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

>Osa06LNT0330400.1

AAAGATCTTCAATGGGAAAGAGCTTTTCCCTTTCCTTTTCTTCATCATATCATTTTTTTCCCAATCTTACACAATTGAACAACCCCAAAAAAAAAAAATCACAAACTTTTCAGCCTTGCAGCTTTACTTCATCTTGAGATGGGCAAGCTTAGCTACCCATCCTAACTTCACCTTTCCTATAACAACAATAACAATCACACCAAATCACCCAAAAATAAAAACAATCTTGCCCTAATCTAACTACATGCAGGGGCAGGGAAATTGTGTATGTGAGCAAACACAATGGAGTAAGGAGCCACAGCTATTGGCTGTGCTGCATCCACTTTGACAGGCTCCAGCCTAGGGATTTCCCCATTTTCATCAGCAACCAATGCCCTGCCATTCAGCAGCATCACTTGGCTCTGCAAGCTGCCATCTTTGGCAGTAAGATGGTATTCTTCTCTCATTGATCCAGCTGCAAGATGCCTGGTCTTTCTGCTATGCTTCTTCACAGTGTTTGCATGAGCACCTTCACTTGTCACTGAAACTTGGCTTGTGGTGTTGCCACTGAGGTTGATCAGCAGTAGTGTTATTCCTGGAGAATCTTTTGCGCAATGCGCATAAGTGCGAATCATGTTGGTGCCATTGAATGTTGCAGATAGAACTTTGGTTCCCATGAGGCGATGCCATAGTAGAGCGCTGTAATAGTCAGGATTTGGTTGGAATGTTTCTTTGTTTAGCAGGCCATAGTTGCCACCAATCAAACTTTGTCTGCAGTAACTCTTCGTGTCATACTTTGCTGACATCCCAAGCTGATCCAAAAACCAGAAACTGAACACAAATGAATCGGTAACAAGATGGCGGCCGCTGTTGTACGCGCCTCCGGACTCTCCGACCCATGCGACAGCCGAAGTCCCGGCAGATTTCAGTATCCCCTGAAGATTGCTGAATGTGCTCACCATTCCATCAAGATAAGATGGATTCAGGATCTTCTCAATCAGATGTGTGTCCACTCCTGGCCCTAAGTTGTAGATGTGATGGGTGACCACATTCAGTAGGTTTGGCCTGGTTTTGACTATAACTTCAGTAAACCAGCCTGCATCAAAGAAACCTCCAGGAGCAAGAACAAGTGGCTTTGATGGATTGCCTTGGTAGATAGTGTCAACTAGTGATTTCAGTGCAATCACATCTGCAGCATATTGGTCAGCCCCAACTTTTGTTCCAACTCCACTGCCACTGAGTTCATTTCCAAGCTCCCATCCATGAATTTTGTAACCCTTGCTCGCGGTGTAACGAATCAGCGATGCAGCATTGGTGTAATCCCATGGCCCTCCCATCGACCCATCCGGCAACGGAACCCGGCCGTTGAGAGCGTTCAGCCCGAACACGATTCTCGCGCCGGATTTTTGGAAGAAGGCGTTGAGCTCGTCCCACCGGTGGAGAGGCAGGCATCCCTGCGTGAAGCCGAACATCTCCGACGTGTTCTTGACGAACGGCGCGCACGGCCCTCCGCCGTCGCCGGTGCCGTACACCAGCTTGTCCTGCAGCGACCCGCCCAGCCGCAGCTTCAACGGCGAGAAGGCTCGAATGGCATTGAGCAAGATTTTGTTGGAGAGATCCAGGTTGAGGAGGGAGGCGAGGCCCCAGCTGCAGGTGCCGTAGTCGCACTTGTCCGGCGGCCACCAGTCCATCGTCGCGCACACGAAGTCCTCGTCGGTGGCGGCAATGGCGCGCCGCCCGTCAACGCCGGCGACCCCGACCACGGCCTCCGCGGCGCCGCCCAGCCGCAGCAGAGCCAAGAAGCATAGCCCACCAAGAAACCGCCTCATCTCCATCCCGGCAAAGCAAGCAAGCAGCAACAATGGCGGAATGCCTCGCCGACGACGAGCCTACCCTACCCTACCCTACCCGGCTAGACCTGAGGTGGGCAGGTGGGCAATGGCGCTTTCTGCCGGCCACCTCCACCTCCACCTACACCATGGCTGCCTAAATACTAAATGGGAAAACGCCAAGGGCGACGCATCGAGTCAGAGCAGCAGCAGCAGGAGGAGGAAGAAGATAAGGGCGGTGGTGGTGGGGAGTAGAATGCTTC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.858398
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0330400.1 6 3926414 A T
Osa06LNT0330400.1 6 3926591 A C
Osa06LNT0330400.1 6 3926612 A G
Osa06LNT0330400.1 6 3926624 A 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
Osa06LNT0330400.1 osa-miR416 Translation 4.5 15.786 1 21
Osa06LNT0330400.1 osa-miR1854-5p Cleavage 5.0 15.802 1 21
Osa06LNT0330400.1 osa-miR1866-5p Translation 4.5 18.239 1 24
Osa06LNT0330400.1 osa-miR1862d Cleavage 5.0 15.012 1 24
Osa06LNT0330400.1 osa-miR5500 Cleavage 4.5 23.298 1 22
Osa06LNT0330400.1 osa-miR5501 Translation 5.0 13.741 1 21
Osa06LNT0330400.1 osa-miR5521 Cleavage 5.0 15.788 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0330400.1 6 qSLL-6 Morphological trait Culm/leaf RM204 RM217
Osa06LNT0330400.1 6 qTLL-6 Morphological trait Culm/leaf RM204 RM217
Osa06LNT0330400.1 6 qTLWR-6 Morphological trait Culm/leaf RM204 RM217
Osa06LNT0330400.1 6 alk6-1 Physiological trait Eating quality RM190 RM253
Osa06LNT0330400.1 6 hr6 Physiological trait Eating quality RM190 RM253
Osa06LNT0330400.1 6 d4 Morphological trait Dwarf nan nan
Osa06LNT0330400.1 6 Qbph6 Resistance or Tolerance Insect resistance RM510 RM314
Osa06LNT0330400.1 6 AsTol Resistance or Tolerance Other soil stress tolerance RZ516 RG213
Osa06LNT0330400.1 6 Lhd1(t) Physiological trait Flowering nan nan
Osa06LNT0330400.1 6 nan Morphological trait Seed RG138 RZ398
Osa06LNT0330400.1 6 nan Morphological trait Panicle/flower RG138 RZ398
Osa06LNT0330400.1 6 nan Physiological trait Source activity RG138 RZ398
Osa06LNT0330400.1 6 nan Morphological trait Panicle/flower RG138 RZ398
Osa06LNT0330400.1 6 nan Physiological trait Source activity RG138 RZ398
Osa06LNT0330400.1 6 nan Morphological trait Seed RG138 RZ398
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