02LNT0145200.1 2 2133845 G C
Osa02LNT0145200.1 2 2134661 C T
Osa02LNT0145200.1 2 2134853 T C
Osa02LNT0145200.1 2 2135390 G A
Osa02LNT0145200.1 2 2135865 A C
Osa02LNT0145200.1 2 2135955 A G
Osa02LNT0145200.1 2 2136385 C G
Osa02LNT0145200.1 2 2136505 T C
Osa02LNT0145200.1 2 2131749 T C
Osa02LNT0145200.1 2 2131773 A G
Osa02LNT0145200.1 2 2131902 G A
Osa02LNT0145200.1 2 2132058 G T
Osa02LNT0145200.1 2 2132475 A T
Osa02LNT0145200.1 2 2132644 A G
Osa02LNT0145200.1 2 2132791 A T
Osa02LNT0145200.1 2 2133036 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
Osa02LNT0145200.1 osa-miR5529 Translation 5.0 15.473 1 21
Osa02LNT0145200.1 osa-miR5813 Translation 5.0 20.996 1 22
Osa02LNT0145200.1 osa-miR396a-5p Translation 3.0 21.522 1 21
Osa02LNT0145200.1 osa-miR396b-5p Translation 3.0 21.522 1 21
Osa02LNT0145200.1 osa-miR396c-5p Translation 3.0 21.522 1 21
Osa02LNT0145200.1 osa-miR166k-5p Cleavage 5.0 21.43 1 21
Osa02LNT0145200.1 osa-miR166i-5p Cleavage 4.5 15.23 1 21
Osa02LNT0145200.1 osa-miR396e-5p Translation 4.0 22.009 1 21
Osa02LNT0145200.1 osa-miR1850.1 Cleavage 4.0 9.69 1 21
Osa02LNT0145200.1 osa-miR2094-3p Cleavage 4.5 14.549 1 22
Osa02LNT0145200.1 osa-miR2099-3p Translation 4.0 16.01 1 20
Osa02LNT0145200.1 osa-miR396f-5p Translation 4.0 21.402 1 22
Osa02LNT0145200.1 osa-miR2105 Cleavage 5.0 7.634 1 20
Osa02LNT0145200.1 osa-miR395x Cleavage 3.5 17.359 1 21
Osa02LNT0145200.1 osa-miR5071 Cleavage 4.5 17.709 1 21
Osa02LNT0145200.1 osa-miR5145 Translation 4.5 21.688 1 24
Osa02LNT0145200.1 osa-miR5146 Translation 4.5 13.209 1 24
Osa02LNT0145200.1 osa-miR5487 Cleavage 4.0 15.066 1 21
Osa02LNT0145200.1 osa-miR5491 Cleavage 4.5 19.203 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0145200.1 2 S29(t) Physiological trait Sterility nan nan
Osa02LNT0145200.1 2 rb2 Physiological trait Eating quality RM236 RM279
Osa02LNT0145200.1 2 qWIJ-2 Morphological trait Seed RM233A RM8
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