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

>Osa03LNT0218200.3

GCCGTAGAACACTATAAAGTATGAAGAATTCAGAAACATATAACAGAGCAGGTGCAATTGATCCAAAAAAAAAAAGTACCACTAGAGAAGAACTTACACTATATGCAAAGGTAAAATCTTTGTTTGACCAGTTCTCAACAACTGCTTCATGGAAGAAAGACAGTTTCTCACCTTGCCTACTTCTTTCCTTCAATGGATGACTTGAGCCCTTCAAAACAATCTCGTTACTCACACCACTATTCAGAGTCAACTGAATTTTTTCCTTTTTCATAAACACTTTTGGCAAAGGGTTCACATATTGCGGAAATTGAAAAGGAATATCAACAGAAAACTGTCCATTGTCATATAGTAACTTTTGTGACCATCTAATCGTGGCAAATATGTCTTCTCCTCCTCCAACCTGTGGTATTGTCAAGGAAAAGAATTGGCGCTTTAAAAGACCCCCACTCTCAGTTTTAGCAATCTTCACTGCACCTTGATCCTCTACATCAATTACATGGGTTTTGTATGATCTCTTCCCAACAGTAACCTCAGCTCCTAGAATTGTACCCTATTAGCCAAATTATTCTTAGATTGAGATCACCAGCAAATTACAAAAGAACGGCAAAAGGTTTGTATGGTAACAACCAAGTTATTAGATTAATATATATATAAGAAGGAAAAAGAAAATCAGAGAAATCCCATGCACTGAGACCTATCTTTAGTCTGTCAACCAATTCACCAAAAGGACAACAGAAATTCATTGGCTTTTGGTAAGACTGTTCATCACATAATAAGTTCCTAATCAACCACCTATTAGTCAAAAAAAAAGTCCACGAAATGAGAGATGATCAAAAAGCATATTTTGGTTGACAATCGACAAGCATTGTACTAGAAAGAAGTGATTTGTGGTTTGCTAGTAATGGAGGCCTAAACGCACCTGAATGGGTTACACAAAGCATATTTTTCTAGTAACGTAAGCATACATTAGTGGTTGATTAAAAGCAACGTTGCTCTCTGTTTTTAGCTGTAACAGAAGGAAATTAAAGAATAAGAAACAATCCAAGTGATGTACTACAAGAAAAAGGAATAGCATCAAGTGCACCAGGTAAAAAGCCTTTATTGGGCAAATGGGCAGACACAGTTATCCCTCCCTTTGCAAGTCAACAATCCAATATTTCTTCCTTGTGGCTTATTATCTAGTAGCAACATGTAAAGCAAGGAATTTATCTTGCTTGCTTCCAAAACCGCGCTGGAACCCACTGCCAGCATAGTAGCCAGGCTGCCGCGCAGAATGTTGAAACGGCATGATCGTCCATATATACTTGGATCATCAACGTGCCAACAAATGCAGCTTCAAGTTGGGCAAACAGGCGCCCCAGTCCAAGGCAAATGATTAAACTACAGCCAATTCATGGGGGCCCCAACCACCAAACAAACAGGAAGCATATCGCCCGCGTGGTAACGGCAAGCAATCAGGCAACTAATCCAGCACTAGTACAGCAACAGCCAACAGCCTAGTATAGAAGATTTCAACCGATCGAACGGAAGAAGAAATAATAAAAAAAAAAGATGAGGAAGGGGATGGAGTAATAATTAAGTGATGACCTGCTCGCCCATGGGCACGACGATGCGGCAGTGGCAGTCGCAGCTGCGGGTGAGGCAGTGCACCCACCAGCGCGCGCGCAGGGTGACCTCGGCGGCGGCGCAGCCGGCGGCGGCGCAGTCGACGGCGAGGGCGACCTCGCGCATGTGGAGCGGGATGAGCGCGGGGGGGTCGAGGCGGCCGTAGACGTGGGGCTGGTAGCTGGGCACGTCGGGGCTGTCGACGGCGGCCGGGTCGACGACGACGGCGTACGCCATGGGCGCGGACGGCAGCAGCGAGGAGGCGGCGGCGGCGTCGGGCAGCAGCCCCCGGTCCATCCCGGGGACGGGGCGGGGCGAGGGCGCGCCGCCGGGGAGGACGAGGCGCTTGGACAGCTTGAGGCCGTCCTCCACCGCCCGCGCGAAGTCCTCCTCCATCGCCGCCGCCGTGCTTCGCCTGGCCGGAGGAGGTGGAGGAGGGGAGGGCGAGGCGTGGGAATGGGGGTTGATACAATGATATGGGGATTAAGTTT

Coding Potentia
Explanation CPC Score
noncoding -1.008
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0218200.3 3 16703232 A C
Osa03LNT0218200.3 3 16702393 A C
Osa03LNT0218200.3 3 16702987 G C
Osa03LNT0218200.3 3 16704100 A G
Osa03LNT0218200.3 3 16704487 A G
Osa03LNT0218200.3 3 16703474 A 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
Osa03LNT0218200.3 osa-miR5533 Cleavage 4.5 14.001 1 21
Osa03LNT0218200.3 osa-miR5824 Translation 4.0 15.608 1 24
Osa03LNT0218200.3 osa-miR7694-5p Translation 5.0 12.488 1 24
Osa03LNT0218200.3 osa-miR419 Cleavage 5.0 19.648 1 21
Osa03LNT0218200.3 osa-miR2929 Cleavage 3.0 14.977 1 21
Osa03LNT0218200.3 osa-miR5500 Translation 4.5 21.361 1 22
Osa03LNT0218200.3 osa-miR5523 Translation 4.5 15.392 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0218200.3 3 qDLR3 Resistance or Tolerance Other soil stress tolerance RM338 RM2453
Osa03LNT0218200.3 3 qGL3-1 Physiological trait Eating quality nan nan
Osa03LNT0218200.3 3 gw3.1 Morphological trait Seed RZ672 RZ474
Osa03LNT0218200.3 3 nan Morphological trait Shoot/Seedling RZ284 RZ403
Osa03LNT0218200.3 3 An5(t) Morphological trait Panicle/flower C1677 R19
Osa03LNT0218200.3 3 nan Morphological trait Panicle/flower RZ452 RZ284
Osa03LNT0218200.3 3 qLWR-3 Morphological trait Seed R19 C1677
Osa03LNT0218200.3 3 qGL-3 Morphological trait Seed R19 C1677
Osa03LNT0218200.3 3 ccfs3 Physiological trait Source activity RM16 RM282
Osa03LNT0218200.3 3 ccf3b Physiological trait Source activity RM16 RM282
Osa03LNT0218200.3 3 nan Resistance or Tolerance Other stress resistance RM4512 RM8208
Osa03LNT0218200.3 3 nan Resistance or Tolerance Other stress resistance RM4512 RM8208
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
Osa03LNT0218200.3 3 16703094 Grain-length(mm) 9.323304176 +
Osa03LNT0218200.3 3 16703615 Grain-length(mm) 9.17711544 +
Osa03LNT0218200.3 3 16703703 Grain-length(mm) 9.205823898 +
Osa03LNT0218200.3 3 16703998 Grain-length(mm) 9.320637703 +
Osa03LNT0218200.3 3 16704606 Grain-length(mm) 21.21233749 +