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

>Osa01LNT0001200.2

TAAAATGAAAACTATGATCACATGCAGTAGTATCACAAAAGTTGCATGCCAACAACTACAAATGCTACAAAAGAATGGAAATTTACACATTTCTAATGTCTCAATAATACCTACAACTACTCAGCCAGGCCTTCAACGAAGATCGATGGCAACGCTGGATCGATAATCAGGTCCTTGCCTTCTGTTTATCTAGGTATAACATTAAGAATCCTTCCAGGCACATAAATTCTCTTCCTGATGCCCTTCCCAGTCAAATATTTGGAGAGTTTCTCGTCGGAGGCTGCTATTTGGAATGCATCATCCTCAGAGCACTCTTTGTCGACAAGAATTGTACCCCTGGTCTTCCCATTGATTTGCACTGGAAGCACGAGCTTTGATTCTTTCAAGTACTCACTTTTTCCCTCTGGAAATTGCTCGTGGGCCAATGATCTTGAGTTCCCAAGGCGAAACCAAAGCTCCTCAGCCATGTGTGGTGCAAAAGGCGAAAGCAACAGAATAAAGGATTCAATAACTGACTTTGGTTGGGTGTCCCACTTGTATGCAGCATTCACAAATTCCATCATTGCAGAAATTGCAGTGTTAAATCTTGTTTCTTGAATTTCCTCTGTGACTCTTGCAATGCATTTGTGAAGAACTCGGAGCTGATCCAAGGTTGGTTCCTCATCAGTAACCGTAGTTCCAACTCCATATGATCCATCTGGTAATGGTGTACCAACTACGAGTCTCCATGTCCTTCCTAGAAATCTATGCACACCTTCAATTCCACCAGTGCTCCATGTTTTTGAATCTCTCAGTGGTCCCATGAACATTTCATATAAGCGGAGAGAATCAGCACCATATTCTGAAACCACGTCATCTGGGTTGATGACATTTCCTCGACTTTTACTCATTTTATAAGCACGAGCGTTTAGACGTATGTTTGCATCATCCTTCAGTACATAATGATCTCCAACTTTTGTGACCTTATCTGCAGGTACTTTTTCTTGGTAGCAATCAATCAAACTTGAGTTGGAATCTGCAGAAACCCATCTCCCTTTATTGTCTCTATATGCAGTATATTCAACTTCTCCTAGAATCAATCCTTGATTTATCAGGCACTTGAAGGGCTCTTTAGTGGAAACTACGCCAATATCATAAAGAACCTTATGCCAAAATCTTGCATAAAGCAAATGCAAGACAGAATGTTCAGCACCACCAACATAGATGTCAACTGGGCCCCAATAACTCTCTTTTGCCTTGTCAACCAACATACTGGCATTTTGAGGATCCATAAATCTCAAATAATACCAGCATGATCCAGCCCATTGTGGCATGGTGCTTGTTTCCCTTCTAGCAGGCTTCCCAGACAAAGGTTCTACGGTTTTAACCCAATCTGTTGCCTTGGTCAGAGGAGGCTCTCCAGTACCAGTTGGAGTGAAATCATCCAATTCAGGAAGAGTTAAAGGCAACTGGTTTTCTTGAAGGGGCAGCATTTCATTGGTATCATCACGGTAAATCACAGGGAAAGGTTCACCCCAATAACGCTGTCTAGCAAAGAGCCAATCTCGAAGCTTGTAGTTCACCTTTTTCTTTCCAAAGCCATTAGCCTCTACCCATTCAGTAACTTTCAAAGCAGCATCCTTGGAAAGCATACCATCAATATTTAATCCAGATGAAGAACTGGATGAGTTTATCATGATACCATCATCTGCATATGCCTCCTCAGAGTCACAATTGCCATTGAGTGGACTTACAACCTTAATGATTGGAAGTTTATATTTCAAGGCAAATTCATGGTCACGTGAGTCATGTGCAGGCACAGCCATGATAGCCCCAGTGCCATAGCTTCCTAAAACATAATCTGCCACCCATATTGGAACTATCTCCCCAGTTGCTGGGTTCTTAGCATAAGAACCACTAAAAACTCCAGTTTTTTCCTTCTGAAGATCAGTTCTTTCCAGTTCACTCTTTCTTGCTGTGAGTTCTATGTATTCCTCTACATGTACACGTTGTTCCTCAGAAATTAGAGATGACAATAGAGAATGCTCGGGTGCCAGAACAACATATGTTGCACCAAAAATTGTGTCAGGTCTTGTTGTGTAAACTAACAAATTAGCACCTAGATCGTGCCCTTCCTTGTCCACAGCTGAGAATTCAAGCTCAGCGCCTTCTGATCTCCCTATCCAGTTTCTTTGCATTTCTTTGATGCTCTCAGGCCAATCAAGTTCATCCAAATCTTCAAGAAGTCGATCAGCATAAGATGTAATCCTCAGCATCCACTGGCGCATTGGCTTTCGTATAACAGGATGACCACCACGTTCACTGACACCATCTATTACTTCTTCATTCGCCAGAACAGTTCCAAGAGCAGGGCACCAATTAACCGGTACCTCAGCCTGATAGGCCAGTCCTCTTTTCAGTAGTTGAAGGAAAATCCATTGTGTCCATTTGTAGTAAGTCGGTTCCGTTGTGGAAATTTCACGATCCCAGTCATATGAAAAACCTAACGATTTGAGCTGTGAGCGGAATCGATTGATGTTCCGTTCAGTGGTAATCTTAGGGTGGGTTCCCGTCTCGATAGCATACTGCTCCGCAGGAAGACCAAATGCATCCCATCCCATCGGATGCAACACATTGAAGCCTTGCATGCGCTTGAACCTCGACAGGATGTCAGTTGCCGTGTACCCAAGGGGATGCCCAACATGCAGCCCAGCTCCACTGGGGTAGGGGAACATGTCGAGGATGTAGCACTTGGGCTTGGAGGTGTCGAGGCCGTGGCCGATGTCCGGGGTGCGGAACGTGCGGTGCTCCTCCCAGTGCCTCTGCCACCTCGGCTCGATCTCGTCGTACGGGTACGCCCTCCTCGCCTGCGCCTGCGCCTTCCCGGCGTCGGCGTTCGCGCAGCAGCGGCACCACCCACCACCTCGCCGCGGATTCGGCGGCGGGAACCCGCTTTGCAGGCGGCGGCGGTGGCGGGCAGCAACAACGGCCGGGGGCCGCGGCTGCAGCCGGAGCTGGAGCGGCGTCTGCATCATCGCTACCGCCATCGGGGTTGGGAGCGGAGGAGGGAGAGGAGTCGTGATGGGGAGGTTGGGGCGTAGCCAAATATAAGCGGGAGGTGGAAGAAGAAGACGAG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.878379
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0001200.2 1 1146628 T C
Osa01LNT0001200.2 1 1147643 T A
Osa01LNT0001200.2 1 1147730 A G
Osa01LNT0001200.2 1 1148238 T C
Osa01LNT0001200.2 1 1149548 A C
Osa01LNT0001200.2 1 1150869 T C
Osa01LNT0001200.2 1 1151085 C T
Osa01LNT0001200.2 1 1152337 T A
Osa01LNT0001200.2 1 1154330 A G
Osa01LNT0001200.2 1 1147741 C G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa01LNT0001200.2 DTM_#DNAt_MULE_japo_Os0103 Chr1 - 1149947 1150101 154
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa01LNT0001200.2 osa-miR5798 Cleavage 5.0 13.905 1 21
Osa01LNT0001200.2 osa-miR5815 Translation 4.5 15.547 1 24
Osa01LNT0001200.2 osa-miR399d Cleavage 4.5 21.2 1 21
Osa01LNT0001200.2 osa-miR399i Cleavage 4.0 21.2 1 21
Osa01LNT0001200.2 osa-miR399j Cleavage 4.5 21.2 1 21
Osa01LNT0001200.2 osa-miR399k Cleavage 5.0 21.2 1 21
Osa01LNT0001200.2 osa-miR160f-3p Cleavage 4.5 20.23 1 21
Osa01LNT0001200.2 osa-miR164d Cleavage 5.0 16.276 1 21
Osa01LNT0001200.2 osa-miR2093-5p Translation 5.0 19.562 1 20
Osa01LNT0001200.2 osa-miR3981-3p Translation 5.0 16.189 1 21
Osa01LNT0001200.2 osa-miR5144-5p Cleavage 5.0 16.046 1 21
Osa01LNT0001200.2 osa-miR5147 Cleavage 4.0 17.951 1 21
Osa01LNT0001200.2 osa-miR5152-5p Translation 4.0 19.135 1 21
Osa01LNT0001200.2 osa-miR5491 Cleavage 4.0 14.114 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0001200.2 1 yd1a Morphological trait Seed R753 C161
Osa01LNT0001200.2 1 nan Physiological trait Eating quality C161 R753
Osa01LNT0001200.2 1 nan Physiological trait Eating quality C161 R753
Osa01LNT0001200.2 1 nan Physiological trait Source activity RG532 RG472
Osa01LNT0001200.2 1 n+p1a Resistance or Tolerance Other soil stress tolerance C161 R753
Osa01LNT0001200.2 1 n+s1a Resistance or Tolerance Other soil stress tolerance C161 R753
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