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

>Osa03LNT0224300.2

TTATAAGTACTTTTTTTACATTTCCACCACATCATGCATGTACATGAGTTACCGCACACATTACCAGTATTCGCCATTCAAGCCATTAATAACTTGCTACGCTAACATAAGTACTCTATATCCTCTACAACTAAGTGAGTTCTACAGTGAAGCTAGGCATAATAATTGCAGATCAAGAGACCAGTTAGCATTATCTCACATCTCCCCATATCATGCACCTGATGAATGAAGCAATTCTTCGTCATCAGAATAGCCAAAATCTTGAGACGGAGAGCAGTCAAAATCTTGTGATTTCCATGTGTGGTTTTTCAGTGTCCTACTACCATCCCTGTGTCCATTCTCTGCCAGTTGTTGGTCTTGCAATTCAAGCTGTCTTCTTACCCAAGGAGGATCATCTGCACGAAGCCACAGCTTCTCGCCAGTGTCCTTGTGCTTGAAATCAGGATAGTAGGAGTATGGCTTGGATTGTCGGTTGTCCCACCATTCGTAAGGGCTAGCGAAGAAGACCTGCCACAAGCGAAGCCGATCTATGTACTTCTTTTCTGTAAGTATTTCATCTAACTGTGGTAGACAGCATTGATGATTTGTCTGAAGAATTCTCATCATTTTGAGGCCTCTGATTTTGATCAAGAACATAGTTTAGGTCTGTGACATGTATCTTGTAGAACGTATGCTTCTCTCCACTTGGATCAACTTTATGATATGAATTCAGAAGGCCAGATACATAAACAAGGTCATTTTGTTTCAAATGCTTTAGGCTTACATGTGCCAGCTCGCCTTGCAAATTCAATGTCACACGGAAGTTGGACGGACTCGAGGAGGGCGGGGATGAGGGCGAGGAGGAGACCGACAGGAAAGTGTACGCCATGGGCCGCTCGTCGGAGCTGCCACCGCACGGGCGCACCGGCCCGTCGAGGCGGCCGATGAGGCTGCACGAGTTCCTCGGGAGCCCCCTCCTCGGCACGACAGGGGGAGGCCGGAGCATGGACATGCGGTACGCCACGCTCTCCACCTCCTCCCGCCCTCCTGCGTGGAGGGACCGCCGGAGCGCCGCGGCCGCCGACGAGCGCCCCGACTCGGCGGCGCCGGCGAGGGAGCGCAGCATGGGGACGTTTCGGGGAAGTGAACGGGGAGAGAGATC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.97164
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0224300.2 3 23093844 A G
Osa03LNT0224300.2 3 23093859 A C
Osa03LNT0224300.2 3 23094380 A G
Osa03LNT0224300.2 3 23095201 T C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa03LNT0224300.2 osa-miR5143b Translation 5.0 12.236 1 24
Osa03LNT0224300.2 osa-miR5821 Translation 4.5 11.141 1 21
Osa03LNT0224300.2 osa-miR5833 Cleavage 5.0 24.043 1 21
Osa03LNT0224300.2 osa-miR395u Cleavage 4.5 12.674 1 21
Osa03LNT0224300.2 osa-miR166l-5p Translation 5.0 17.964 1 21
Osa03LNT0224300.2 osa-miR444b.2 Cleavage 4.0 14.549 1 21
Osa03LNT0224300.2 osa-miR444c.2 Cleavage 4.0 14.549 1 21
Osa03LNT0224300.2 osa-miR444f Cleavage 5.0 14.549 1 21
Osa03LNT0224300.2 osa-miR1883a Translation 5.0 15.56 1 24
Osa03LNT0224300.2 osa-miR1883b Translation 5.0 15.56 1 24
Osa03LNT0224300.2 osa-miR5143a Translation 5.0 12.236 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0224300.2 3 qGL-3 Morphological trait Seed R19 C1677
Osa03LNT0224300.2 3 qLWR-3 Morphological trait Seed R19 C1677
Osa03LNT0224300.2 3 qSV-3-1 Morphological trait Shoot/Seedling RM156 RM168
Osa03LNT0224300.2 3 qSV-3-1 Morphological trait Shoot/Seedling RM156 RM168
Osa03LNT0224300.2 3 ccf3b Physiological trait Source activity RM16 RM282
Osa03LNT0224300.2 3 ccfs3 Physiological trait Source activity RM16 RM282
Osa03LNT0224300.2 3 nan Resistance or Tolerance Other stress resistance RM4512 RM8208
Osa03LNT0224300.2 3 nan Resistance or Tolerance Other stress resistance RM4512 RM8208
Osa03LNT0224300.2 3 nan Resistance or Tolerance Insect resistance G332 R19
Osa03LNT0224300.2 3 An5(t) Morphological trait Panicle/flower C1677 R19
Osa03LNT0224300.2 3 nan Morphological trait Shoot/Seedling RZ284 RZ403
Osa03LNT0224300.2 3 nan Morphological trait Shoot/Seedling RZ452 RZ448
Osa03LNT0224300.2 3 nan Morphological trait Panicle/flower RZ403 RZ452
Osa03LNT0224300.2 3 gw3.1 Morphological trait Seed RZ672 RZ474
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