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

>Osa04LNT0277900.1

GTGGGACTCAAGTGCAAAAGCACTAAACATGTCAGGCTTTACAAAATTTCTATTGATCGTAAATATAGCTTGAGATTATCACACCAAACCAGCTTTGTTGAGGTGGCAGCAAGCCCTTATCCAACCGGCATGCAAGCAGGTGAGTCACAAAAGAAAAAAATTATCCCATATATCAACCCAGCTACTAGAGAACCAGTCTTGGTTACATCGGTTGGAAACCAATCTCAAGCAGCAGCCATAGTAAAATACTCCTCAGTCGCAAGAACAATCAACCACAGAATCAAGCAGTAGTAGCCAGCAATTCGGCTAGAGACTCAGCTGAAGACAGAGAAATAATCATAGGTAGCATATCAATAGTAAACACCTCAGTCATGCAACACCACAGCCGTAGCAGCCTAGAGTGAGCAGCAGAGGAGACTAGGGTGACTCAGAGAGAGAGAGAGATAGTTGCTGTTGTAGTTCATTAGTTTAGTACAAAACAATCAGAGCAACCATAGCGACCATGGCCAGGAAATCATATAGACAAATCAAAGTAGATGAGTAGGAGATGCTTGAGATCCAGGAGAAGCAAGAATCTGAGCTTCAAGAGGAGAGGGGTTTCAGCTCCAGGAGGAGGAGCTGAGTTGGTACATCAACTGCAAGGGGAGAAGCTAGAGTTCCAATAGGAGAATCCTTGAACCGGAGTCCAGGGGGAGTATCTTCACTGTAGAAGCTGTCAGCAAAATAGTATATTGCAATTTTCAGTGTGACGCAATGGGTTTGATCTGCCGGAGCTCTCGCCGGTCCAGAAAACAAATTGCACTGACGCAGCGGCCGCGCACCACTCGGCTGGGAACGCTGAGGGTGAGGGCTGGGAGGATGAGTTGAATCTACGACACAGCACCATTGAAGATTTGATCTGGACGGGAGGGACTCAGATCAACTCAGAAGAAGACTATATATACTACTTGTCTACCTCCTCCATGGATCCGCCGAGGATTAGAAACTGCAGCACTCCATTCGCTGTCGACGGGGAGAAGTGGAGCACGTACGACCTCACCAGGGAATCTCGTCGGAGATGCCACCACAACCGCCGACGACGATTGGTACAGGAGGGACGAGAGCTAGCCGCCGCTCGTGGCGACGTTGAAT

Coding Potentia
Explanation CPC Score
noncoding -1.06727
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0277900.1 4 30095135 T A
Osa04LNT0277900.1 4 30090878 A C
Osa04LNT0277900.1 4 30090984 A T
Osa04LNT0277900.1 4 30092543 A G
Osa04LNT0277900.1 4 30092843 C G
Osa04LNT0277900.1 4 30093609 T C
Osa04LNT0277900.1 4 30093644 T C
Osa04LNT0277900.1 4 30093727 G A
Osa04LNT0277900.1 4 30094070 T G
Osa04LNT0277900.1 4 30094507 A G
Osa04LNT0277900.1 4 30094742 C T
Osa04LNT0277900.1 4 30094763 A G
Osa04LNT0277900.1 4 30094883 T C
Osa04LNT0277900.1 4 30094919 T A
Osa04LNT0277900.1 4 30094940 C T
Osa04LNT0277900.1 4 30095658 C T
Osa04LNT0277900.1 4 30096192 G T
Osa04LNT0277900.1 4 30096533 A C
Osa04LNT0277900.1 4 30096465 C T
Osa04LNT0277900.1 4 30095488 G T
Osa04LNT0277900.1 4 30096381 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
Osa04LNT0277900.1 osa-miR159a.1 Translation 4.0 21.631 1 21
Osa04LNT0277900.1 osa-miR159b Translation 4.0 21.631 1 21
Osa04LNT0277900.1 osa-miR159c Translation 5.0 21.631 1 21
Osa04LNT0277900.1 osa-miR159d Translation 5.0 21.631 1 21
Osa04LNT0277900.1 osa-miR159e Translation 5.0 21.631 1 21
Osa04LNT0277900.1 osa-miR529a Cleavage 4.0 22.321 1 20
Osa04LNT0277900.1 osa-miR2876-5p Translation 4.0 13.361 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0277900.1 4 nan Morphological trait Root RM3288 RM5503
Osa04LNT0277900.1 4 rfw4a Resistance or Tolerance Drought tolerance RM349 RM1136
Osa04LNT0277900.1 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0277900.1 4 OsAOX1a Resistance or Tolerance Cold tolerance R2737 R740
Osa04LNT0277900.1 4 pss4.1 Physiological trait Source activity RZ740 RZ590
Osa04LNT0277900.1 4 nan Morphological trait Panicle/flower RM303 RM348
Osa04LNT0277900.1 4 nan Morphological trait Panicle/flower RM303 RM255
Osa04LNT0277900.1 4 qPN-4b Resistance or Tolerance Drought tolerance RM317 RM255
Osa04LNT0277900.1 4 Xa2 Resistance or Tolerance Bacterial blight resistance RM317 RM349
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