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

>Osa07LNT0386800.1

AACCGGTTTAACCCACATATCTGAGCAAATCTACACTCGATAGGCATTCAACCACCTTGTCAAAAAATAGGTAATCAGCCCCCCAAAGAATGTACACTCAAGAATGAAACTGTCACAAGATTAACACAGTTTCATTCTTGTCACAGAAAGATTAACATGTATTGTATGGCTACACTCTTAAGTGCACTAAGCTGTTTCAGCATTAACATCAACTGCTACTTAACCATGTTTACGTGTAGTAGTATATCCTAACGACTTCAGTGTGACGCCAAAATCAATCAACTAAGAAACATTCCTCCGGGCCACTGTACACAAACTTTCCCTTTTGTTTGACTGGCTTAGGTGGCTTGGAACTAGCAAAGTCATACAAGTGCTGCTTCACCTTCACTGTTCCTCACTAAATAGGTCATCTGGAAGACAGCGCTCCCTTTTGTTTGTCTGTCATAATGGTCCATGGAGAGGTGTTCACTATCCCAAGTTCAGTCTTCAAGGTATCAAGAAACCATGTCCATGTGCTGAAAGACTCAACTTCTACCACAGCCATTGCAATGGGGTATATGCAGTCATTGGGATCAATTCCAACTGCTGTCAACAATTGACCTCCAAATTTGGTCTTGATGTGGCAACCATCCAGACAAATGATTGGCCTGCAACCACTGAGGAATCCTCTCTTGCATACATCTAGTGAGAAGTACAAGCTACTAAATTTGCCCTCATCTAACCTAAGATAGAAAGAACTCCCAGGATTGGACCTCCTTAGTTCATTGCCATAATCCCACAACAAGTTGTATTGGGCTATTTCATCACCATATATCTCTTTTAGGGCCAGCCTCCTAGCTCTTGCAAGCTTGCTTCTTGAAGGAGTCAAGTTCCACTCTTTTTGTACTGTCTTTGCAAAGCTAGGAATGGTCATCTTCCCATCAGCCCTAAATGACTCAGTGTACTTTTCAGCTAACCATTTTGCAGTACACCTTTTTAGAATCCACTCCTTCTTGCATTTGTGATGGGGCTCATATGTCTTAACAATGAAGGCCTTTGCCCTGCTGTCCATTGAAGCATAAAAGTTCCAGGGGCATCCTTCTGCACAATGTGCCTTGATCCTAGTTCTATCATTCCTGGGCATCTTTATGTCCACCCTGTTCTTCATGCTATATTCAGAGATAGCCTTTCTAACTAATTCAACTGAAGAGAATACCATGCCTACTTTGAAGATTGGGTTGTTAATGTCTTCAGGATTAAAAGACTTAAACTTCAAGTTGAACTCATCATCATCATCATCACTTGGCAAGTGCAGTTGTTCATCATCACTTGTGTCACCTTCTGACAAATCTGCCACAACTTTCTTGCCCTTCAACACACTACCTGCAGCCTTCTTATGGTTGAATTTCTTCCTATCCCCCTCTTCCACATCACCATCCACATTTTCCTCAAAGAGGTCATCATCATCATCCTCCCACTCATAATCACTATCAACAAAATCAGAATCAGACTCACTGTCATCTGAGTTTATATGAAAGCTCAACTATTTCTTCACCAACATCCAATTCTTCATGCACTACATGTCCATCAGGTGCATTCCTAGGGTTTCTATCCTCGCTTTCTGCCTCCTCTGTCTGCTGGCACTGTCTACTAGGGTTGAACACCTCTGGCAACTCAGCTTCTGGGCTCAGAACAATGTCATCTATATTTCTTCCTGAGACATGATTAGTATGATCAAAATAGATGACAAAATTCTTGATTTTATTTGACACTGATTTCATGACATTGATCTCAACTTCACTGTCTATGATCCTCAATCCATCAGACATGTTCTTTCCAGGCAATAACCAATAAGTTTTCAACTTTCCATCAGAGTCATATCCAAGCATGGCAACAAAGTCTGCTAAATGTAGACATCTACCCCAATCTCGAGAATCAATATTGTCAAACCAGTCTACTTTGCCATCCATATATGTGCGGTTCACTCCCATACCACAGAAAAACCCCCCATGATGAAACTCAATTGAAAAGTACTTTGATCCAGGACCTTCTGGAGATTCTGTTTTCTTCTCAGAGAGGTTATGTGTTAGAGGTGAATCAAAATCTCCAAATTGATGTGTCAGTGTCTCCTGGGAAAGTTCAATGAAATTCGGCATTTTTTGTCCAGAGTGACCCTCAATGGCATTGTCACATGATGTCCTGTGTGCAACATTGTCAAAACGGTCGTTTCTCTGAGGAAGCTGCCTTTGCTCTTGTTTGGTCCTATCCAGGTAAGGCTTTGACTCTAACTTCTACTCCACTGATGGAATGCGATGTGCTCTTTGATAAGAGAAGCCCCACTGTGTCATCATTTTCGAATGTCACAAAACCGAAAGTGTGCTTCTCATTGTCTGGCTTAAAGGGGATGTAGACATTGATCACAGGTCCGAACTTCTTGAAGTAGTCCCGAATATTTTTCCAAGTCAATATGTTCTTAGCGATGGTAATATAAATCGTAAACTCGGTACTTTGACCGAAGAAATCCCTCTGTGAGCCATGAGGATGGGATTGCCTCTGATTGTGACCAAAGAAATCCCTCTGTGAGCCACGAGGATGAGATAGCCTCTGATTGTGCAACTCAGGGACACCAGACCCGAGAACTTGTGCATTTAGGTAATCCCTTGGCATGCCATCGAAGGCATTGGCACATGATGTCCTGTGTGCAACATTGTCAAAATGGTCGTTTTCTTGAGGAAGCTTCCTTTGCTCTTGTTTGGTCCATTCCAGGTAACGCTTGACTCTAACTTTTACTCCAAAGATGAAATGAGGTGTGCTCTTTGATAAGAGAAGGCTCACCGTATCAGCATTTTCAAATGTCACAAAACCGAAAGTGTACTTTTCATTCCCTGGCTTACAGCTAAGGTAGACATTGATCACAGGCCCGAACTTCTTGAAGTAGTCCCAAATATTTTCCTTAGTTAATCTGCCGCCATCAAAGTTGATGGTAATATAAATCGTAAAATCGGAACCTTCACCAAAGAAATCCCTATGTCGGCCACGAGGATGAGATTGCCTCTGATTGTGCATCTCATGGACATCAGACCCGAGAACATTAACTTGTGCATTTAGATAATCCCTTGGCAAGCCATCACCTGGAATGTTCAAAGACTGAAACTGAGGCTCCAAATAGAGCGATGGGGATTCATAATCATACCGCGTTGAAGGTGACTGCAGTAAGGGTAGCTGCTGGAGGTGTTGTATTGGGGGGAACCTCATGTAGTATGACTTCGCCTCATTAATCAAGGCTTGTATTGCCTCATCCCGGGCTGAAAATGCATACCAACTGATCCAACTTGGCTTTGATATGTTGGCGTACTGAACAATAGCATTTGCACATGATGGCTCCAACTGATCCAACTTGGCTTGTGCCGCAAAACCAGTTGACATTGGAGCATATGCCCCCCGTTCCCGTTGCGCCGGCGGCCGGAGCCAGGTGCCAAGCGGCGGCGGTCCCCGGCCGTCCGTCGGAGACCCGCCGCCGCTCATTGAGACCTAGCCGATCGCCGCCGCCCGCGCGCTTCGCCGACCTCGAACAAGAAAGAGATTTGGG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.821858
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa07LNT0386800.1 7 23637813 G T
Osa07LNT0386800.1 7 23637917 C T
Osa07LNT0386800.1 7 23638257 A C
Osa07LNT0386800.1 7 23638287 C T
Osa07LNT0386800.1 7 23638316 T C
Osa07LNT0386800.1 7 23641972 A G
Osa07LNT0386800.1 7 23642010 A G
Osa07LNT0386800.1 7 23642245 A G
Osa07LNT0386800.1 7 23642389 T C
Osa07LNT0386800.1 7 23633598 C T
Osa07LNT0386800.1 7 23634198 T A
Osa07LNT0386800.1 7 23635689 G A
Osa07LNT0386800.1 7 23635886 T C
Osa07LNT0386800.1 7 23636115 T C
Osa07LNT0386800.1 7 23636128 A C
Osa07LNT0386800.1 7 23636135 T C
Osa07LNT0386800.1 7 23636145 G A
Osa07LNT0386800.1 7 23637737 G A
Osa07LNT0386800.1 7 23632835 T C
Osa07LNT0386800.1 7 23632961 C A
Osa07LNT0386800.1 7 23633032 A G
Osa07LNT0386800.1 7 23633157 G A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa07LNT0386800.1 DTM_#DNAt_MULE_japo_Os0208 Chr7 - 23632470 23636197 3727
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa07LNT0386800.1 osa-miR5526 Cleavage 4.5 12.864 1 21
Osa07LNT0386800.1 osa-miR5541 Cleavage 5.0 11.355 1 21
Osa07LNT0386800.1 osa-miR396c-3p Cleavage 3.5 11.125 1 21
Osa07LNT0386800.1 osa-miR171i-3p Cleavage 5.0 9.99 1 21
Osa07LNT0386800.1 osa-miR390-5p Cleavage 5.0 16.613 1 21
Osa07LNT0386800.1 osa-miR1428a-3p Translation 5.0 18.991 1 21
Osa07LNT0386800.1 osa-miR1852 Cleavage 4.0 12.355 1 21
Osa07LNT0386800.1 osa-miR2874 Cleavage 4.5 17.417 1 24
Osa07LNT0386800.1 osa-miR2907a Translation 4.0 15.344 1 22
Osa07LNT0386800.1 osa-miR2907b Translation 4.0 15.344 1 22
Osa07LNT0386800.1 osa-miR2907c Translation 4.0 15.344 1 22
Osa07LNT0386800.1 osa-miR2907d Translation 4.0 15.344 1 22
Osa07LNT0386800.1 osa-miR2928 Translation 4.5 18.514 1 20
Osa07LNT0386800.1 osa-miR5076 Cleavage 4.5 15.749 1 22
Osa07LNT0386800.1 osa-miR5507 Cleavage 5.0 17.637 1 21
Osa07LNT0386800.1 osa-miR5508 Translation 5.0 16.078 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa07LNT0386800.1 7 nan Resistance or Tolerance Other soil stress tolerance C451 R1245
Osa07LNT0386800.1 7 nan Others Others RZ395 RZ264
Osa07LNT0386800.1 7 qSDS-7-2 Physiological trait Germination/dormancy RM320 RM234
Osa07LNT0386800.1 7 qCIVG7-2 Resistance or Tolerance Cold tolerance RM336 RM118
Osa07LNT0386800.1 7 grb7-2 Morphological trait Seed RM505 RM336
Osa07LNT0386800.1 7 qLCC-7 Physiological trait Source activity R2394 R2677
Osa07LNT0386800.1 7 Ph7a Morphological trait Dwarf RG650 C285
Osa07LNT0386800.1 7 qLVG7-2 Resistance or Tolerance Cold tolerance RM336 RM118
Osa07LNT0386800.1 7 qCDS-7 Physiological trait Source activity R2394 R2677
Osa07LNT0386800.1 7 Ra7a Others Others RG650 C285
Osa07LNT0386800.1 7 QRl7 Morphological trait Culm/leaf CDO497 CDO385
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