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

>Osa03LNT0205900.2

GCCGTCCATGAAATGAAATTGACACTTTATTAACTGAAACATCGAGTAATTGTACAAAGCTTTTTGTTGGTGATAAACGATTCACACCACGTTCAAGTACAACAAAAGGACAGTACCTTTCACGCCCTTATCTAATATACTCGTGCTTCAAAAATAGCTGACAGCACTAATATGTGTTGGGCATTGTACAATAGGCAGTAGCACTTAATAATAACAACGGCATCCACGTTACTGGAGGAGAAAAGGCTACTGGTTTGGCTCCATAAGCTGACATTAGCCTTGAGGAAAGCTTCAAATGTATCACCGCAATGATACAGCACAACAATAGGAGCACCCTCCTTGTCCAGCCGCCACAGAATTTCATTACCATTGAGAGAATTTTCTTGTCTGAGAGGTTCGCTAAAGACACTGAAGCACTTGGCAGTAGATATCCTGACTCAGGGTTTGAATTTGTTGGGTTGACCGTGTTTTCTGTTCTTCTGCTGTGCCGCAAACAAGCAACAGCCTTCTCTGCAAACAAACTATATATTACAACTACAACTGGGACAACCACCAGGTATAGGAAAGGCAGTGTAATAACCAGCACATCTGGGTTGCTCGATTTGTTCCAGGTCAAGTCTTCACCAAGAGATGGGATGCTCCATCCGGATAAGTACATTTGAGCAATTTCTCCTTTCTCAGATGTCGCATGACCCCAAAACCATGGCATTTCAATAAGCCAAATAACATATATGAGCAAAGAAAACCAGATGGGTCTACTCCTTGCACCCTCCATTAGAAACCAGACCAACCAAAAGTAAGCTTTCCTCGGCTGGATAGGGGATAGCATAACTGACACGGTCCATCTTTGGTATGTCAAACTTTTCTTCATAAAATGATACAGCAATTTGGGAGCAAACAATAGTACAATTATGAAGGCAAAATTACTCCACAGAAGAACTTGATACATGTCTTCCCATTGGACTTCAAAAATCAAGTAGTTCAGACATGGACGTGATTGAATTTGCACTTTACCCTCAACTGAAAATGGTCGTCGCTCGCTTGATGTCTTCCCACCCTGAGAATCCTGAGCAAAAACTTGCAGCCAGTAGCGAGTAGGGGATGGACTTTTGTAGTTTTCAGCATTCCATTCCGCATGGAACAAAGGTTTGTGAACAGATGGTGTGGCAACAAGCTGCAGTGGTATTTCTTCAACTATCTTAAACTCATTATGAGAGTCAAAAACTCTTGCACTCACATTGCGGATCACCTGATTAGAGAAAACAAGAACATTTATATCATTTCTCGTTGACCAATTCATTGATTCCAATGTATTCATACTTCTTGAATCTGTTGGGTATGTGATCAAGATGGAAGTTTGAAATGCCTGTTTTAGTGTGTGGTCTATGAAAGAGATTGCACCTCCATCAATTGCTAAAATCCTCATCAGTCTTGACTCTTTCCAGTCTCCAAGTTCCCATTCCCAATAGCTTGATTTCTGCTCTTGTGTTGTTGCACTCATTTCATGAAACCGCCAAAGCTGCTTACTAATTTTCGCGTGCAGATGGCCACATAGGTATGCTGAAATTGACTGCTTTGCAAATATACTTTCATAACGTTGTCCTTTTTGAGATGAAGTAGTGAATGACATAGGGTAATGTCCAAAAACTACTTTTGTTATTGGAACATTGGAATGATTGGACCAGTATTGAAGTTCTGAATTAACAGCGTCTATCCTCTTATCAGTAGGATGGCCAAATAAATTAGCTGGATATCGAATGCCAATACTCATTGTATCATCTATGCCAAGGAAGAGATAATTCCTGCGTCCCTGAAGCAAAATGCTACTGATGGTGCTTAATCGGTCAAGCTGTGAGTTCACACTGTAAGTTGAGAAGAAATCCAATTTTCCTCCCCTATAGGGAACTCCATATGTATCATGATTACCTCTAATATCAAATATCCTGCTCTTATCAATACCACCTATTCCAACAATTGCATCAATAGCTTTTTTGTATGTAATCCATTCCCTCTCATCTTGTCTTGACGTAGTTTTTCTCCTATTCTTTGCATCTTGTTAACATCCCACGAAAAAACTGGAAATTATTATACAGTCATAGGAATATATAAAACTACAAGAACAACATATACATTCAATTGCATCAACCATATATGTGCTTGTTTCATTTCCTTATTATTCTAGCAAGGGCTTTCTGTCTAACAAATTAACATGTACACTCAAGGTGAAAAAAGGAAATGCATTATAGCAAGGGACGAAAATTGAAGTTATCCAAATTTACTACCAAATCAACTTTCCAATATTTGACCTTCCACATACAAATAAATATTTTCCAAATATAAAAAATACAGTTAGTAATGTTTTCAAGTGATTTGGGATTTATCTCCATTTGTTGTAACAAAGCAGCTTTCATGTATGTCGCCATTAGATACGATATTGGAGAATTTAATGGTTTATACAACAAATTCAGAGTCATATTCTTCATGCAAATAGTTGAAATGAATGTTAGGCCAATAACTCCAGGATATTTCCAGAATATGTTTATGGATGTTACGCTAGCTGAGTTTATTAGAAAAATGATCTACTAACCTTATGGTAGTTTGTAAGTTGTATGCTTTACCTTGCATTAACTAATGAAGCTATTCTCAAGTTTCATGGCATGGAGCCATGGACTCTGAGTTACTGTATCATTTGATCTTTTTAGGCAATACTTGGCAACCACAAATACAAATTCAACCTGCCTACGCTACATGGAAATGAATCAGAATTTTCTGCAGATTCTCATTAACAGAACATGATATTCCTTCGTAGTCAGTGCCATCATGTACTAGATGGGATTAGTTCAGAAGTACATGCGCATTTAACAGCACAACTGTAACAAAAAGCTCATGCTGTGAGCATAATTTCCCACATAGCTAATCGAGTTCACAGCTTATACGGAAGTTGATTCTACGTTCACAGCATAGCTAATCGAGTTTATATACTGCTATTTCCCACATATAACAATACCACTCAACACCGATCACTTGCAATATGTCAAAACCAGAGTAGATACGGTCTATTTCTCGGCAGTTGCCATGCTCCTTACCAAACAACTGTACAAAATGGATGCATGAAGGAACAATTCGTGACTTTTTTTTAATCAAATTTGACGATACATGAGAAGGGGGCTCGCCGCTCACCTGTGATGTCGCCGGTGACGAGGAGCAGGTGGGGGCGGATGGCGCGCAGGGCGGGGCCGAGGATGCTCGCGAGGTCGTCGGCGCGGTCGGGGTGGTAGGCGCTGATGTGGAGGTCGCTTACCTGCACCACCCACGCCACGTCGCCGTCCATGGAGAAGGCCGACCTCGCCACCGAGGCGCCGTCGTCGGCGACCACCAGCCACGGGGCACACAGCCGGTGGAGGGCGAGCAGCAGCAGAAGCACCAGCGGGGAGCGGAGGTGCGAGGCCATCGCTGGGCGGTGAACGGGTTCGGGATCCGGCGCGGCGGGGAATCTCTACGCCGCCGCGTC

Coding Potentia
Explanation CPC Score
noncoding -1.01563
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0205900.2 3 8440214 C A
Osa03LNT0205900.2 3 8437637 A G
Osa03LNT0205900.2 3 8437872 T C
Osa03LNT0205900.2 3 8438951 T C
Osa03LNT0205900.2 3 8439476 T C
Osa03LNT0205900.2 3 8439490 A C
Osa03LNT0205900.2 3 8440664 C T
Osa03LNT0205900.2 3 8441546 G C
Osa03LNT0205900.2 3 8441570 C G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa03LNT0205900.2 osa-miR5536 Cleavage 3.5 13.524 1 22
Osa03LNT0205900.2 osa-miR5817 Translation 5.0 11.986 1 24
Osa03LNT0205900.2 osa-miR6248 Translation 3.5 3.045 1 21
Osa03LNT0205900.2 osa-miR6248 Translation 5.0 15.854 1 21
Osa03LNT0205900.2 osa-miR166g-5p Translation 4.5 17.676 1 21
Osa03LNT0205900.2 osa-miR166j-5p Cleavage 5.0 17.309 1 21
Osa03LNT0205900.2 osa-miR390-5p Cleavage 5.0 14.701 1 21
Osa03LNT0205900.2 osa-miR1428a-3p Translation 4.0 12.239 1 21
Osa03LNT0205900.2 osa-miR1857-5p Cleavage 5.0 14.483 1 21
Osa03LNT0205900.2 osa-miR1428b Translation 4.5 12.239 1 21
Osa03LNT0205900.2 osa-miR1428c Translation 4.5 12.239 1 21
Osa03LNT0205900.2 osa-miR1428d Translation 4.5 12.239 1 21
Osa03LNT0205900.2 osa-miR1874-3p Cleavage 4.0 15.803 1 24
Osa03LNT0205900.2 osa-miR5487 Translation 5.0 12.587 1 21
Osa03LNT0205900.2 osa-miR2275c Cleavage 4.0 9.577 1 23
Osa03LNT0205900.2 osa-miR5518 Cleavage 5.0 19.636 1 21
Osa03LNT0205900.2 osa-miR5487 Cleavage 4.5 16.352 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0205900.2 3 qGW3 Morphological trait Seed C706 C12534S
Osa03LNT0205900.2 3 qOE3-1 Physiological trait Eating quality nan nan
Osa03LNT0205900.2 3 qTA3 Physiological trait Eating quality nan nan
Osa03LNT0205900.2 3 S34(t) Physiological trait Sterility nan nan
Osa03LNT0205900.2 3 Gy3a Others Others RG266 C63
Osa03LNT0205900.2 3 qTAA3-1 Morphological trait Shoot/Seedling C316 C63
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