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

>Osa07LNT0388100.1

TTAAATCATCTTCCTTGTGCATAAGCAGACCCCATCTGATAAATTATGTGATGTATTGAATCTGCCAAACGATTACACATTGTTCCCTACCAAAATTGGCACAGCTTCCTTTTGCAGGTATCTTTCCATACATAACATTCTGGTCAAAAACGAGGGAACATCATCACACTATTTCAATCCCTGAAGCTATACACAGCTTGGAATCAGCTCCCCCACTGATGACGCTATCCCCTTTCCACCAGTCCGCACATAAAACCTTGTCTTTGTGTGACTCCACAGAAGCCAGTGGCCATGCTGTCCTTAGATCCCACAACATTACTTTCCCATCAAATGAAGATGATACCAAATGAAACCACGAACTTGGATGCCATTTGCAAGCACTGATCCAGCTTTTATGGGAGGAAAACTGAAAAATTGGAGCTAGAGTTCCAGGTTTACGAGGGTCCCATACCCTCAAGACAGGGTCAGAGCCACCAGCAGCGATTAGTGAAGAGCTCTCACCACCACAATCCAAGCAATTCAAGGCCTTCCCAGATACCATATTCCATGTCTCTTTCCCTGTTTGGACATCCCACTGCCGAACAGAATGGTCCCAAGATGCTGAATATATTGTTTGTCGCTCAGGCCAGGTAACAGCAGAAACGCACTGCGTATGTCCCAGAAATGTTGAAGTGGCAGAACCCTCAAACAGAGATTCTTCAGGTCCAGATGAATCAGAATTTGTCCTTCTCTTCTTCACTGAGACAGTGTCACCATCTTCTTCCGACCCTTCGACTGACCATAGCTTAATTGAGTTATCCCAGGAACCAGAACATATCATGTTTGTGGAAGGGTCTACTGCAACACTCTGAACAGATGATGTGTGGCCACGGAGAATTTTGTAAGCCCCAATTTGCTTTGGAACACTGACTGATGTATCAAACTTGAATAAGCGCAATGACCTATCCTTTGATGCAGTGACTACATGCAGCCTGTCTTCAGTTTCACCTTTATTAATGAAGCGAGCAGAAGTGATTCCGTCACTATGTCCTTCCAAAATATGTGTACATTCAGATGCATCTCTCCATATTCTTGCAAGACCATCATAGCAACCTGTTAATACGAAACTCGGGTTCGATCCATCAACTGCGCTAACCCAGTCATCATGCGGGCATGGATCCTCCTGCTTCCTCGGTGCCACAGCTTTTACATATTCAAGCTCAAGCACCCTCTCCACTGAGATGCCCTTGGCGAGGAGGAACTCCTGGAGCGGGAGCCGCACGAGCTCGCCGTCGACGAGGAAGTCGAAGGGCTGCGCCTGGTGATCCGGGGAGGCGGCGAGGAGGAGGCTGTTGACGATCTCAGAGAGGCCCATGCGGGTGAGGTCGGCGGGGACGGCGATGGAGGTGGGCGGCGCGCGCAGCGGCGCGGGGAGCTTCGTCAGGAAGCGCACCCGCACCTGGCGCGAGGGGTCGGAGGCGCCGCCGGAGTCCATGGCGGCGGCGGCGGCGTCGGCCGGCGGAGAGGAGGCGGAGGAGGCGGCGGCGGCGGGAAG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.712422
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa07LNT0388100.1 7 24496190 A G
Osa07LNT0388100.1 7 24494065 C T
Osa07LNT0388100.1 7 24495305 T C
Osa07LNT0388100.1 7 24495741 C T
Osa07LNT0388100.1 7 24496229 G A
Osa07LNT0388100.1 7 24496903 T A
Osa07LNT0388100.1 7 24497334 T G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa07LNT0388100.1 osa-miR5808 Cleavage 5.0 14.564 1 24
Osa07LNT0388100.1 osa-miR396a-3p Cleavage 4.5 19.429 1 20
Osa07LNT0388100.1 osa-miR396b-3p Cleavage 4.5 19.429 1 20
Osa07LNT0388100.1 osa-miR169f.2 Translation 4.0 14.971 1 21
Osa07LNT0388100.1 osa-miR2094-3p Cleavage 4.0 22.087 1 22
Osa07LNT0388100.1 osa-miR3979-3p Cleavage 4.5 11.978 1 20
Osa07LNT0388100.1 osa-miR2878-3p Cleavage 5.0 17.6 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa07LNT0388100.1 7 QRl7 Morphological trait Culm/leaf CDO497 CDO385
Osa07LNT0388100.1 7 nan Resistance or Tolerance Other soil stress tolerance C451 R1245
Osa07LNT0388100.1 7 nan Others Others RZ395 RZ264
Osa07LNT0388100.1 7 qPH7-2 Morphological trait Dwarf RZ626 RG650
Osa07LNT0388100.1 7 qSDS-7-2 Physiological trait Germination/dormancy RM320 RM234
Osa07LNT0388100.1 7 qCIVG7-2 Resistance or Tolerance Cold tolerance RM336 RM118
Osa07LNT0388100.1 7 grb7-2 Morphological trait Seed RM505 RM336
Osa07LNT0388100.1 7 qLCC-7 Physiological trait Source activity R2394 R2677
Osa07LNT0388100.1 7 qCDS-7 Physiological trait Source activity R2394 R2677
Osa07LNT0388100.1 7 qLVG7-2 Resistance or Tolerance Cold tolerance RM336 RM118
Osa07LNT0388100.1 7 Ph7a Morphological trait Dwarf RG650 C285
Osa07LNT0388100.1 7 Ra7a Others Others RG650 C285
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