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

>Osa04LNT0264400.1

GAGGATTAGAAAATTCTAGCAAAAATATGTGATTGATAATAAATAAAGCCCGAATGCATTGAAAAAAAAAATCAAACACAAGCAAACTAAACAAAAGCGAAGACAGTAAAATGCTTGCTTATGATAGTAGTTTTTGTTGAGTCACCATGAAATACACATGAGGAATCAATCCATTAATCCAAAGCTGACCAAGTGACCTTCACCGAGATTGAGGCGAACCCGATCTTTATTTCTTCACTAGCACATCCATGATTGGTCGCTTTGAAAGATAGACAATGTTCAGCGAAATAGACAGAACCTACCTTAAACTTCAAATCCATACACTTATTCTTCATGACAGCAACCACATGCGGACATGCCTCCTCAAGCCACGCGACTCACCAATCACACCATCAAAGAGCTGGATTTCCTCATGTAACCCACTGGTAAAACAGCCGACACACAAATTGAAACCGGTTTGCACTTCTGATATGACAACATCTACTGTCGCTTCAAATGCGTAGTCAAGACACGCTCGAGTTATGTCTACCGCGCCGTAATCTCCATGAATGCGATTTATCACTGGATTGCTTGATGTCAGTATTTCGTTAACACATGATACACCATCAATCAGCTGTAGATCATTCTCATCTCGTTCTCCTGTCTTGATCCTCATGTCATATTCAACTAGAACAGCACGAGACAAATCGATCCCTCTCTTAGGGCCAATTTCGATGATGGAACCCTGCTCCACAATTATGGGATTATCTCTGCCAATATTGACAATATAATTAAGTAATGGGTCCCGAAGATCCCGTGCCGCAATGTATCCATACAACTCCATTGAGCCATCAACCCCAAAAACTTTAGCCAACTTTATTGAGAAAATTTGCAACATGGAATGTTGAGTATGCCTCGTGCAAGTTCCATCACTCAGGCTGCAATCTTTGTTGGAATTTGATAACATCATTGCCTCCAATCGAGTCTCATTACGGTCCGCGATACGATAGTCCCATTTCCACCCAGATCCAAAGGTGGTGTCGTATATATAACCATCACGGTGGCTGCTCCATTTAAATGTCGTTCAAGAGACAGGACCATAACAGCTGTAGTTATCTACGCGATCGTTGAACTCTTCATATTCATCATCATCATCATCATCATCATCATCATCATCGGCCTCGCTGGCACTTTGGTTCCTTGCATCTTCTTCACCATCTGTTAGCTCCTTAATTGCCCCCCTTGGATCTTGTTTGACACCTGGGACCTTCACGGTTGTCCTACAAAAAACTTCATCGCTATACTTGGCATTAACAATTTTGCGTCCATTCTCTTCAACATTGGCAGGACGGCCATCGCCATAATGAGCAATGAACTCAGTTGCAGCCCCATTCTCTTCATTGTCCATGCCTCGGGTGATGGGAAAGTGCTTGTCCATGGAATTTATAATACCGTTGGTTGTGTGGATAGGATCGTTGGGAGAAGGGGTGAGTTGGCGCTCGTCTGATTTACCCAATTGCTCACTTTTCACTGCATTGCCGCTGGCCATGTTCCGAGATCCACAGGGGAATCGGGAAACATGACGGACAGGAGGGTTAAGCGCCGCCCTGCTGATCGAAGCGGCTCGTCGCGCAAGCGTCGGTAGCCACCCGCGAGGCGGACCGGAAGCCATGGAGGAGACTAGAGAGGAGAGATCGCGGAGATGCGGCGCCATCCGGGCGGTAGAAGCCGCGGCGTTGGGGGCGTCGGAAGAGGCGGATCAATCGAGCGCGATGGGGTTCGCGTGCGTGCTCACACAGAGAGGAGCGCGCGGCGGCGGTGAATCCGGTGATGGCTGCTGGTGGGTATAGTGTTGCGCGCAGCCGCGCACTGGTCCGGTTCGTGGCTTGCTAACCCTAAGTGAATTCAACAAGAGGGAGGCAGCCCAAACCCAAGCCCACTC

Coding Potentia
Explanation CPC Score
noncoding -1.19141
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0264400.1 4 22563520 A G
Osa04LNT0264400.1 4 22564014 T A
Osa04LNT0264400.1 4 22564415 T C
Osa04LNT0264400.1 4 22565168 T C
Osa04LNT0264400.1 4 22565277 G A
Osa04LNT0264400.1 4 22565461 G A
Osa04LNT0264400.1 4 22565895 A G
Osa04LNT0264400.1 4 22566038 C G
Osa04LNT0264400.1 4 22566441 C G
Osa04LNT0264400.1 4 22566630 A G
Osa04LNT0264400.1 4 22566199 G A
Osa04LNT0264400.1 4 22566293 A 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
Osa04LNT0264400.1 osa-miR530-3p Cleavage 5.0 12.238 1 21
Osa04LNT0264400.1 osa-miR1850.1 Translation 5.0 19.668 1 21
Osa04LNT0264400.1 osa-miR1880 Cleavage 4.0 11.05 1 24
Osa04LNT0264400.1 osa-miR2118d Cleavage 5.0 24.375 1 22
Osa04LNT0264400.1 osa-miR2118o Cleavage 5.0 24.375 1 22
Osa04LNT0264400.1 osa-miR2118p Cleavage 4.5 24.375 1 22
Osa04LNT0264400.1 osa-miR2871a-3p Translation 4.5 16.891 1 21
Osa04LNT0264400.1 osa-miR2871b Translation 4.5 16.891 1 21
Osa04LNT0264400.1 osa-miR5489 Cleavage 5.0 20.603 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0264400.1 4 orl1 Morphological trait Culm/leaf S10628 C377
Osa04LNT0264400.1 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0264400.1 4 nan Resistance or Tolerance Other soil stress tolerance RM5586 RM3916
Osa04LNT0264400.1 4 nan Morphological trait Culm/leaf RM3337 RM3785
Osa04LNT0264400.1 4 gpp4 Morphological trait Seed RZ569 RZ565
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