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

>Osa03LNT0208500.4

ACAAACGAAAGCACATCAATTATAAAGCAGCCATGAATAGTACAATAGGAATATGTAAAAAAATGGAATTTTAGCTCACAGGGCAGCAAGCTCACACTCTACATCTGAAGCTTTATGGGATCAAGGAAATAATATTTCATTATATTTAACCTTTTCATTTTGTTGAAGAGCATGGCCATCCACAAGCAATAATCCATGAAGAGACCTTGGTTGCCTGTAAGTGAGAAGCTATAATGACACAGAGACAGGCCAACTGGCCAAGCGAGGTCCTCTAAAGTTCTTCAGGTTCCACTTCTTCTTTTTTTAACGCAATAGAGTGCACATGAAACAAAAGCATTAGGACGATAATCTCTTCATTGAAGGTATTGTAATTAGTTATGAAACACTACATTACTTCCAAAGTCATTAAGAAAAAGATAGCTTCAACAAAATGTCATACTAAACAAATTAGTTCAATGTTTATCCTATAAAACGTAATCTGGTAGTTTTTTTCTTCTGTCAAGCTAATAACACATTTTTTTTTACAAATAAATTCTATGCCTCAGCAATAATCACAACACATTGTGGCACAAATTTGGTTCTAGTGTGGGTAATACTCATGGATTTGACATAACATTTTACACAACATCACTAAAAGATTATATTGGCCAATGGAATCAAACTTGTTGCCTGCAATTTTCAGTAATGGAAATATACAATTCTGAGCAATGGAAAATCCAAGCAAATTTAACACCTTAATCACCAGTAATGGATACCCACCTCCGCAAGACCACCACAACATCTTCTATAACTTTGCATGATCAAACTGTGCAAACCAACATTAGGATGGTCTCAATTCATTCACAGGAACAGAGTATCGTGCCTTCCATTTCATCCATGTAAAAAAATCAATTGCACTCCTAGGACTGCTATGGGAATACGTGTACTACATTTTTCTCTATAAATGGTGCATCTTGTTCTAGAAATTGTTACACCATGTCCACTTTGTCAGCTGTGTGCTTCAAAATCTTAGGTGTCGACACTTTCAGATCATTTGAAGTGTACCTCTGGATTTGCCGAGTTCGTTTCCTGGTTAACAACAATAATTAGGTATGATATCCATGAGTGTTCCACTTTGTTGATCATACACTTAAACCCGATCTGCGGCAAATGAAAGCAGGCTCTACCTAACACTTGTCAGAGGATGCTTAAAATGTCACAGAAAGAGCAGTAATTAGTTTAGCATAAATGTGTAATCAACAATTAAGCAAAAAGAAGGCATAGAATTAATTTTGGTCATTCAAGAGAAAAATATTTATTGTAGAAAAACTGAATGAGGTAATTATGTTTCTGGTTTGTAACAATTTCCAAGAGCTTAGCACCTATCAATATCACTTAGCATGCAAAAACAACATCTGCCTGTGAGTATTAAGCCAACATAATAGCAATAAGCTTGCAACCTTTCTAAAATATGAACTAATACCAAAACGATACCAACATTATCACCAGCTTTTCAATCAGCAATTCAGCACCATAACACCAGGCCTAATCAAGCAATTCTCATGTGCATATTCAATTAATCTACAGATAAAAAACTACATATGTGAGAGGTACGGTTGTACACATAATTTATATATGTTTGCTCACATAAACAGAGTGTGTTGAGATGTTAGTAGTGGAGTAGAGTAGGGTAAAGCATTTTTTATAGAAAAATGATTTGCTCCGAAAAATAACGAAAGGAATGTGCTAAGTGGAAATTGTTTGACTCGCCCAAGAGCAGTCCTGTCCTTGACTGATAAAAGGGGACCAAACCCATACAACCATGGAAAAATGGGGGGGAAACAGAGATATGGGGAGGGACAATACATTTTTATTACTAACCATTTATGTTCTAATCAAGGAGCATGAGCAGTTTGGTGATCAGGAAGCTATGTTATTCCGAAAGATAAGAAAGGAAAATTAAGCCAAAATAATACCATTTCCACAAGATTGACTAAGATCAAATATTTATAAAGCTTACATTGCTAGACATGAATCAGGCTGGAAAAAAAATGTAGCTCATCCCAGATTAGCTACAAATATGTACCCCAGCTATACCTTTCCATCTAGAGGATAGCAAACCATAGTTGGCTGAGAGTTACCTCATGCATTTTTTTTTCATGGCATATGTTTAAGCTGAAGATAAGGATCATATCAAAGCAGTAGACATTTAGAGTAATAATAATTAAGGGTTATAGGATTTGAACCATAAGTGTTTGTTCATAGTCTGGATTGCAGTTTTATGTAAAGCAAAAGGATTCTAGGAAGCAAACGCCATATATATGGTAGCGGCTATTCCAGGATTCTAGTCGTGGCTGATGTGTGGGGACTCAGCAGCGTCCACGCCGGCAGCAAACAGTACGGGACAAGTAGACCTGAAATGAGAGCAGAAACAAACCAACTATGCTTCCACCAATTTCTACACCTATAAAACAAGGTAAATTAATCATCAAAAGATCACAAACATTTAGTATGCGTCCGACTTGACCAGCACACTATCACACAGCCTATAGTATAACAACTGCAGTGTTAACATGTCACTTGCATAAGAGCAAAGCTGCCCTGCTGAAAGCACAGAATGAGAAATGTCACTAAGCAGCAGCAACAGCAAGAGAATGTTAAAAAAAAAGTTCATATATAAGCAAAGGGCTAATCATATAGTGCAAAATTAGCCCATTTGAAAGCCTTCACAACAAACTGGATTTTTATCTACTCACTGAACAAATATCTTGTACTATATAAAATAAATAAGTACTTTGTTTCAAAAGGGGACAAATGTCTTGCAAGTAACTGTGCTACTCTCCTATAAACTCCATCATACACACGAGTGTTTTTCATCTTCCAAAATCACTGGATGAATATTTAGATTTCAACTTAATTTGAAGAAAAGCAAGAACAAGTAAGGAAAACTAAGTAAGGAAAACTTTTGCTTTAAGGTTGCAGTGCCCAGATTGATTAACTGTATACTTGCTTTACCAGCGAGAACCAATAACTAATAATAGAGGTTATATTTTAAAAACTCCATATATCTAGCTTGTCTTTAAAATAATTACTAACTTTTACCCAAAATTCAGAGATAGTGTGCAAATATTGTGCAGCCATGTAGGATTCAAACGCCAAATACATAGTATTTTACAAACTTTCAAATGATATTTTCAATTTTACCTTGAATGAAAAGGGAGGTGGAGCTAAAAAAATAGTACTCAATAGTTGGGGGGACATAGCTTCCAAATGAAGGGCTATGCAGATTGCCATGGTTCACATTCCTCGAGGCTGCCCTGTATCCTGGCGATCTGTCCCTGCAGCTCTTCAAGCAGGAGCCACTCCTTTCCATCCTTCCCTGCGTTAGAAGGTCGCAGTTGGCCGAGCTTCTTCCCTAGAATTACAAGGTCTGATGGAGGTGCGAAAGATAAGCTTCGGCCGTGGCCTCATGCTTGTCACCAGTGGGGAGGAGGGCATGTCTGAGACATTGCTGCCATCATCGCCAAGCTGCTGCCGCTGCTGAGCTCAACAGATCCGGCGGCCTTGATCTGTCACATCCAACTTCCCCACCGGCTCTGGATCTAGATTAGAGAGAGAGAGAGAGAGAGGGAGAGCAAGAACAAAAAAAAAGAGTTAGGGAGGAAAGTCTTTCCCCATAGAGAAAACGATGAGCATCATGTGCTAAACCATCCCAAGCCTCCGGGTGATCGGATCTGCCGGCAGGGAGATCGTGGTTGCCGGATCAGGCGGGCACGACCTCCCCTCCACCAGAACCTGCCTCGCGGTGGCAAGAGGGAGGTGCGGTGATGCACCTGGGTGCTAGAAGAGTGCGGGAGGCGCGGCGGCGGCGACGCAGTGAGGAGAGTTTGCGGCGCGGCGTAGCGGGGGCGGGAGGCGCGAGGAGGAGGAGGAGGCGGCGGCGTGGGCTAGGGAGAGCGCGCGAGAGAGGA

Coding Potentia
Explanation CPC Score
noncoding -1.23544
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0208500.4 3 10236307 A C
Osa03LNT0208500.4 3 10236806 C T
Osa03LNT0208500.4 3 10237326 A G
Osa03LNT0208500.4 3 10237352 T C
Osa03LNT0208500.4 3 10238416 G A
Osa03LNT0208500.4 3 10238515 A G
Osa03LNT0208500.4 3 10239880 C G
Osa03LNT0208500.4 3 10240402 C A
Osa03LNT0208500.4 3 10237527 C A
Osa03LNT0208500.4 3 10236237 C 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
Osa03LNT0208500.4 osa-miR812r Translation 4.5 17.503 1 24
Osa03LNT0208500.4 osa-miR5808 Cleavage 4.0 10.701 1 24
Osa03LNT0208500.4 osa-miR5143b Cleavage 4.5 11.745 1 24
Osa03LNT0208500.4 osa-miR5834 Cleavage 3.5 8.932 1 21
Osa03LNT0208500.4 osa-miR156a Cleavage 4.5 9.388 1 20
Osa03LNT0208500.4 osa-miR156b-5p Cleavage 4.5 9.388 1 20
Osa03LNT0208500.4 osa-miR156c-5p Cleavage 4.5 9.388 1 20
Osa03LNT0208500.4 osa-miR156d Cleavage 4.5 9.388 1 20
Osa03LNT0208500.4 osa-miR156e Cleavage 4.5 9.388 1 20
Osa03LNT0208500.4 osa-miR156f-5p Cleavage 4.5 9.388 1 20
Osa03LNT0208500.4 osa-miR156g-5p Cleavage 4.5 9.388 1 20
Osa03LNT0208500.4 osa-miR156h-5p Cleavage 4.5 9.388 1 20
Osa03LNT0208500.4 osa-miR156i Cleavage 4.5 9.388 1 20
Osa03LNT0208500.4 osa-miR156j-5p Cleavage 4.5 9.388 1 20
Osa03LNT0208500.4 osa-miR156k Cleavage 3.5 9.388 1 21
Osa03LNT0208500.4 osa-miR168a-5p Cleavage 3.5 21.449 1 21
Osa03LNT0208500.4 osa-miR417 Translation 4.0 16.94 1 21
Osa03LNT0208500.4 osa-miR1424 Translation 5.0 11.438 1 21
Osa03LNT0208500.4 osa-miR1429-3p Translation 4.5 14.157 1 21
Osa03LNT0208500.4 osa-miR1439 Cleavage 4.0 15.774 1 21
Osa03LNT0208500.4 osa-miR1858a Translation 5.0 11.122 1 21
Osa03LNT0208500.4 osa-miR1858b Translation 5.0 11.122 1 21
Osa03LNT0208500.4 osa-miR1860-3p Cleavage 4.0 23.956 1 22
Osa03LNT0208500.4 osa-miR1878 Cleavage 4.5 16.83 1 24
Osa03LNT0208500.4 osa-miR1882e-3p Translation 5.0 8.656 1 24
Osa03LNT0208500.4 osa-miR2094-5p Cleavage 4.0 11.641 1 21
Osa03LNT0208500.4 osa-miR2118i Cleavage 4.5 22.112 1 22
Osa03LNT0208500.4 osa-miR2868 Cleavage 4.0 9.907 1 20
Osa03LNT0208500.4 osa-miR2874 Translation 4.5 24.04 1 24
Osa03LNT0208500.4 osa-miR3980a-3p Translation 5.0 18.445 1 21
Osa03LNT0208500.4 osa-miR3980b-3p Translation 5.0 18.445 1 21
Osa03LNT0208500.4 osa-miR5143a Cleavage 4.5 11.745 1 24
Osa03LNT0208500.4 osa-miR5338 Cleavage 4.0 11.046 1 21
Osa03LNT0208500.4 osa-miR2275d Cleavage 5.0 18.011 1 22
Osa03LNT0208500.4 osa-miR5518 Translation 5.0 17.66 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0208500.4 3 qLVG3 Resistance or Tolerance Cold tolerance RM251 RM282
Osa03LNT0208500.4 3 ccs3 Physiological trait Source activity RM282 RM251
Osa03LNT0208500.4 3 dcf3 Physiological trait Source activity RM282 RM251
Osa03LNT0208500.4 3 qGL3-1 Physiological trait Eating quality nan nan
Osa03LNT0208500.4 3 qOE3-1 Physiological trait Eating quality nan nan
Osa03LNT0208500.4 3 qTA3 Physiological trait Eating quality nan nan
Osa03LNT0208500.4 3 qGY-3 Morphological trait Seed RG369 RG745
Osa03LNT0208500.4 3 nan Physiological trait Germination/dormancy nan nan
Osa03LNT0208500.4 3 qBM-3 Physiological trait Source activity RG369 RG745
Osa03LNT0208500.4 3 nan Morphological trait Seed RM251 RM554
Osa03LNT0208500.4 3 nan Morphological trait Seed RM251 RM554
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