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

>Osa02LNT0170300.1

GAAGAAATGTTTCCATTCACGAGGCTGGCAGCAGGCTCAGTCAGTTACAAAAGACCTAAGTCAACAACTGGACTAAGATTTTCTTTACTGTTTTCCCTACAAAGCTGCATACATACAGATCAAAGAAAGGCCAGCATTGCAGTTCTACCCAACTATGAACATATGGCTGCTTGATTGGCAACATCGTGTTGTTTTGAAGGCCACCATGATTGCTGGGGCACTTCATTCTTCTATATTTCAGAGGCTGAAAGGTTCCGTAGATCAATATTTAGACCGCAGGAAGTTCCAGAACTTTTTTGTTCTGGAAATTGCAGCAGCACTTTCGATGGACCGACAAAAATGGTCAAATATTTAACATGCAATTCAAATACTCGAGGTATTTGGCAACTGATCAAGCCGGCTGTTCAGTATTTGGTGAGCTCGCGCACTTCGGTATTGCAGTCGCTGGTGTAGTGCTTCTGACATTTGATCAAAAAAATCAGGATCCCATCTCTGAATTAAACGGGGATCCTCAGCATAGCATATGTATATCGATGTAACTGCACTTTCGACAACTACAACAGTTACCCCAACCAGTATCATGCCCATCAGCATAGAGGTTGAGCCAACCATAATAGCTTTATCACTTTGTTTAAAATATGTCCAAACACCCGTACATGTTCCTGTAATTAACCCACCTAAAATGGTGCTCATCAGAAGGACAGCACCTGAACAGTCATAAGCAACAAGTGCTTCAACGCCAGTTGATTGGAACAACTCCCAAGCATCCCTAGCTGAGCGATTGAAACTCTGGCCATTGATAGCTATCTGTACATATGCATATTTGTTGAAGAAGCGAACAAGAGTTTCCACGATATGAAACAAAAAGTCAACACAGCACAGCAAACACTCATTGTTGCCTATTTTAGAACGAATTCCTCGAATCTCCCAACGTAAAGTCCTAATAGCAGCCGTAAAAAGTGATCCATAGCAAATGCTCCCAAATGAAGTTGTTACAGCGTACTGAAGTGATTTTAGAAGTGGTTTTGGGGGCATCGATGCAGCAGCTTGACCACCATGAATGAGAACAAGAAAAACCATCCCTGATACTATGACATGGACTGTGTTACTAAGGACAGCTCCAGTCCAAAATAAACTGACTGAGAAAATCCGCTCACCAAAAGAGCCCACCATTGCCCTCCATTAGGTATGTGAAAAGCAAGAATGCCAGACACTCCAAAGGACCATAATGCCATCCAACAAAGCATGACTAACACAAATGCATATGCTATCCTCATCACATCAGGAAGTTCCCATACCATTCTTACTGCCTTCTGCAATACAAGCATTGTGAAGGGGAACCTATCAAGAACTGACATGACGTAGAGGAAGTGCAGCGCTCCGCCGACGGCGAACGCCACGCCCCAGAAGAAGTGCTTCCCCCAGAAGCAGAGCACGCTGACCACCGCGAGGTAGGCGGTGAGGCTGTGCACGGCGGCCCTCATGACCACCCTCCCCCCGTCCTTCTTCCCCGCGGCCGCCGCCAGCCACGCCCACGCGAGGGCGGTCCCCACGGCCCCCGCGGCGCCGTAGTAGGGCCAGTACGACTCCGTGAGCTCGGACTTGGGGGTGACCTCCTCGGCCTCGAGCGACGGCGGCGGGGGCGCCTCCCGAGCGGGCTCCGGCGACCCGGCGAAGCGAGGCGCGGCGGTGAGGTTGGTGAAGCGGTCGATGTTGAAGCGGTCCGCCTGGCCGAAGCGGTTGAGCCCCGTCAGCGCGAGCGCCCCGCCGAAGACGAGCAGGTGGAGCAGGAACACCACCAGCCAGAACACGTCCCGGCACCGCCGCCTCGGCCACGCCGCCGCCCCCACCCCCACCCCCGCCGCCCCAGCCACCGCCGCCGCCGCCGCAGGCCCCGCGGGGCAGGGGCTAGGGTTCGCGCTCTCCCCCTCCGACGACGACATCGCTCCCCGCCCCGCCCCGCCGGAGATCAGCAGCAGCGGGGACCGCACCGCACCGCACCGGAGCGAGGGATCAGCCGCGAGCGGATCGCGGGGAGGAGGCCGGAAGCGGAGGGGATGACTTGGAGGAGAAGAAGAGGATGGGGAGGAGGAGTAACTGC

Coding Potentia
Explanation CPC Score
noncoding -1.07209
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0170300.1 2 22327308 A G
Osa02LNT0170300.1 2 22327383 T A
Osa02LNT0170300.1 2 22327728 A T
Osa02LNT0170300.1 2 22328208 T A
Osa02LNT0170300.1 2 22328361 C T
Osa02LNT0170300.1 2 22329274 G A
Osa02LNT0170300.1 2 22329399 A C
Osa02LNT0170300.1 2 22330667 A C
Osa02LNT0170300.1 2 22329370 T G
Osa02LNT0170300.1 2 22330214 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
Osa02LNT0170300.1 osa-miR820a Cleavage 3.5 15.996 1 21
Osa02LNT0170300.1 osa-miR820b Cleavage 3.5 15.996 1 21
Osa02LNT0170300.1 osa-miR820c Cleavage 3.5 15.996 1 21
Osa02LNT0170300.1 osa-miR1879 Cleavage 4.5 18.228 1 24
Osa02LNT0170300.1 osa-miR1882a Translation 5.0 22.536 1 24
Osa02LNT0170300.1 osa-miR1882b Translation 5.0 22.536 1 24
Osa02LNT0170300.1 osa-miR1882c Translation 5.0 22.536 1 24
Osa02LNT0170300.1 osa-miR1882d Translation 5.0 22.536 1 24
Osa02LNT0170300.1 osa-miR1882e-5p Translation 5.0 22.536 1 24
Osa02LNT0170300.1 osa-miR1882f Translation 5.0 22.536 1 24
Osa02LNT0170300.1 osa-miR1882g Translation 5.0 22.536 1 24
Osa02LNT0170300.1 osa-miR1882h Translation 5.0 22.536 1 24
Osa02LNT0170300.1 osa-miR2863b Cleavage 5.0 16.744 1 21
Osa02LNT0170300.1 osa-miR812o-5p Translation 4.5 15.788 1 21
Osa02LNT0170300.1 osa-miR5505 Translation 5.0 15.317 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0170300.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0170300.1 2 nan Resistance or Tolerance Insect resistance RG157 RZ318
Osa02LNT0170300.1 2 yld2.1 Morphological trait Seed RM262 RM263
Osa02LNT0170300.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0170300.1 2 qCSH2 Resistance or Tolerance Cold tolerance RM262 RM263
Osa02LNT0170300.1 2 qRTT2-1 Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0170300.1 2 nan Resistance or Tolerance Drought tolerance RG157 RZ318
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