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

>Osa03LNT0227900.2

CCAAAAGTATCACCAATCAATTGAAGAATCAGAACTTTTGTATGGCCAAAAGGATCTGACACAAGTTGCTCAGGCACTAGTTAAAACTTAAAACAAACAAAATTTTACCCTAGCAACTAGGACAGATGGCGCTCTCTTTCATTTCTATGCTTCTTTTCTTTTATATGCATCTCTATGCCTTTTTTTTTTGTATATTCATTTGTATGCTTCTTTGGTCACTGTATGTATGTCCTATCTGCAAAACTTATGCAGTTTGCGGATTTACATCGGCGGAGGGTCCAGCGGGCTGTGGTGACAGGCCTCTCTTCTGTAACCTGATGATGGAACTGAGCGACCTCACTGCATGCCGTAGCCGGTTTACAGGGAGTCCTTCCAGTGTAGGGTGAGAAATGTCACTGGTTGTGGGTTGGTTGGTGTCTTCTTTGCAGCTAGATTCACCGGAACTTCCGCTTGCATCTGCATCTCTGTCAACGTGAACTCCTTTCAGAGGTATGTCGTCAGTGTCAGCAAACTGGCAGTAAGCAGAATGAAGACGGTGGTGAATGTCATCCATTCTTCCCGATTGCTCGTCCTCCCTGTCCATGTCAATTAAATCCTGTGCAGGGAGAGTCTTGAATAATGGCCGAAGACGATTGCTGCAATACTGGTTGAATAAAAGAGTGAGGATGATGAGAGGTACAGTGAAGCCTGCAGCTACTGGGGATTCTTTAAGCCCAAAGACACCAAGACAGATGATCTGGGTGAGCACAATAGAGAAGATTGTTGTATAGTGAGCAATCGGCCAATACAGACCACCTGTGTCGTATTTCGTGCAATAAACATTGAGGAACTGGTTGCGGTACACAACATAACCAAGAAAAAAGTACACCAGTAAAAAGGGCAAGATGAGAGGTGCTAATACAGAGCATGTGAATCCCAGTAGTCCAAACAACAGAACTTTTGGCACTTCAGTATGATAGGGAAATGACGGGACAAAGTAGCTATCCTCTTTCATTCTCAAAACATACTTCATTATAAAGTTCCATGTGAGACCAAAGAGTTGCATAAGTTCTGATGATAAACTAGCCCAACCAGAAGTCAGTACATAGGTGGTAAAGAATGTAGCCTGTACAGGTACCGCTCTAGCAAGCACCATAGGAATGTCCTTTGGGCTTGATAACGCATTCACTTGGCTAATTGCAGAACCTGATAGGACATTCACAAAGAATACATTCCAAATAGTGAAGTATAATACTTTACAGCAGGCACTTCTCTTCCTTTCACTGTGGGACACGGGTCCTTCTAATGTAGAAAAAAACATCATGGTTGGGGGAACAGTGTATAAAAATATTTGCAAGATGACACTGGGAAGGTATCCGGTCACTAGCTGGGTTATGTACTTCTTTTTTAATATGCCATTTAGGAAAGGGAGCCTTTGCTGCAGCTGCTCCAACTGAGTTAGACCTTGTATAAATGTCACAGGTATGAGAAACAGGAACATAAAAACAATAGAACCCGAAAGTGTAACTATACGGCGAATCCAAAGCTGCTTGTAGGGTAACCAAAGATTTGACCAATATACGTCATCTCGATCTGGAGCAAGACTAGTAACCCATTCCATAGGATTGGATGTCTGAACAATTTCTGATACGACCAGGGCTGCATACCGAGTTTTGAAAAATACAAAAGCAGCACCACAATCCTTATCAGGTAAGCTCAACTCTGAATCTTTCACATCATGTTTTTTCATCTCTTGCTCAGGTTCAACAGGCAGCAACTCGAACGACTTTGATGAAGCTCCACAAAGACCACATCTATATGTAATTGGTCCGCATCTCTGATCAACTGTGGTGCCCTTGAAATGTTTAAATTTCTTATAAGCCTTCTTTGCACCAGTCACAATCTTCTGAAGTTTCCCGACTTTATAAATAATCTGATGAGAAAGGTAACTCGACACATGATACTTGGTGAAGAAACTCTCAACAGTGCAACTAATTGATTCTTTAGTTGATTTTGGTACTCCACGAACAAGCACAGTAAAATGGCTAGGATTGGTCGATGCTCGAGAAACATGAAGTAACCTCAGCCTAGCAATATGCTTGTACTCAAGGTATAGAAGAAGGCAAGCCACACCAGATATGATGTACAGTGCAACACAATGGACCCAGAGCCATCTTGATCTCTCTTGCATATTTCCAATTGTAAATGTCTCCAATGATGCTGAAGGAATCCGTACATGGAGCATATCTTGTCCAAAATAATTCAGTGGAAGAACTCCAAGTACACAAAGGAAAGCGGCTAAGGAGAATATGCGTATGCTAAATACAAGAATCCTATTGAAGACAACTGCATCCAACCCAGCAGTAGCTAAGAGTTCATCCTCCGTGCATCGAAGACTTCTCAAAATCCAGCTAGCGGATGGAACAAATCTCTCCAAAATAAAAGCCTCCCTGAGCCTACTATTCTCCTCAGCAATCCTTCTTCCAAAATAGACCTTAACATTTTGCGGTTGCTTCCTCAGAACGGAATACAGTGACAAAAAAAGTATACAGAGGCTAATGTTGATTCCAGCTGAGGTCAAAAGAGCGCCGACTTTCATCTCTGTCTTATGTCATCTAAATGCAACAAACTTCGTATCTCCTTTAATTCCGTCGCGACGCGCGCCGAAAAAATCCCACCAATGCCCCCCGGCCGCGCCTCCTCAAAACCCCTGCACCACTCCACTTCGCCAGTCGACCACCGCCGCCGCCGACGCGCGATCGGGATTCGCCGGGGGGGATCGGAGAGATTTCGAGAAAGCAATGTGTGGTGGGAGATTTGCGATTTGGTGGGGGGTTTGGGTTGGAAGTTTCGATCACAAGGAAGAAGAAGAGGAAGAAGAAGGAAGGCAGAGAGACGAAAAGGGAAAG

Coding Potentia
Explanation CPC Score
noncoding -1.12409
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0227900.2 3 26623799 T C
Osa03LNT0227900.2 3 26623828 C T
Osa03LNT0227900.2 3 26623990 A C
Osa03LNT0227900.2 3 26624303 T G
Osa03LNT0227900.2 3 26626008 C G
Osa03LNT0227900.2 3 26627706 A G
Osa03LNT0227900.2 3 26627943 G T
Osa03LNT0227900.2 3 26629767 T C
Osa03LNT0227900.2 3 26630070 T C
Osa03LNT0227900.2 3 26630825 A G
Osa03LNT0227900.2 3 26631032 T C
Osa03LNT0227900.2 3 26632011 G A
Osa03LNT0227900.2 3 26627739 T C
Osa03LNT0227900.2 3 26632113 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
Osa03LNT0227900.2 osa-miR5794 Translation 4.0 17.055 1 21
Osa03LNT0227900.2 osa-miR5837.2 Cleavage 4.5 9.669 1 21
Osa03LNT0227900.2 osa-miR415 Cleavage 4.5 8.258 1 21
Osa03LNT0227900.2 osa-miR528-5p Translation 5.0 6.789 1 21
Osa03LNT0227900.2 osa-miR530-3p Translation 5.0 23.178 1 21
Osa03LNT0227900.2 osa-miR812g Translation 4.0 16.277 1 24
Osa03LNT0227900.2 osa-miR812h Translation 4.0 16.277 1 24
Osa03LNT0227900.2 osa-miR812i Translation 4.0 16.277 1 24
Osa03LNT0227900.2 osa-miR2105 Cleavage 3.0 9.901 1 20
Osa03LNT0227900.2 osa-miR2864.2 Cleavage 4.5 14.775 1 21
Osa03LNT0227900.2 osa-miR5338 Cleavage 5.0 15.21 1 21
Osa03LNT0227900.2 osa-miR5338 Cleavage 5.0 11.244 1 21
Osa03LNT0227900.2 osa-miR5338 Cleavage 4.0 12.245 1 21
Osa03LNT0227900.2 osa-miR5492 Translation 3.5 9.926 1 21
Osa03LNT0227900.2 osa-miR5494 Cleavage 4.5 14.753 1 21
Osa03LNT0227900.2 osa-miR812j Translation 4.0 16.277 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0227900.2 3 nan Morphological trait Shoot/Seedling RZ403 RZ630
Osa03LNT0227900.2 3 nan Morphological trait Shoot/Seedling RZ452 RZ448
Osa03LNT0227900.2 3 nan Morphological trait Panicle/flower RZ448 RZ403
Osa03LNT0227900.2 3 qSB-3 Resistance or Tolerance Bacterial blight resistance R250 C746
Osa03LNT0227900.2 3 nan Resistance or Tolerance Blast resistance RM16 RM168
Osa03LNT0227900.2 3 qSV-3-1 Morphological trait Shoot/Seedling RM156 RM168
Osa03LNT0227900.2 3 qSV-3-1 Morphological trait Shoot/Seedling RM156 RM168
Osa03LNT0227900.2 3 QFlw3 Morphological trait Culm/leaf RZ474 C746
Osa03LNT0227900.2 3 Yd3-13 Morphological trait Seed RZ403 CDO337
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