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

>Osa01LNT0007200.1

TTAGCACTGCAATCTCGCCGTTAAGTACCTTTTTTTTTACCCTCAAAAGTTAACAAAACACGTACAATTCTGGGTTGCTTCACAAATTACAACATGAACATACAAAGTCAGGGAGGGGCACATCAATCTGGAACACATCAGGGTGTAGGAGAGAATGGAAACCAAGGGAAAAAAAAAAACAAGGATAAGGTAGATGAGTTAGCTGTGAAGAAAGTTTTTGTCAGCTGCATCGGTGGCCGTCTTCTGAACATTCAGAACTTTGAGATGATCCCTGACCAGCAGAGGATGTCATGAGTCTCTGACGATCTTAACATTTCTGAAGGACAGCATCACAGTAAGAATCAAGGTAACCATCGCGAAGCAAAGGTGCTCCAAGGAATGGCCGCTGATGAAGTACCGGTTCACACTGTATACCTTTCTGTCAGCAAGGCCTTCAAATCTTGCAAGAAGGTAAAAACCTGTGGCAAGAAACCAAAATCTTGAGTGTGTATATTTTGGAGGAAACAAGAATAGCATTGCAGGAATTGCAATGCAAGGAGCGGAATTCAAAACTACCCATAACCGCATATCATCAAGAACCCTTTCACATGCGCTGCTCACCAGTATGAGAGATAAGAGTGATAGCAAACAAGATAACCCAGCCCTTTCATCAACTCTTTCAATTACCAATATAGACAACATTGAAGAAGCTGATATCATCATCTGCGTTCATAGCATCCAGTGAACATTCATATCGAGGAAAAGGATAGATACATATTCATTAATAGCATTGGTTATGCACGATAACATGATAGTCAGATTGGCTGCCTAGCACAGTAGTATGGAAACTCAGACACATCCTTTTTTTTCTCTTTTTGCCTATGGTTAATACTTCGATGATATTAAGGACATTCAAGTAGGTGAACTGCATTTTTTGAACATGAACTACTTAATACAGTTTTTTCTCCCAATGGACTCGAAGCATAAAATGACAACATATCAAAAAAAATTCCAAGTCCAGAAACCATGGAAAACACCACGAAATAAGTAAACAGTAGATGGGGAAATTACAGAAAGATGAGATATTTAGATACCGGCAACCTGTCCCAAATTAAGCGGTCATCATCTGGTTTGAGGTGATAGTAAGCCGAGCCAAATGCTGCTGCTACATTCCCAGCATAGAAGAGGAACCATCCCAAGGCCTCCCATCTCAAGCTGATGCCGAAGCACCCACTGCCACAGAGGCAGAGGACGAGCCCGGGCACGCCCGCCAGGAGGAGCGGGTAGGCGGTGAGCACGTTGAGCGTGTTGGGGACGCCGAGGAGGTTGCGCATGTCGGCGAAGAGGTGGAGCGCGGGGGAGTGGCGGAGCCGCGGCGTGGCCACCAGGAGCAGCGCCGAGGCGAGGACGGCCCCCCCGGCGAGCGCGCGGCGCCGGTGCTCCCGGCGGAGCGCCGCGGCCGCGAGGTGGCCGAGGCCGAGGCCGAGGGCGGCGCGGCCGCCGCCGCCGCGGTGGGGGTGGTCGGCGGCGGCGAGATGCATGTGGCCAGGGGGAGTGCTCAGTGGAGCAGAAGAATGCGGTGAATTTTTTCTGGTGT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.288333
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0007200.1 1 5263994 A G
Osa01LNT0007200.1 1 5264192 T G
Osa01LNT0007200.1 1 5264642 T C
Osa01LNT0007200.1 1 5265399 G T
Osa01LNT0007200.1 1 5265336 C 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
Osa01LNT0007200.1 osa-miR7693-3p Cleavage 5.0 24.188 1 22
Osa01LNT0007200.1 osa-miR7694-3p Translation 4.5 13.033 1 22
Osa01LNT0007200.1 osa-miR444d.3 Cleavage 5.0 24.491 1 21
Osa01LNT0007200.1 osa-miR2275a Cleavage 4.0 19.925 1 22
Osa01LNT0007200.1 osa-miR2275b Cleavage 4.0 19.925 1 22
Osa01LNT0007200.1 osa-miR5488 Translation 5.0 13.292 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0007200.1 1 qTNSP-1-1 Morphological trait Panicle/flower RM1 RG532
Osa01LNT0007200.1 1 gn1 Morphological trait Panicle/flower G359 RG532
Osa01LNT0007200.1 1 gp1a Morphological trait Panicle/flower G359 RG532
Osa01LNT0007200.1 1 gw1a Morphological trait Seed G359 RG532
Osa01LNT0007200.1 1 qLS1-2 Morphological trait Shoot/Seedling G359 RG532
Osa01LNT0007200.1 1 qSS1-2 Morphological trait Seed G359 RG532
Osa01LNT0007200.1 1 qSSB1-1 Morphological trait Panicle/flower RG532 G359
Osa01LNT0007200.1 1 qSW1-3 Morphological trait Seed G359 RG532
Osa01LNT0007200.1 1 qFLL-1 Morphological trait Culm/leaf RZ543 RG532
Osa01LNT0007200.1 1 qFLP-1 Morphological trait Culm/leaf RZ543 RG532
Osa01LNT0007200.1 1 nan Resistance or Tolerance Lodging resistance R1944 C955
Osa01LNT0007200.1 1 ph1.1 Morphological trait Dwarf RM220 RM272
Osa01LNT0007200.1 1 nan Morphological trait Root RM7383 RM243
Osa01LNT0007200.1 1 nan Morphological trait Root RM7383 RM23
Osa01LNT0007200.1 1 Rf3 Physiological trait Sterility nan nan
Osa01LNT0007200.1 1 ppp1.1 Morphological trait Panicle/flower RG140 RM243
Osa01LNT0007200.1 1 prg1.2 Physiological trait Source activity RG140 RM243
Osa01LNT0007200.1 1 spp1.2 Morphological trait Panicle/flower RG140 RM243
Osa01LNT0007200.1 1 dn1a Morphological trait Panicle/flower G359 RG532
Osa01LNT0007200.1 1 nan Resistance or Tolerance Salinity tolerance RM1 RM5
Osa01LNT0007200.1 1 nan Physiological trait Source activity RG532 RG472
Osa01LNT0007200.1 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0007200.1 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0007200.1 1 sp1a Morphological trait Panicle/flower G359 RG532
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