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

>Osa06LNT0338200.1

CAAAAATAAAGCTCGCAATATTCTCATTGCATATACACAAGTGTAGAATTTATACACATTTCGTGGTTCGTAATTCTTAAACAAAACTGTATTGAAAAAAAAAAAAGAATAACAAGGTTTCAGATGAAACTAGTAGGGTCATTTGCGATGTTAACTCTTGATTCCGACGAATTTGCATATTTTATGGAGAAAGCCGCCATCACTAGTACTAACTGCAACAGGCTCCTGCACAGGCTCTTTGAAGTTAGCCTTATCACTCAACTCTTGAAATGCATTAACAACGTTCTGTAGTCGGGCAACAAACTCGATTAGAAGGGAGGCAAATGTGGCCAAGGACAGAGCACTTGCACTTTCATATGTTTTTGTTTCCTCGTCTTCAAGTGGCAGATTTGGATGGAATGATCTTCGAGCAGGCCAAGACAGTAACTTGAAATCTACAGTTGATGATGAATCATGTCTGCTCAGAAATGAATTAACAGCAAAGCTTTTTGAATGATGCGCTGTAGTTTGTTCAACAATTGTAGGCTCCTTCACTTCGATCTTGTTTTCCTTTCCCATAATGCCAGTGCCATTCAGAACTTCTTTGATACCTTCGGCTTGCTTGCTAGTGTCCCATCTTTCAGTATTCACAAGAAGGTACGACTTCTCATCAATCCTTTTTTGCAACTGTTCAGCAGCCAAGTGGACTTCTGCTAGAATATCTGAAGAGCTCAATTTGGTCATTGTCTTGACTTTGTCTCCAAGCTCGCGCAACACTTTTGCACCTTCTATACCAACTCTCTGAATTTCTGCACTAAAAACCTTTCTGCTTTCTGGTGGTGCCTGAATTTCGGAAAGAATACAGCCATGCAATGCCATGACTGCAAAGGAGCAATGCCTCAATGCCCCACCAACTTTGGTGAAATTCCTCCAGGGGTACTTCATCATTTTGTAAGCGCCATGGGGTGGCTCCCATATAGCAAAACCCAACAGAGTTTCCTCTTGTGCTGATGCCTCAACTGCTGCCCTATAGCCACTATATAGAGGATCATCAGATGCTTGATATACAAGTATTTTCGAAGGAATCCTTTCATACTCCATGCATTTCAAATATCCATCAACGCAACCTTCCAAGGATTTTGCAACACCAATGAAGTTTTTTGCAACCAAATTGTGCAAATCTTGTCCAGCCCATATTGGGTAAATACCTACATTGATTCCTAGACTGACAGCAGCACCAATAGCAATTAATATAAATCTACTCACAGCCGTATCAGTGAACTTCCCTGTGTTGTACCCAGAAACCATGACATAGCAGAATGTCAACAAGAATACGCGGAACCCATACTCATAGGCCTTCATTTTTGGATGCAGTTTCGTCAAGGTTGTGAAAAAAGCAACAATAAATATGCTAATTATAAGAATTACTTCCTCCAGCTTTCCCAGGTGTTTGGACAATTCGGCGACTGCTAGCGCAAGCCCTCCAGCGGTAAGGGTACCCAATCCCCTATTAAAACCTTTGCTAAATGTTGCACCGATGCTGAACTCGAAGACGACGACGACGGTGAGGATGGCCCAGACGGAGTGGCTGACGATGTCGCGGGGCTCACGGAGGAACACCAGCAGCGAGATGAGCGCCAGCGCCAGGCCGACCTTGGCCGCGAACACGGCCTTCCGCGGGTCGGCCCGCGCGAACGCCCACAGCTCCTCCGCCGCGCCGCGCACGGCGCCCCACACGCGCGCCGCCGCGGCGCCGGCACGCCGGACCAAGCCCTCCTTCCACCCACCCCCTTCCCCGCCCCCGCCCCCGTCCCCGCCCCTCCCGCCGCCCGGCAGGCCCCACGCCGACGACAGCAGGGGCACCTCCCGCGCCCCGCCGCGCTGGTCCTCCAGCGTCGACCACAGCGTCCCCAGCTGCCCCGGCGGCGGCGGCGGCGAGGACCCCGCGCTCCCCGCGGCCGCCATGGCCGGTGGATCCGGAACGCTCTAGAAGGTTCCCGCG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.859586
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0338200.1 6 8961578 G A
Osa06LNT0338200.1 6 8960133 C A
Osa06LNT0338200.1 6 8963773 C T
Osa06LNT0338200.1 6 8963793 G C
Osa06LNT0338200.1 6 8963833 C T
Osa06LNT0338200.1 6 8963837 T C
Osa06LNT0338200.1 6 8964128 G A
Osa06LNT0338200.1 6 8962290 T C
Osa06LNT0338200.1 6 8962796 C T
Osa06LNT0338200.1 6 8962815 G A
Osa06LNT0338200.1 6 8960809 G C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa06LNT0338200.1 DTM_#DNAt_MULE_japo_Os0312 Chr6 - 8962098 8963011 913
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa06LNT0338200.1 osa-miR5536 Translation 2.5 12.55 1 22
Osa06LNT0338200.1 osa-miR5805 Cleavage 4.0 14.257 1 24
Osa06LNT0338200.1 osa-miR397a Translation 5.0 13.071 1 21
Osa06LNT0338200.1 osa-miR166k-5p Cleavage 4.0 15.777 1 21
Osa06LNT0338200.1 osa-miR172a Cleavage 4.0 14.884 1 21
Osa06LNT0338200.1 osa-miR172b Cleavage 5.0 14.884 1 21
Osa06LNT0338200.1 osa-miR172c Cleavage 5.0 14.884 1 21
Osa06LNT0338200.1 osa-miR172d-3p Cleavage 4.0 14.884 1 21
Osa06LNT0338200.1 osa-miR1865-5p Cleavage 5.0 14.536 1 24
Osa06LNT0338200.1 osa-miR414 Cleavage 3.0 18.358 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0338200.1 6 S5 Physiological trait Sterility RG213 C235
Osa06LNT0338200.1 6 qNFGP-6 Physiological trait Source activity RM136 RG456
Osa06LNT0338200.1 6 qSF-6 Physiological trait Source activity RM136 RG456
Osa06LNT0338200.1 6 nan Resistance or Tolerance Blast resistance R2171 RG64
Osa06LNT0338200.1 6 nan Resistance or Tolerance Blast resistance R2171 RG64
Osa06LNT0338200.1 6 gp6 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0338200.1 6 qRS6-1 Morphological trait Shoot/Seedling RZ667 RG424
Osa06LNT0338200.1 6 qGY6-1 Morphological trait Seed RZ667 RG424
Osa06LNT0338200.1 6 qLVBSL6-1 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0338200.1 6 qLVBTL6-1 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0338200.1 6 qSL6-1 Morphological trait Culm/leaf RZ667 RG424
Osa06LNT0338200.1 6 qTL6-1 Morphological trait Culm/leaf RZ667 RG424
Osa06LNT0338200.1 6 nan Physiological trait Eating quality RM253 RM162
Osa06LNT0338200.1 6 qHD-6-1 Physiological trait Flowering RG424 RZ667
Osa06LNT0338200.1 6 qPH2-6-1 Morphological trait Dwarf RG424 RZ667
Osa06LNT0338200.1 6 qTN2-6-1 Morphological trait Culm/leaf RG424 RZ667
Osa06LNT0338200.1 6 nan Physiological trait Flowering R2171 R2123
Osa06LNT0338200.1 6 amy6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0338200.1 6 asv6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0338200.1 6 sd6 Morphological trait Panicle/flower RG138 RG64
Osa06LNT0338200.1 6 nan Physiological trait Eating quality RG64 R2171
Osa06LNT0338200.1 6 qPHw6-2 Resistance or Tolerance Other soil stress tolerance RG424 RZ667
Osa06LNT0338200.1 6 qSFWd6 Resistance or Tolerance Other soil stress tolerance RG424 RZ667
Osa06LNT0338200.1 6 tns6 Morphological trait Panicle/flower RG138 RG64
Osa06LNT0338200.1 6 qLDLJ-6-1,2,3 Physiological trait Source activity RM217 RM3
Osa06LNT0338200.1 6 sd6 Morphological trait Seed RG138 RG64
Osa06LNT0338200.1 6 ph6 Morphological trait Dwarf RZ667 RG653
Osa06LNT0338200.1 6 tns6 Morphological trait Seed RG138 RG64
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