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

>Osa04LNT0280400.1

TTCCTCTTTTTTTCTTAAACGTTGGAACTGTCAAAGCAAAAGCAGTTCTGGTGCAAGAACATAAAAAGGAGCTTTCTTGCTGTCCTTGTTTCCACAGCATTAAAGAATAAGCACAGCACCCTTAACAGCCAATGACACTAACACACAAACAGTTCCTCTTGTTTTCGAAGGTTGGACTAACCATGCTACCTATTTCTAGCCTAAATACCTAGGAGATCTTCCCTACTTGCAATTCACGGGTAGATAAGGTTATTATTGTTGTGAATTGCAGCAATCAGACTGATTTATATCCCCATCATGTGATCCAGGCCTGGCTGAGGAGCAGCTCCCATGCCTGCGCCTGTCACATTAAGAAGCAATTGCTGGAGCCAGCGCCTTGTTGTAGGATCATCCCTAAGACAGTTATTGAACGTGCCATCCTTCAGCATGTCAGGGAGGCAAGTTTGTAGTGCAGCACATGCCCTGGAATTGTCTGACAGCCTAAGGTAACATCGGATAATGTGCTTCAGCAACCTTGTGGAAGGCTGCTCAGCAAGTGAAACCACCATGTTTGCTAAAACACTGCCTACAGCAAAGAAACGCTCAGCAGTGGCACAAATGTAGCGCAATCCAACATCATCGAGGAGAATCTTCTGAACAATGAAGGTGGCCACAGTTTTTGACAGCTCACTTCCCATTTCCATGGTACGCAAACACAGAGGAATTATTTCAGTTTGCAGCAGAAAACTGATAACTTCAGTATCATCAACCTTAACAAGTGCACCGATGACACCCAGGCTGGTGAGTCGCAGGTATTCAAAAGGTCTTGTCTTGCTGGTAGTATTCAAGAATGGGTACAGGTACAGGGGAATATGAGCAGTTAAGAAAAGGATCCTGGTCTCAGGGTGAGATGCAACACACTGAAGAAGTGCAAGTGCATTGCAGACTCGGTTCGATGCACCTGGTGACAATGTTGGGGGTGAAAGTGCAGAGTAGATTGACACAATTTCCTGAAGAAGTGCAGCAACTGTTCCAAAAGAATGCCAAAGAAGTGGGGCCAGATCTTGAAATATCTCTCTTTTCTTCGAGAGCTCGAGGAGGGCGTTCTCGCGAAGCTCGGGGTCGCAGAGGTCGAGCACCAGCTGCTCCGCCGACGCCATCTTCATATCCTTGGCTGGCTGCCCCACCCCGCCGCCCACGCCACCGCCGCCGATCGGAGAAGGCGATGGCGGCGAGGCCCCGGCGAAGGAGGGCGGAATGGAAAGCGAGGGCTGCAGATTCGCCATTATCCCCACAGCAAAGGCTATACAGCACGGAGCGAACTAGGACGAAATGGAAGGGATCACCCGAATTCCGCGACGGATCACCACTCTCCGCTCCTCTCCGGCGGCGCCGCGGCCGCCGTGGGCTCGCCGCGACGGGAGGAGAACGACGGCGAAGTCGGAATAATGCGAAACTGCAGCCGAGG

Coding Potentia
Explanation CPC Score
noncoding -1.05011
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0280400.1 4 31098729 G A
Osa04LNT0280400.1 4 31099093 T G
Osa04LNT0280400.1 4 31100462 G A
Osa04LNT0280400.1 4 31100592 G A
Osa04LNT0280400.1 4 31100630 C T
Osa04LNT0280400.1 4 31100657 G A
Osa04LNT0280400.1 4 31101021 C T
Osa04LNT0280400.1 4 31100110 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
Osa04LNT0280400.1 osa-miR5827 Translation 4.0 15.736 1 21
Osa04LNT0280400.1 osa-miR5827 Cleavage 5.0 20.113 1 21
Osa04LNT0280400.1 osa-miR5833 Cleavage 3.5 22.555 1 21
Osa04LNT0280400.1 osa-miR396a-3p Translation 5.0 14.56 1 20
Osa04LNT0280400.1 osa-miR396b-3p Translation 5.0 14.56 1 20
Osa04LNT0280400.1 osa-miR413 Cleavage 5.0 16.366 1 21
Osa04LNT0280400.1 osa-miR1879 Cleavage 4.5 19.615 1 24
Osa04LNT0280400.1 osa-miR2864.1 Cleavage 5.0 24.005 1 21
Osa04LNT0280400.1 osa-miR5145 Translation 4.5 16.971 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0280400.1 4 Xa2 Resistance or Tolerance Bacterial blight resistance RM317 RM349
Osa04LNT0280400.1 4 nan Morphological trait Root RM3276 RM3335
Osa04LNT0280400.1 4 rfw4a Resistance or Tolerance Drought tolerance RM349 RM1136
Osa04LNT0280400.1 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0280400.1 4 OsAOX1a Resistance or Tolerance Cold tolerance R2737 R740
Osa04LNT0280400.1 4 nan Morphological trait Root RZ23 RM255
Osa04LNT0280400.1 4 pss4.1 Physiological trait Source activity RZ740 RZ590
Osa04LNT0280400.1 4 nan Morphological trait Panicle/flower RM303 RM348
Osa04LNT0280400.1 4 nan Morphological trait Panicle/flower RM303 RM255
Osa04LNT0280400.1 4 qPN-4b Resistance or Tolerance Drought tolerance RM317 RM255
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