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

>Osa04LNT0281400.1

CCTTAATCAACTTACAAAACACCAACACTTTGGTGTATCCACAGCACCAATCACACAAGGAAATTTACCATCCACCTACTCGTATCCTACTGTTAGATTGGCCACCTTACACCAGAGAAAGGGCATTGCCAAATTCTGAGACGCTGTCCTTTGAGCTCCCCGAATCGCTCGCGACCTCAGTATCCTTCTCAATCTCCACTGATTGGTAAGTTGCTGTTGGCATTTTTTTCGCCGGGCCGGCGAATAACCGGCCGATGTATATTAAGAGAAAGAGTTGCTGTTGGCATTTCATCCCCGATATCTACATACTCATCCAACTGCTCGGCCTGTGTAGTGATCTTGTCAGGATCCTTGCTCTCTATTGCCATTGCCACGTCACCGTTGTCCACCATCGTAGCGGTACTGCCATTCACCAGCACATAACTATCATTAGCCACGGAAGCATCAATGACATCGGCATTTTCACCATTAACAATGGCAGCCCGTCGACTCTTGTTGAGCGCCTTCTTGAAGTTGTTGACGAATCGATCAAGCTCCCACTGTGTCTCGACATCCATCTCATCAATATCCAGCTCGATCTCACCCCCAACCAGCTCAGGATTGCCGTTCCTCTTCCGCACAATCTGCAGCACATTATGCATCTTCTTCTCTGGCAAGCTCTCCAACCCAACCCTCAGCAAGTTCTTCTCCTCCAGGGTAATCTCCCACTTGATGACGGTGTGGTAGTCGTGGAGCCCGAGGCGGTCGACCTCCACGGGGGCGTTGAACCAGATGCTCCGCTTGTCCTTCCCGCAGCGTCGCCAGGATCTGGTCGCACCGCTTCCGCATCGCCGGAAAAGGATGTTTATCTCCCAACCCAGCGGCGAGGTTCGGCTTCCCCGTGGCGAGATCCGCCGTTGAACCAGATGCCCCGCCCACTTGCCGTTCCGCAGCTTCGGCGGGATCCCGGCCGCTCCGCTTCCGCCTCGCCGGCTTGAGTTCCGGCGGCGGCGGGGGAGGTGAGGCGACCCATGGGTAGCGCTTCGGCTTGAC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.578762
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0281400.1 4 31609566 G C
Osa04LNT0281400.1 4 31609584 T C
Osa04LNT0281400.1 4 31609967 C T
Osa04LNT0281400.1 4 31609972 C T
Osa04LNT0281400.1 4 31609980 A G
Osa04LNT0281400.1 4 31610029 T C
Osa04LNT0281400.1 4 31610032 C A
Osa04LNT0281400.1 4 31610159 A G
Osa04LNT0281400.1 4 31610171 G A
Osa04LNT0281400.1 4 31610184 C T
Osa04LNT0281400.1 4 31610287 A G
Osa04LNT0281400.1 4 31610320 C T
Osa04LNT0281400.1 4 31610394 A T
Osa04LNT0281400.1 4 31610590 C G
Osa04LNT0281400.1 4 31610592 C T
Osa04LNT0281400.1 4 31610635 T C
Osa04LNT0281400.1 4 31610123 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
Osa04LNT0281400.1 osa-miR5536 Translation 4.5 12.191 1 22
Osa04LNT0281400.1 osa-miR531c Cleavage 4.0 22.707 1 24
Osa04LNT0281400.1 osa-miR399h Translation 5.0 21.903 1 21
Osa04LNT0281400.1 osa-miR399k Translation 5.0 21.903 1 21
Osa04LNT0281400.1 osa-miR531a Cleavage 4.0 22.707 1 24
Osa04LNT0281400.1 osa-miR1429-5p Cleavage 5.0 19.11 1 21
Osa04LNT0281400.1 osa-miR531b Cleavage 4.0 22.707 1 20
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0281400.1 4 nan Morphological trait Panicle/flower RM303 RM348
Osa04LNT0281400.1 4 qSN-4b Resistance or Tolerance Drought tolerance RM255 RM349
Osa04LNT0281400.1 4 Xa2 Resistance or Tolerance Bacterial blight resistance RM317 RM349
Osa04LNT0281400.1 4 rfw4a Resistance or Tolerance Drought tolerance RM349 RM1136
Osa04LNT0281400.1 4 Gm7 Resistance or Tolerance Insect resistance nan nan
Osa04LNT0281400.1 4 nan Morphological trait Root RM3276 RM3335
Osa04LNT0281400.1 4 nan Physiological trait Source activity RG143 RG329
Osa04LNT0281400.1 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0281400.1 4 OsAOX1a Resistance or Tolerance Cold tolerance R2737 R740
Osa04LNT0281400.1 4 pss4.1 Physiological trait Source activity RZ740 RZ590
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