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

>Osa12LNT0139000.2

GTACTAGAGGTAAACGCACGAGCCAAGCATGCAAATATAAGATGCATATGTATACGCTAGAACAGAATGAAATGAGCAAATGCATTGCAAATATTAGTATTAAATATAAGAGGAGTATTTCCATTGGCTGGTCCAACAATTACTTGGGTTGCGACGTTGATCATCGATCAGCAGCGCTGGAGGGCTGACGGAAGGTGAGCATGCTGGGAGAATCGACTCTGACAATCACCTCTTCCCCGGCCGACTCATCGCTCGAGTTGTCCTCGTCCTCTTCTATTGCCTTGCGTTGTCGCCGCCGCCGCCGTCCTGCCTCCTCCGGCTCCGGCGGCAGAGAAGCACCAGCAGCAGCAGCCTGCCTTGCCGTCGTCATGTTGGCACCCTCGGACTGCACAGACAGCAGGGGCCTCTGCGTGTTGGACGACCTCGAAGGCACTCTTGGGTACGACGAGCTGTGCGCTTTATTAGAGCTTGCTTTCGTGTGACGATGCCTCTGCCTCCTCTGACCCTGACCCTGACCGGACTTCATGTCATTGATCATGCTCCCGTACATGCTCAGCTGCAATGCTCTTGCAGAGAAGCTTGCTGGATGGTCTCTGATTTCAGTTAAGCTGGCACCATTCTGAGCTCCCCTGGATTTTCTGAAGCTTTCCGGCCAGCTGAGCAAACCGCTGTGCTCCTTGCTTTGTGTCCGAGGCAGTTCAAGGGTTTGAGATATCAATGACGCACTCCTTTGCAGATCCGCCTCTATTTCGGGCCTCCCTATCTCAACGAACAAAATCCTTGCTCTAGCCTCCACCTGATAGCTGGGTGCTGTATAACAGTAGTCAATGCGGTTTATAGCTGATGACTCGAGACCAAATAAGTTCAAGTCGGCATTTGGTGGTAGCAGTAACCCTGGAGGTGTGATCAAAGTTTGGTTCTTGGTCTTCAAAAATCCTTCCAGTAAGATGCCAATGAAATTCTGCTCAAGTTCAATTTCTTCGCCCTTAATGTAGATGTTCATAGTAGATCTTTCAGTGATGAGAACCCTGAGCTCATGTGTTGCCATTTTCTCAAACATCATAGGGAGCAAAAGCCTGGCAACGACTAGAGCACTTTCCTGCCACAGAAAAATCTCAATAGAAGGATCTGATTGACGCAATTGCTCTATCTTTTCAGCTTCAATGAAGAAGCAGTGCACCACAGAATCTGTAATCATGTCACAGATATAAGGTTTTCCAATCAGCACCTCATACAGGCCCAAAGTGCTGCCATGTGATAAAATTGGATCCAATGAATGCCTGCTGCTTAATCTCTGACTTGTCCACTTTACTACTCCAATCGAAACAAGCCATATACCAGTTGGCCTTGAGCCCTCTCTATAAAGGATTGTGCCATGTCCTTTTACTGTTTCTTTTGTGCTACTTAATAAAGGATCACGCATCGCAGCAGGCAGTGCACCAACTAACGGATGAGTGTTCAAAAGATCACTGACTCTTGGCATTTTTACCAATGGTGGATTCCTCTTGAACTTCTTCAAGTCTGTCTGCAAAGCATCATCTAGATGGGCCATTTCCTTTTCTTCCAGCAACCCAGTCTTCTGGAGATTTTGAATATACTCACTCAAGTGGGTCAATACCGAATATGTTACTTGTCGAGTCTTCAGCACACGAAGCACCTGAGGGAATGTAACACGAACATCTTCCAAGAATTTTCTAGCCTCCTCTCCCTCAGCATTACTTTCATCAATAACAATTCTGGCAACCTCACTATCACCAAGAAAGTCATGTAGCTGCCGTCTTGCGATTCTATGAGCACGGAGAAATGCAGCACAGATGTAACATCCTGACTCCAGTCTTTCTACTGTGAAGTAAGTGATAAGCCTTCGTGGCAACCTGCTCATTTGAAGGAACCTATAGTAATTTGGAAAATGGACATTGGACCGCAAACCCTTCCAGTCACATAATTCTTGGGTAGGAACAAGATCCATAGCTTCATCAACCGATCTCATTAAAATATTTGCAGTGGTTTGAGTTATTCGTCCTTCTTCAAGCATTCCCCAGTAAGCAGCTTGGACACCATTTAGAAGCCGCACACGGATGTCCCTTAAGTTCATGGTATGCATGCGATCATTTCTGTCAGAAACAGCATGAGGATGCACAGGCTCATCGTCCAAGTCGTTCAAGCATGTGATATATTTCTTTACAGTAACCCAATCAGCAGGAGGACCAAGTTCCTCATCATCCCTAAGATCACCAAAAGCCTCCAATGCCTTGTTTAGCATTTCATATTTTGTATAATTCAATATGCGAAGCTTTGTTGCTGCTAATCTGTCCATTCCAAGTAGATGCAACAAAAATTGTGTAGTAGAACCATTAAAAATCAATGTCAAAAACACGATGCCACCAGTGAAGAACACAAACATTGTTCCGTCAACTGGTTTCAGATGGGTCTGAACTGCATCACTAGCACGCTTAACAGATAATGATAGAGACAGAGCAACAGCCCCTCGCAGTCCCGCCCAAACAAGAATTGTGGCTTCTTTCAAGTCCAAACCATACCCAAAGTGGCGCAACAATGGATACAAAATAACAACAACTAATATCCGAGAAATTTGCACAAATACATAGAGCAGAAGAAGGAAGCCCCATGAAGCACCTGAAACAGTAATTAAAAAAATGCAAGCATAAATAAGAAATTCAGAAACAATGTTCTATTCCAGAATGTCCATGTCAGCAATTGCAAGGTATCTTTCAAGTCTGCGGTCTCTCCCTCCTCTAAAAGGAAGCAGCGCATTCTAGCCATTCTCCTGGTTATCCGTGCCTCTCGAAATGGACATTATTTTCTAGTACTCCATCTGCAATAACAACCCCACTCAGTATAAATATAAGTGTGTTTGCTATATAAGCAACCATTTCCCAGAAATGATGCAAGCTTTGCTGACTGTCACCCTTAAAAGCAGTTTTTGCAAAAGCGGCATAGAACATTCCCAGTGTCATGACGGTCAAAACACCAGAGACCTCCAGTGCATCTTGTGCCTGATATAACCACATTAGTAAATGAGAAGACTCCAAGAAAATAGAGGGAAATAAACACTTATTATTAATTGGCATAATTTTATCCAAAACACAGACGAATTCCTATTGCAGAAGGTATCAGAAAAACCAGTCCATGATGGATACTTGCACAGGTGATCAAACAAGCTAACAATAATCAGGGGTACTGATATGTTAATGTTATATGTGCAAATGCTCACAGAAAAATATACATGCAGTCAGTAGTTGCAAAAATATGGGAAGAAGACAAATGATTGGGCTAGTAAAAATGATGACTGATCCATTTATAGGCACATTATAATGTACAGACATGTACCCTTACATTTCTTAGCATATGCTCATTTTACAACCTATGTTCAAATAATTTCTTCACAGATCCATTCACCTATCCAAAGTTTCACCCATCATAGCCCAAATTATTAGAACTATAAATCAGAGATGCCATCAGTAGTAACCCTCAATAATAATAATATTTGAACAAATCATTTGACGCTCTGTAATTGCATATGCACATTTCAAGAAACCATGAATCCCTGACCGATTATGCATCTTTAAATATATCATAGATATTCAAGCTATATGTGCATGTAGCAACTACCACTGCTTAGCAGTAAAATGACATCTCTAGCAAAATTGCAAAACAAAAAAAAAGGCCATCATGAATTGTAATTATAGGATGAACCACAACTTATTCTGTTTGCTGCAACGTAGCTCAAGTAACTTAACCAGAAATGCCCTTCTGAAGAAAAGAACAGGTGGAGAAGGTTGGATGTATTATTTATCTTACAGTGAAGAAAGCAATGTAGCTGACAGCAAGAGTAAGCGCGATCTCTATGATTGTATCATTAAAAATAAAGCCCAGCCACAGTACTGATGCAATTCCAAAAGCAAGGCCCAGAGCAACAGCTCCAAGTGAAACTTCTGACAAGAATTTTATTATTGATCCTGCATCGAAAGTTCTTCCAAGCACCATCCTATAGAATAACTGATACACAACAATAGCAGTCCCATCATTCATTAAGGATTCTCCCTCAATTATGGTACTAAGCTTTTTACTTGCGCCAAGTTCTTTTAGCAGTGCAACAACAGCAACGGGGTCAGTTGCACTAAGCAATCCACCAAGCAACAATGATGTTTTCCAGTTCCAGTTGTATGGAAAAGTGAGCTTTAGAGCAGAGCCTAGGAAAAAGGTTGATATTAGCACACCAGGTCCAGCAAGTAACACCATTTGTGCCATACATTTCTTGATTTGGTGTATTTCCATGGAAAAGGAACTTTCAAAAAGAAGAGCGGGTAGAAAAACAGCCAGAAGAAGATCAGGATTAATGTTAGCCCAGATACGAATGCCGGCTCCGAGTTTGCCCATGCCATGTTTTGTGCCAAATTCGAGCGATCCGAGGGCGACGCCGAGGACGAGGAGGGCGACGGTGTAGGGGACGCGGGTGCCCCGGAGGAGGTGGCGGGAGGCGATGCCGAGGACGAGGGAGACCCCGACGAAGAGCACCGCGTCATCAGGCTCCGCCTCGGGATTGTCCATGGATTACTGATGAGGAGGAGGAAGTGCAAGTGCAAGTGGAAAATCCAAGGCAAAGGGAGGAAGAAGAAGAAGATGCAGCAGCCTCCTCACTTGAGCTCCCTTTCCTTTTGTTTTGACTTGTTGTTTTGTCACCCCTTTTTCTCTTTT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.631119
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa12LNT0139000.2 12 27497172 C T
Osa12LNT0139000.2 12 27497344 T A
Osa12LNT0139000.2 12 27497741 T C
Osa12LNT0139000.2 12 27498547 C T
Osa12LNT0139000.2 12 27499135 T C
Osa12LNT0139000.2 12 27500328 A C
Osa12LNT0139000.2 12 27500361 A G
Osa12LNT0139000.2 12 27501093 T C
Osa12LNT0139000.2 12 27502348 C T
Osa12LNT0139000.2 12 27502371 T C
Osa12LNT0139000.2 12 27503721 A C
Osa12LNT0139000.2 12 27506048 T A
Osa12LNT0139000.2 12 27506874 T C
Osa12LNT0139000.2 12 27507230 T A
Osa12LNT0139000.2 12 27507949 A G
Osa12LNT0139000.2 12 27504825 T C
Osa12LNT0139000.2 12 27505802 G A
Osa12LNT0139000.2 12 27504424 T A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa12LNT0139000.2 osa-miR812s Translation 4.5 17.827 1 24
Osa12LNT0139000.2 osa-miR5799 Translation 4.0 17.827 1 24
Osa12LNT0139000.2 osa-miR5512b Translation 4.0 10.176 1 21
Osa12LNT0139000.2 osa-miR395f Cleavage 4.5 15.508 1 21
Osa12LNT0139000.2 osa-miR156l-5p Cleavage 5.0 16.338 1 21
Osa12LNT0139000.2 osa-miR530-5p Cleavage 3.5 17.749 1 20
Osa12LNT0139000.2 osa-miR814a Cleavage 4.5 17.251 1 22
Osa12LNT0139000.2 osa-miR814b Cleavage 4.5 17.251 1 22
Osa12LNT0139000.2 osa-miR814c Cleavage 4.5 17.251 1 22
Osa12LNT0139000.2 osa-miR529b Translation 4.0 21.371 1 21
Osa12LNT0139000.2 osa-miR169r-5p Cleavage 5.0 15.937 1 21
Osa12LNT0139000.2 osa-miR1881 Cleavage 3.5 15.878 1 24
Osa12LNT0139000.2 osa-miR1882a Cleavage 4.0 21.254 1 24
Osa12LNT0139000.2 osa-miR1882b Cleavage 4.0 21.254 1 24
Osa12LNT0139000.2 osa-miR1882c Cleavage 4.0 21.254 1 24
Osa12LNT0139000.2 osa-miR1882d Cleavage 4.0 21.254 1 24
Osa12LNT0139000.2 osa-miR1882e-5p Cleavage 4.0 21.254 1 24
Osa12LNT0139000.2 osa-miR1882f Cleavage 4.0 21.254 1 24
Osa12LNT0139000.2 osa-miR1882g Cleavage 4.0 21.254 1 24
Osa12LNT0139000.2 osa-miR1882h Cleavage 4.0 21.254 1 24
Osa12LNT0139000.2 osa-miR2097-5p Translation 5.0 21.121 1 22
Osa12LNT0139000.2 osa-miR2105 Cleavage 5.0 16.343 1 20
Osa12LNT0139000.2 osa-miR2863b Cleavage 5.0 15.392 1 21
Osa12LNT0139000.2 osa-miR5144-5p Cleavage 5.0 15.687 1 21
Osa12LNT0139000.2 osa-miR5160 Cleavage 4.5 17.115 1 22
Osa12LNT0139000.2 osa-miR5509 Translation 5.0 16.1 1 21
Osa12LNT0139000.2 osa-miR5512a Translation 4.0 10.176 1 21
Osa12LNT0139000.2 osa-miR5512a Cleavage 5.0 8.095 1 21
Osa12LNT0139000.2 osa-miR5518 Cleavage 5.0 10.188 1 21
Osa12LNT0139000.2 osa-miR5512b Cleavage 5.0 8.095 1 21
Osa12LNT0139000.2 osa-miR162a Cleavage 4.5 16.843 1 21
Osa12LNT0139000.2 osa-miR162b Cleavage 3.5 16.843 1 21
Osa12LNT0139000.2 osa-miR2101-5p Translation 5.0 12.721 1 22
Osa12LNT0139000.2 osa-miR5494 Translation 4.5 17.0 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa12LNT0139000.2 12 qLEI 4 Resistance or Tolerance Submergency tolerance RM5479 C901
Osa12LNT0139000.2 12 qDRS12-1 Resistance or Tolerance Drought tolerance RG181 RG958
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