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

>Osa04LNT0248900.1

GTCCGTCACAGATGAGTATAATCCAAACAGATGAGTATAATCCAAAAAAAATAAGTATAATCCAAAACAAAATAGCTAGCCTCAGACCTTTGAGGTCCATGCCATGCCGTCCCGCCTCTCCCAGGCCTGTCTTTTTTGTCCTCACTCGCGTGCACCCGGGAAGGTCGGTCACCTATCCCAAAATTGCTCCAGGCCAAGCACGCTTAACATCAAAGTTCTTTGGAGATCAGCTTCCGGAATAGTAGTTGTAACTTGTTGGTATGAGTATTCTATTAATCCTATTAAGCCCTATGCCAGGATGTCACACCCCAACATCCTCCATTCATATACATTCATTCATTCACATACATTAACATCAATATATTTAACATAGCCACATTCACATAACATCTATTTTGATCACATATTTCATATCCATTCACATATTTCACTAGCAAAACCGAGTTAATTGGATCAAATATATATAATTCTAAGAAAAATGAATTTTGAATTGAATTTTATAATACTAAATAAACTCATATGAAAAAGCTGTCAAAAACAAAGTTGTAGAACTCATTGAGATCTGTCAAAAATAAAGCCCGTCATAGATGAGAACTTTAAATTTAATTTTAGGCCGGTGTGTCAAATGCAAAAATCATAAACAAAAAAATTGTATAATTCATCGAGATCTACAACTATTCTATCGGTTCTTTGTACAAATAAGTTCATTTGAACGATTCAAATTTTGAATTTTCAAAATTTGACAACTTTGAACAAAATTTGGGGTTATTAAATGATTTCAAATGGAAAAATCACCAAAACCAAAATTGTAGAACTCATCGAGGTGCAAAACTTTTATTTTGGTCATTTTTCTATATAACATT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.429417
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0248900.1 4 5164243 A G
Osa04LNT0248900.1 4 5164255 G C
Osa04LNT0248900.1 4 5164304 G A
Osa04LNT0248900.1 4 5164314 T G
Osa04LNT0248900.1 4 5164604 T C
Osa04LNT0248900.1 4 5164610 T C
Osa04LNT0248900.1 4 5164617 A G
Osa04LNT0248900.1 4 5164628 T A
Osa04LNT0248900.1 4 5165207 C T
Osa04LNT0248900.1 4 5165252 T C
Osa04LNT0248900.1 4 5165266 T G
Osa04LNT0248900.1 4 5164241 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
Osa04LNT0248900.1 osa-miR5532 Translation 4.5 4.335 1 22
Osa04LNT0248900.1 osa-miR5825 Cleavage 4.5 20.055 1 24
Osa04LNT0248900.1 osa-miR395f Cleavage 4.5 18.916 1 21
Osa04LNT0248900.1 osa-miR2099-5p Cleavage 4.0 15.398 1 22
Osa04LNT0248900.1 osa-miR5162 Cleavage 5.0 13.007 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0248900.1 4 spp4-2 Morphological trait Panicle/flower RG449 CDO456
Osa04LNT0248900.1 4 qCTS4-1 Resistance or Tolerance Cold tolerance RM335 RM261
Osa04LNT0248900.1 4 qSNP-4a Morphological trait Panicle/flower RM401 RM335
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