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

>Osa02LNT0152900.1

CAGCGAACGCGGAGTGAGTTGAATGCAAGATATATAGAAATGCGAGACGCGACTGGAGTTTATGGAAGACACAGCAGGAGACTTCACTTCCAATGTTTGAAATGGTACACTTTATTGCCTAAGGCCCTGTTTAGTTCCCAAAACAATAACTTTTCACCCATCACATCAAATGTTTAGACACACATATATAGAGTATTGAATGGTACACTTTATACTCAAACTGAAAATCAACAGTACTGAAATTTCAGACAGGTATATATGGCTCTTCCTACCATGTGCCTTGTATTTATAGACATCAGGCTGCAGTCATAATAAGTAAAGACTACATGATAAGAACACTACTACAAATATAGTACTACTCTGGAAAACCTCTATATTAAATAACAAGAATTGAGCATTTCTGATAGTGCTACATTCTATGGGGGCGCTTTTTAACTAGCAGCCTCTGGGTATTGGGACAGCTTACAGATACAACAGTGCCACAAATCTGCATTCCCCGTTACCTTCTGTTTGTGACCAAAGGGGTACACATGGACAAGGCACAAGGCCGGAACAAGGGCTCTCCGTGAACTGTGTGAATGGGGAAATTGGGAAAAAGGAGCCAGGCAGCAGCAGTACATTCCGAGCCGCAGAATTGCAACGAAGCAAAACTGATTCCGAAGCAAAACTGATGGCCAAACCATGCCTAGAGTATCCTGACCATCGAGAGAGGCCATTGGAGGCTTCTTGTCGAGGATCACTCGCCATCTCCGTTGCCAAAAACTCCGACGCGCTGCCTCCTCTTATCGAAAACTGCCCTGAAGGATTCACCTTCGTCACGAAGTTGTTCGCTGAATCGCTTCTTTGTATCGGTGTTGATTACCCCCTTTGCCTGCTTGGAATTATCTTCAGCCAAGGGGTTGGAAACCAAATTGTACCCTGATCCGGGTCCTATGATTAATGAAGAAGTGAGTCTTCTTTTAGCTGCACCAATAGAAAAACCACCCTTTTCTAGCCGATCTCCCCAGGTAACTGTTTTTCGATGCGTGCTGTAGGTTTGAGCCAATCCAGAAAGAGCATGCGTACTTCCTTCTGCATGGTCAGACTTCTCGGTATCCTCATCAAAATCTTTTGACCATTTACTCTGTCCTAGCTCTTTGTAGCCATCCAGGTCGTCTTCTTCTGACGAGTCCCACTTCTTCCCTGCTCCTGAGATGTCTTGATCATGTCCATTATCTAGTGATTCAGACACAGCCTTCTGTGTGTTTTCAGCTTCAGTACTAGTTGCTGTGTTACTGGCCCCATCAGTGTCTTCTGTCTCCATATCCACCTCTTGAATGGAATGCTCGCGTAGATTGTCATCGTTGAATAATGAATGGATGTCTAGTCGAAGATATAGTGGTGGAGCCTCTTCCCAGTCTGCTGCCATCTTGTTCACATCATCTACTGTAAACCCATGCACATTCCTAGCAGCACAGCCTGTTGGATCCTTGTATGGTGCCTCCAGCAGGTACACTTCATAGCCTGATTTCAATCACAAATGTAAAATTCCCTTCATCAAGGGTCTTCTTAAATGCGTTCAACATGCTTGATCTGTACGTCTCCTCCATCTCAGGCTCATAACAGTACTCGATCACTTTCTTGGTCAGCTGCTTTCTTCCTTTGGATGTACTAGAAGATTTTGACCCTTCATTGTCTTCAACTTTCTTCTCAACCTCAATCATGAAATAGTCATCCATCGAATGAATTCTAGGTGCATTTCCACCATTCTCAACTTCAAGGTCACGCAATGCCTTTGCAAGATAGCTCTTTCCACTACCTGGCAGCCCACGGAGGATGATAACAATATGATCAGGCCGTGACCCACGAAGTGGCTGCTTGAACAAGTCACAGGCACTAATTACACTGATTTTAGCATTGTTGATGGAATGCTGAGCTTGGGTTTGCCTTCCACCTCCTAAATGTTGCTCTAAGTGTGGTTGATATGCCAAACCTGGTACCTCATTGTGGATAGGTCCATTGTAACGATTTGCATTAGGCATCAGGTGAGCTTGATGCAAAGTATGAGAACTAGGTGGGCGCGCAGTTGCGGCTGGAGAACCGGAATGAATAGGAAACAAAGATGATTTCACAGCCTGCAAAGGTGGCTTGGCATGGTAATCTGAGGAAGACGGTACAGGAGGCTCCAGTGGTGGTGGTGGTGGTGGAACATCCGCCTCAGGATGCCAACCGTGGGAATCATAACGGCTTCTCGCCTCAGGGTATCGAGCCGGTGGAGGGAGCGGCGGCGCAACAGGCGATTCCGAGCGTTGGAAGCGATTGTAGCGGTGATCATGGTTGAAATACCCCTCCTGAGGTCCTCCAGGCACAAAACTTGAACCTAAGGCGGCAAGCCTTTCATGCGCAGGTGGAAACCTCCCGGCGTGCTCGTAATCGGGAAAACTGCCTTCATGCGCATAGGGATTGTCATAATTTGGAGGAGGAGGATAGCCTCTCCCTCCTCCATAGCCGAACCGATCAGGAGGTGGGTACGGTTCGCCGTGCAACATCCCAGGCGGCGGCGGAAACGGAGGGCGGCCGTGATCCCGGATCAAGCCGAGCAGCCGGTCGCCCTCCACGGGAACCATCCCCGGCGGCGGCGGCGGGGGCAGCGGGGGAGGCATCCCGTCGCCGTACGGATCGCCCACGCGCATCCGCTTGTGGGGGGCCTCCATGTCGAGGACCTCGTAGGGGTGCGGCCCCGGGGGGGCCCACATCGGCGGCGGAGGGTGGAAGGGGACGTGATACTCCGGCGGGGGAGGAGGAGGAGGAGGAGGGTGGAAGGGGGCGTGGTACTCCGGCGGAGGAGGGGGCGGAGGCGGGTGGAGATCGTAGGGGAAGGGGTGGGGCGGAGGCGGGCAGAAGGGGAAGTGCGGCGCGGCGCAGACCGGGCAGAGCTCGTCGCCGGCGGGGAACCGCCATGGATGGTCCATGGGGGAGATGGTGGCGGTGGTGGTGGCCGAATGGGGTTAGGGATCTAGGGTTTTGGGGGAGGAGGAAGGATCAGGGAGCTTCGAGAAGATTCGAGAAGCTTCCTTCCTGGGCTTGGGGTCCGCGGGGGTGGACGGCTGCGGCGCCGCCCGCCTCGTCTGGGTAGCCAGAAAAAGCC

Coding Potentia
Explanation CPC Score
noncoding -1.05598
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0152900.1 2 6433851 A G
Osa02LNT0152900.1 2 6434241 G A
Osa02LNT0152900.1 2 6434648 A T
Osa02LNT0152900.1 2 6434851 C T
Osa02LNT0152900.1 2 6435238 C T
Osa02LNT0152900.1 2 6435251 G A
Osa02LNT0152900.1 2 6436349 C T
Osa02LNT0152900.1 2 6436744 A G
Osa02LNT0152900.1 2 6437599 A G
Osa02LNT0152900.1 2 6437874 G A
Osa02LNT0152900.1 2 6438136 A G
Osa02LNT0152900.1 2 6440697 C T
Osa02LNT0152900.1 2 6440863 C T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa02LNT0152900.1 osa-miR5529 Cleavage 3.5 19.634 1 21
Osa02LNT0152900.1 osa-miR156c-3p Cleavage 5.0 17.434 1 22
Osa02LNT0152900.1 osa-miR156f-3p Cleavage 4.0 17.434 1 22
Osa02LNT0152900.1 osa-miR156g-3p Cleavage 5.0 17.434 1 22
Osa02LNT0152900.1 osa-miR156h-3p Cleavage 4.0 17.434 1 22
Osa02LNT0152900.1 osa-miR156l-3p Cleavage 4.0 17.434 1 22
Osa02LNT0152900.1 osa-miR408-3p Cleavage 5.0 12.799 1 21
Osa02LNT0152900.1 osa-miR2092-3p Cleavage 4.5 20.527 1 22
Osa02LNT0152900.1 osa-miR2118l Translation 4.0 22.672 1 22
Osa02LNT0152900.1 osa-miR3979-3p Cleavage 5.0 20.699 1 20
Osa02LNT0152900.1 osa-miR3979-3p Translation 5.0 14.383 1 20
Osa02LNT0152900.1 osa-miR5502 Cleavage 5.0 18.374 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0152900.1 2 tms5 Physiological trait Sterility Jan-39 Feb-39
Osa02LNT0152900.1 2 tms5 Physiological trait Sterility nan nan
Osa02LNT0152900.1 2 nan Resistance or Tolerance Drought tolerance RG83 RG171
Osa02LNT0152900.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0152900.1 2 qLER-2 Morphological trait Culm/leaf R2344 R712
Osa02LNT0152900.1 2 qEML-2 Morphological trait Seed R2344 R712
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