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

>Osa07LNT0387600.2

GTGCGCTGACCACGCTGGACTAGCGCTCCTCCTCGCCCCGCCTCAGTCCAACGCTGCTCCCGCCGGCGCTCCGCCTCCTCCGCCCTCTTCCTCCTCGCCGGAACCGATTTCGTCCCCTTCCGGCGTCGCCGGCGGCTTTTCCCGCCGGTGCTCCTCCTCCGCCCTATTCCTCCTCACATTCCCCGTTCGCGCCGCCGGAGGGTCGTCCCCTTCCACCGACACCGCCGTACTCCACCGATGCCCTCGCCGGAATCGATTTCTTCCCTTTCCGCCGTCGCCGCAATCCACTTCATAGGTTCATCTTGCGCTGATTGGTTCCCGTCAGATTTGAGTAGGAACTAAAGGAACCAACACTGTTCCCCCTGAACCCTAAGTTGATCCTGTGCAGCCCCTATCAATGGATTTGCAGCCGTGGTGCGAAGGCATCGTATCCCCTCATGGCGTTGCAATCCCAGTAGGAGCTTGCCATCGGCCACATCTGGCGTTTCACAATCCTGCTACCGCTGATTTTCAGATGATTTCACGAGCGTGTAGACAACAGCAATTATCAAACAAGGTTCATCCCTAAATCAGGGAGCTTCTTTGGTATACGCAGGGAGCATCAGTACTGTCTAATATTGCACCAATGTTATCATTGAAGCAAAACCAGTTTTATTGTGTTTCAGTGCTGCAATCGATCTAAAGCAATACCTTGAAGTACATTTTGTATATTGTCTAATGCCTCTCCCTGGACATAAAGGGATGAACTTCGTAAACTATTTGCAGGGACAAGATGAGCAAGCAGCTAACCATTTCATTAAAATTGAGGTCTTTGTTGTTTGCATGGATATGAACTGAAGAATTGAGATCTTTGTTGTTTGCATGGATATGAATTGAAGAAGGATAATATTATACTCTTGGAGTTCCCAAAAGGACAGTGCAATGGCCGATGAAGGCATTCTTTGATGCTCTGTCTACTAAGTTAAACTAAGGTGTAGTATCCTGTGATGGAATTGCAGTTGCGGATACTACAAGTGCTGCAGCTGATGTACATGAGTACAAAAAGACCAGAATGTGTTAAGATAACGACTGCACTGCGACTAAAGATGTCAATTCAAATTATTCCTGACCTGAATGAATTATCTGGAATTAGGTCCACAGTCTTGGAGCACCAGTATCTTCGATCTTTCACTGGAGGTTTGCTTTTTCACGTGTAATTAAAATGTTGCACTGCATCTTACAAAATTATCACTCTAGGAAGCTTACTTTTTGTATGTCAGAATTTGTTTGATCGTTTTCTCCAAGAAGCTTACTATTTGTATGTTCTCAGCCAATTTTTGCATTTACTGTCTGGTTAGACAATTACCCGTTGCAGAGCAGGTGTCCATAATGGAGAGGTTATTATATTTTTCCTTTTGCACAATTCTGTTTCCAAAGTATTTAAATTGTGCCTGTACAATTTGTTCACAGGCAAGTTCACACTTTTTTAATTTAGTTCAGATCTTAGTTTCCATCTGAATATATGGTGCACCATAGCCGTGGAAAACGGTATATACAGCTCTATAGCAAGAATTTGTTGGATTCATGCTATTGATACTTGGCTCGGTCAATTTATTTTACATGTGCAAGGGAGATCAGGTGCATATGCAGTGAGAAGAGTCAACAGAAAGGAATGAGGAGTAATGAGGCTTGAAGGAATAATAATATGCAAGATCAACTCTGGATTTAGACTTCTTTGGCCAAGCACTATGGCTAAAATGGCATGCCAAGCTTGGAATAGAAAGATCCAAGTTGATGCTGGCACAGGCTTTGGTGAATCACTGATGGGTGAGAGACCTGTAGAGTTCCTTGTCCAACAGAGCAATGGTTGAGTTCTTTCAGTTGTGGGATGAAATTCAGATGGTGTAGCTTCAACCAGGAATAGCCACGACTCCATTCGGTGGTAGCTAACAGGTGGGAGCTATTTGACTTGTGTGGCTAGAAGTATTCGAGTCAATCATCTGCTTGCCTCGGCCTACTTCAATAGACAACGGAGGATGCTCTACATCATAATCGTATGCAAAGACAGGTTACAAAAAATGCATGAAAAACGTGTAGGCTGTCGAAGCAAATCCATCAGGAGGACACCATGGCATCTGATGTTGTCTACTATGCATTAAAGAGATTACTGGTTGTTTCTATTCCTTCTTTTTGGTTGAAATAATTTACGTTAATATAATGTTTTCATAGAAGTGAGCCAATCTTGATTTGTTTGGTTAACACGGGTTATGTGTTGAACGTGTGATCCAATAGTATGGCTTTGTTACGTTCTCTTATCAGCTAATTGTAAGTCCTTAGCAGCTGGAATGCTGGATCATGACTAACAAGTGAAAAGGATCAGTGATAGTTTTATGCTGGTGCAGACATGCAATGCCAAATAAAACATGGATAATTCCTTCTTGTTTGTG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.435333
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa07LNT0387600.2 7 24119352 T G
Osa07LNT0387600.2 7 24122799 T C
Osa07LNT0387600.2 7 24119582 A T
Osa07LNT0387600.2 7 24120036 T C
Osa07LNT0387600.2 7 24120955 C T
Osa07LNT0387600.2 7 24121392 A G
Osa07LNT0387600.2 7 24122248 T C
Osa07LNT0387600.2 7 24122300 T C
Osa07LNT0387600.2 7 24122302 G A
Osa07LNT0387600.2 7 24122663 C T
Osa07LNT0387600.2 7 24124032 A C
Osa07LNT0387600.2 7 24124474 G A
Osa07LNT0387600.2 7 24123888 T C
Osa07LNT0387600.2 7 24124957 T C
Osa07LNT0387600.2 7 24122539 T C
Osa07LNT0387600.2 7 24123524 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
Osa07LNT0387600.2 osa-miR5837.2 Cleavage 5.0 15.06 1 21
Osa07LNT0387600.2 osa-miR397a Cleavage 5.0 12.789 1 21
Osa07LNT0387600.2 osa-miR397b Cleavage 5.0 12.789 1 21
Osa07LNT0387600.2 osa-miR171e-5p Translation 4.5 21.236 1 21
Osa07LNT0387600.2 osa-miR437 Cleavage 4.5 16.034 1 21
Osa07LNT0387600.2 osa-miR1425-5p Cleavage 4.5 18.867 1 21
Osa07LNT0387600.2 osa-miR444b.2 Cleavage 4.0 13.935 1 21
Osa07LNT0387600.2 osa-miR444c.2 Cleavage 4.0 13.935 1 21
Osa07LNT0387600.2 osa-miR1879 Cleavage 4.0 16.947 1 24
Osa07LNT0387600.2 osa-miR2092-3p Cleavage 5.0 17.886 1 22
Osa07LNT0387600.2 osa-miR2905 Cleavage 5.0 15.507 1 21
Osa07LNT0387600.2 osa-miR2905 Cleavage 5.0 11.006 1 21
Osa07LNT0387600.2 osa-miR5498 Translation 4.0 24.361 1 21
Osa07LNT0387600.2 osa-miR1872 Translation 5.0 20.834 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa07LNT0387600.2 7 nan Others Others RZ395 RZ264
Osa07LNT0387600.2 7 qPH7-2 Morphological trait Dwarf RZ626 RG650
Osa07LNT0387600.2 7 qSDS-7-2 Physiological trait Germination/dormancy RM320 RM234
Osa07LNT0387600.2 7 qCIVG7-2 Resistance or Tolerance Cold tolerance RM336 RM118
Osa07LNT0387600.2 7 grb7-2 Morphological trait Seed RM505 RM336
Osa07LNT0387600.2 7 Ph7a Morphological trait Dwarf RG650 C285
Osa07LNT0387600.2 7 qLCC-7 Physiological trait Source activity R2394 R2677
Osa07LNT0387600.2 7 qLVG7-2 Resistance or Tolerance Cold tolerance RM336 RM118
Osa07LNT0387600.2 7 qCDS-7 Physiological trait Source activity R2394 R2677
Osa07LNT0387600.2 7 Ra7a Others Others RG650 C285
Osa07LNT0387600.2 7 nan Resistance or Tolerance Other soil stress tolerance C451 R1245
Osa07LNT0387600.2 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