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

>Osa06LNT0331900.3

AACACCAGGAACCGGCGTTTATTTGAGGCAAGCACTGCCCAAAATCTCGCAAAAGTACTGAAACCTTAGACATAGTACACATCCATGGCAAACATGGATGCCAAATGACAACTACAGAAAATTATCAAATTCGAATGCAGCTGACGGCTTCTCCTGCTGAAGATGCATATTTTCCCCTCCATTACTTGGATGTGCTCTCTCCATCGACAGCCAATGGGACGGCGCTGGCCAGGCTGCGGTATTTCAGAGCATAGAACATCTCAATGTAACGGCGAGTCTCGCGCCTCTCAAGGTTGCTTACGTACTTCCAGAATCCGTATACACCAGTCAAGGTCATCAGCCTCTCAGAGTACAGCTTCCAGGTGTACTTCTCGTAAATCCTCTGCAGACCTCCCTGTGAAATATTGTCCCAGTAGGTTGAATCCTGCTTGCACTTCTCAAAGAAGTTGACCAAGATATCAGCAGCCTTGTCACTGTGGTAAGGATCAATGTGCAGACCAGACACCCCATCAACAATAATCTCAGCAGGGCCACCATGGCATGTTGCGATTGTTGGCAAACCACATGTCATGGCTTCGATGACAGTCAGACCAAACGCTTCATAGAATGCAGGCTGGACAAAGACTCCCTTGGTGTCACAAATGTATCGGTACAACTCCCCGTTACGAACACGGTTCATCTGAGCTGAGATCCAGCGGATATGCCCCTTCAACTTGTACTGGTCAATGAGACCGTACATCTTCTTGAACTCAGCCTGCTCCTCCCTGTCCTTGGACTGATTGCCGTGGTCACCACAAACAATCACAAGGTTTGCCAAATCCCTGAGATGTGCATTCTTACCATACATCTCAACCAGACCTGTCATGTTCTTCACTCGGTCAAGACGAGCCATGGAGAAGATGATTGGCTTGTTCTTGTCCTTCAATACAAACTTGTGTTCATCGTTCTCGACTTCACTGTAGAGAAGCTCCTCAATTTCAGGGTGGAAAGCAGTGAGCCTCTTGTCAGCCTCGGTGTACGGGAAGTAGACACTCATGTCAGCTCCAGGAGAGACAATGTTGAACTTGGGATCAAAAACATCTATGCCATGCACAACTCGGTAAAGCCCAGGAAGGGTGAATGCAATGTGTGATTCATACTGCCCCACAGTGTCCTTGCTTCCAGCAATTTCTTGGAATGTACTGGTGATGATGAAATCAGTGTGATTCATGGCGATAAGATCAGCAGTGAATTGGCATGAGAAGTGGTACTGGCTGTCAAACTTGTCCAAGTATATGTCTGAGTTGGGGTATTTGGTTTTCTCCAAGGCATGAGATCAGGTTTGGCTTGCATTTCCCTCATAATTTCGTTTGCAACATCCTCAGTGTATGTTTCCAGGAATGGCCAGACATCAAAACGGGAGATCCACTTGCGGAGGATACCATTCTCACTCCTGAATGGAACACGAAGAATGTCAGTGTGCTCAGTTCCAATAACCTTCTCCACACGCTGGCCGCATGTAGTACCAACAGCATCAGGCAACAGCCTGGTTACAATGAGGATCTTAGGTGTGATATCAAGGCCTTGCTGCTTGATCCTCAAAAGCATCTCATTCTCCAAAGCGCGGACTTGGTCCAAAATGTACACAACCTGACCACCAGTATCAGGGTATCCCAACACATTGGATTGGGCAAAGTATCCATGCGGAGACAGGATAACAACATTGAACATCATTGGAATAGTTCCAAGGAACTTCTCCAAGTTGGCCGGATCAGGGGCCTCAAGAAGGTCAAGAAGCAAGTGGATGGTGTCAAGCACACGCTTTGCACAGTCACCCCAACCCTTCTCCAAACCGAGCTCTTGGAACCTGTGGTTGAACTCCGAGTAGGGCGTGTCTTGAGGAATGCCCATCAGATATTCTTCTGCCTTTCTAAGGGATGATTGGAGCCCACGAAGGCTCTGAATTCTGTCATTCAGCATCATTGTCGTGCCCTTGTGGTTATGGGCTTTCAGGAAGTTCAGCAAGGGGTAGAGGCTCTCCTTGTCCTGGAACAACTTGGACGACAGGTGACGGTTAAGGAACTGCACCCCATTTCCGATGGACTTGGACATGGACGGGCGCGGGAAGGAGGCATTGAAGGGCTCAAAATCAAGCTCAAGAACAAAGTTGCTGTTGGTGTGTCCATCAACAAGCTGTTCCTTGAATGCCAAGTACTCAGAAACACTCAGCTCTTCCACTGCCAACTCACTTACATTCACCCGAATGTAGTCCCAGACACCAGGCCTTGGCCTGATGGCCAGTGCAACCCAGGGCGGCAGCACAATGGCTTCCTGAGCAGCCCGGAGAATGTCTTCAAAGGGAGCATATTTCTCTTTGTCAGCTTCGATCAAGGCATCGAACTCCGCAAGCAGCTGGTGACGCTGGAGCATTCCCTTTCCCTGGTTAACATACCTAGAGAAGAGTGCAATCAACTCATTGGGATGAGACGAGAAGGTGGCACCGAGGCGTTCGCGGAGACTGTGGAGGCGAGCTAGCTTGGCAGCCATGACTCAATTTCAGGAACTGAGAAGGAGTAGGAAGCATAACAAATCTGAATAAATATATATTCAAAATTGTAGTGGGTTGGTTTTTTCCTAGACGAAGGGAGTATCCTATTAGCATATGCCGGCACCATTGTCAGCTTTGGAGAAAAAAAGCTTCAATCT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.60919
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0331900.3 6 4797496 C T
Osa06LNT0331900.3 6 4797499 A G
Osa06LNT0331900.3 6 4796988 T C
Osa06LNT0331900.3 6 4798087 G A
Osa06LNT0331900.3 6 4799053 A G
Osa06LNT0331900.3 6 4799302 A G
Osa06LNT0331900.3 6 4799710 T C
Osa06LNT0331900.3 6 4799711 G A
Osa06LNT0331900.3 6 4799776 A G
Osa06LNT0331900.3 6 4800577 A G
Osa06LNT0331900.3 6 4800943 G A
Osa06LNT0331900.3 6 4801386 G C
Osa06LNT0331900.3 6 4801528 A T
Osa06LNT0331900.3 6 4802745 C A
Osa06LNT0331900.3 6 4802833 A C
Osa06LNT0331900.3 6 4802924 A C
Osa06LNT0331900.3 6 4802988 G C
Osa06LNT0331900.3 6 4798299 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
Osa06LNT0331900.3 osa-miR5791 Cleavage 4.5 18.233 1 21
Osa06LNT0331900.3 osa-miR5813 Cleavage 5.0 23.876 1 22
Osa06LNT0331900.3 osa-miR5822 Translation 4.0 16.839 1 21
Osa06LNT0331900.3 osa-miR5837.1 Translation 4.5 19.185 1 21
Osa06LNT0331900.3 osa-miR167a-3p Cleavage 4.5 23.865 1 22
Osa06LNT0331900.3 osa-miR396a-5p Translation 4.0 20.662 1 21
Osa06LNT0331900.3 osa-miR396b-5p Translation 4.0 20.662 1 21
Osa06LNT0331900.3 osa-miR396c-5p Translation 4.0 20.662 1 21
Osa06LNT0331900.3 osa-miR166k-5p Cleavage 5.0 20.811 1 21
Osa06LNT0331900.3 osa-miR1851 Translation 4.5 24.496 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0331900.3 6 alk6-1 Physiological trait Eating quality RM190 RM253
Osa06LNT0331900.3 6 hr6 Physiological trait Eating quality RM190 RM253
Osa06LNT0331900.3 6 Qbph6 Resistance or Tolerance Insect resistance RM510 RM314
Osa06LNT0331900.3 6 amy6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0331900.3 6 asv6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0331900.3 6 AsTol Resistance or Tolerance Other soil stress tolerance RZ516 RG213
Osa06LNT0331900.3 6 qRCRJ-6 Physiological trait Source activity RM217 RM402
Osa06LNT0331900.3 6 qLDLJ-6-1,2,3 Physiological trait Source activity RM217 RM3
Osa06LNT0331900.3 6 nan Morphological trait Panicle/flower RG138 RZ398
Osa06LNT0331900.3 6 nan Morphological trait Seed RG138 RZ398
Osa06LNT0331900.3 6 nan Morphological trait Panicle/flower RG138 RZ398
Osa06LNT0331900.3 6 nan Physiological trait Source activity RG138 RZ398
Osa06LNT0331900.3 6 nan Physiological trait Source activity RG138 RZ398
Osa06LNT0331900.3 6 nan Morphological trait Seed RG138 RZ398
Osa06LNT0331900.3 6 qNP-6 Morphological trait Culm/leaf RZ450 RZ588
Osa06LNT0331900.3 6 qLW-6 Morphological trait Seed RM217 RM111
Osa06LNT0331900.3 6 qSPTF6 Physiological trait Sterility RM217 RM111
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