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

>Osa04LNT0279900.2

GAAATGTCTAATCCGGTATTAGGTTTCTAATTTTGGAACAAAGAGAGTAATAAACAAAACGTGAAGAGATGAAGCTATTCTGGCCATCTGGGTCAAGAGCCAAGAGATGAGTTTCACTATCGATCGGAGTCAGCGTAGCAGCGGGAAATACCACTGCTGGCAGTGCATTTCAGCATCTCTCCAAAAGACCAGGGACAGGGAAACAGCATTAGACGCAGGTTTATATATTACATGGCCAAAATTCTACGCGGCGAGGCAGATCAATCGCTTGTAGACACCACTTCCTCCTCCTCAACCTCATAATCTTCGTCATCGTCGTCGTCATCGTCGTCGTGGTGTCTCGCAGATTGACGCCTTTCAACATGCTGTTTGTCTGATTCGTCCTGATGTTTTGACTGGTCCTGTTGAACATCTCCTCCAGCTGCCGAAGACCCAGGGGCATGCTCATGATCAACACCTAACAATGGCGCACCACGCACACTTTGCTCCAGGGATTTAAACTTCTCCTCCCAGGATTGATTTAAACCTTGCAGAGCATGATTGATCATCTGTTGGACCTCCTCCTGCGAGAACTTCTGCTGACCCCTTTTACCAGGGATGGACTTTGCTATCTCCGCGATTTTGGCCTTGTCGATGGTGCCAGTGAGTCCATAGTACCTCCCACGGTTCCGGCCCCCCACCTGCTGTATCCATGCAGCATCGGGATCTGCAGGTTTATCACCAGCCTCCTCCATTCGCTTCTTGAAACCCTCCACAATCCGTTTCGCTTTCTCACTGACAAATTCTCCTGTGCCACCATTAAACTTATGGGTCTTGTTGAATATCTCAAGTTCTGACACTGGCTTCCCACCATTCTCTATGACCATAAGCTGCCGTTGCATGGCAAAGCTCCGAGAACCTGATGTGTGATGAGCACGACCTCCAACAAACCGATTCTTCCTATACTTCAGAGACATCTGCAAGACTTCTTCTTTGGCCCAATATTCACACAATCTCTCCCACCAATTCGGATGCATCCATGCAGGGGGGAAGGGTTTCCACAGTAAAGGGTCCTCGTCCTCATTTACCTTTTCTGTCTGATTGTCCTTTGGCTCTTCTGTAGCATCTTCCTCCTCTGACTCTGCATGACTATTGGAGCTACGAGAACCTGAAGCTTTTTTGGCTTTTTGTACTGCAGCCAATTCTGCTCTAACCCTTCGCTTCTCTTCGCACAGGAGGCCAGTAAACTGTTTTACTGCTCTGCGCTGAAATATCTTCAGGCACTCGGCCTCACGGCCAGGGGCCCACTTGTACCTTTGAAGAAATTCATTCAAAATAGCAGCCCTCGTCTCTGCAGGATAATGTTTCCAGCGGTAAACCAATTCCTCATTAGCTGGAACATCACCATGCTCACCAACCGGCAAATAGGTTGATCCAGGGTACTTCTGCTTCAAAAGAGCAGTGATGGTAGAGGACACCTTGGGACAAAGTGGGTTGACATCCCAGTTATCGATATTATTTGGTGTCAAGACAGGCCTGTCATATTCCCTGCGTGGTTCAATCAGTCCTCTAGGACGGCGTCCCCTGCCCCTACCTGATGATTTACGACTATATTTTCTTAATACGGGATGATAGCTATATGCGTCCTGCTGTTGCGCATGCGTAACCTGCTCTGGTGACTGTGGCTGCACCTGCTCACCACTTTTATCAAGCTGGTGTGTACCCCTGACCTCTGGAGGGCACAGTTGATTGTAGCGGTGCGGGGATTGCTCGGCTTGAGGCATCTCACGATTTGAAGATGCTGGTAAAACAGATGCATCAGCATTGCCTGACTCACTTGAGCATGCTTGAGGCATTTGGCACTGAGGTGATGGACTGGGACACAAATTGGCAATGAGTCGGTCAATGTCTGGAGGATCAGAATTATATTGGTTTGGAGAAGCAGCTGGCTGCTGGACTGGATCATCATTTATTGGTTGTTCTGGTTGTTTCGTCAAGCGCTTGCTACGCCTAAGATAGAGTCCTTCATTTGGAGAACTCGGAAAGCCCTTATTTTTCCTCTTATTCTCACCAGCATTCTTGCTGCTCCTTTTTCTCTTCGGGCATCCAATCGTCTTACCAGCTTGTGCTTTTTTCAGTTCACTAGCTTGATTGAGGGGCTCTGCTTTTTCCCGCTCCATAGTACTTGAGACATTTTTTGCCCGCTGTTCACGACTTGAAATGTCAACAAGAGGTTGCTGCCCTTGTGCGTGGTCCCCACGAACTGAATTACTCGGAGGGCAAGCTTGTGCCTGTGGTGTGCTTTCCTGAATAGGACGCTCTGGTTGTAGTTTTTCAATATATATAGATTCAACACCTGCCTGCAATCTAGCCTTCCTTGAACTAGACCTTGCAGTGGTTTTATCAAGTGTCTCATTGCATGATTCCCCCCTATGAATTGAATGGTTAACAGGCTCCTTTCGTGCCAATGTGTGTTGGACTGCTGCTGGGGAGTCGTTTCTGAAAGAACTGAATGTCTCCTCTCTTGGAACTGAACGAATGGAGCATTGTGCTGGTATCTGCTCTGAACGAATTGGATGGTGTCTTTCTATTTGTGACTGCTCCGGCCGATGGCGCAGGGAAGACGCCGTGAGCGTGACGCCAGCTGGGGGCGGCGCCACGACGGAGACCGTGGGGGCGGCAGGGGAAGCGAAGTAGAGGCGGAGGCGCCCGCCGTCGACGACGAGCTCGGCGGCGCAGACCGGGCAGGCGAAGCGCACGAGCCCCGCCGGCACACTCAGCAGAGCGCAGCAGCCACCGCACGGCATGCGCGCGGGCGCGGGAACCTGCACGGGGACCGGCACGGGAGCGTGCAACACCGCGGCGGGAGGAGGCCCCCGTCCGGGGATGGGCAGAGCCCGCCGCGGGCGCGGCGGCGGCGGAGGCATGAGCTCGGGCGGGAGCGCCTGGTGGGTCCCGCAGTCCGGGCAGGCGAACTCGGTGAGGCCCGGCTCCACCTCCAGCGTCTCCCCGCACCCCGCGCACCGCACCTCCACGAACTCCGGCTGGCCCCCCGCCGCCTCCGCCATGGCTTCGGGGAGCAGCGGCTAGGGTTTCCTTCGGTGCGCCCTCGGGGAACAGAGTAGTAGTTGGAGTGAGGTGTGAGTGCGAGATACTAC

Coding Potentia
Explanation CPC Score
noncoding -1.06396
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0279900.2 4 30925170 T G
Osa04LNT0279900.2 4 30920978 G A
Osa04LNT0279900.2 4 30921380 A G
Osa04LNT0279900.2 4 30922993 T C
Osa04LNT0279900.2 4 30923494 A G
Osa04LNT0279900.2 4 30923698 A G
Osa04LNT0279900.2 4 30924508 T A
Osa04LNT0279900.2 4 30924772 A T
Osa04LNT0279900.2 4 30924934 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
Osa04LNT0279900.2 osa-miR5534a Cleavage 4.5 15.804 1 21
Osa04LNT0279900.2 osa-miR7694-5p Cleavage 2.0 9.647 1 24
Osa04LNT0279900.2 osa-miR396c-3p Cleavage 4.5 21.278 1 21
Osa04LNT0279900.2 osa-miR169i-5p.2 Translation 4.0 19.209 1 22
Osa04LNT0279900.2 osa-miR1428a-3p Translation 4.5 15.14 1 21
Osa04LNT0279900.2 osa-miR5072 Cleavage 4.0 23.317 1 22
Osa04LNT0279900.2 osa-miR5507 Cleavage 5.0 20.702 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0279900.2 4 Xa2 Resistance or Tolerance Bacterial blight resistance RM317 RM349
Osa04LNT0279900.2 4 pss4.1 Physiological trait Source activity RZ740 RZ590
Osa04LNT0279900.2 4 rfw4a Resistance or Tolerance Drought tolerance RM349 RM1136
Osa04LNT0279900.2 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0279900.2 4 OsAOX1a Resistance or Tolerance Cold tolerance R2737 R740
Osa04LNT0279900.2 4 nan Morphological trait Root RZ23 RM255
Osa04LNT0279900.2 4 nan Morphological trait Panicle/flower RM303 RM255
Osa04LNT0279900.2 4 nan Morphological trait Panicle/flower RM303 RM348
Osa04LNT0279900.2 4 qPN-4b Resistance or Tolerance Drought tolerance RM317 RM255
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