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

>Osa01LNT0035000.2

GGCACTGTCTCGACTCTCGAGTCGACGAAAGCAAGATCCATTATGTAACATATATTTAGGTATACATACACATGAAACACGACGGCACTACTAGCCCCACAAGCGGCCTCTAGTTTGTCGAGCAAACAAACACGCAACCAGGGGCTTTTTCTTCGCTGCCTTTCAGACTATAAACAAAGCAACCAAAGCCCACAGCTTCCTCCTGAAGCTGAACCTTACGGAAATTTCGGGATGAGAACTCCTGATCCCGAAAGGGTTTCTTCTTCATTATCATCTTCATCTTTCTTCTTTTCACAGGGAGTTATGTGTCAGTAACATCGCACAAGTTATGTGCAGCACAGGCCTTCAGGTACGACCTGACGCCTTCAGGCAATTCATGAAGTTAAAAGTGCTTGCTTCTTCTGCCAATACTGCTCGAATCTCTGCCTTGCATACTCCTTGTAGTCGAAGTCAATATCATTGACATGATCCGATATTATTCCCCAGAGGCCCCAAACTAGATGACTGGCGAGCGTGTATTTCTCAATGCTTTGGAGAAGGTTCTCCACCTCTTCCGCATCAGGTTCTTCACTTACAGAATTGCTTAGGTACGTCTTCACAAAACGCTTCTGCTCATCAGTGTCTGGATATTTACTGTAGTCCAGTCTATGTGGCTTCTCTGAATGATAGTCTGCTGCCATCTCGCAGAAATGATTAGCGATGTCATACGCAACTGGATTGAAGCTGGCATATTCATAATCCTGTATATATATGAGAAGAACAGAAAGGATCAAATTGCCAACAATTAATTGGGGCTTGTCATATATGTAAAGAAAAAGGAATCAGATTTCCTTAAGAAACAGTCGTGACAAATTGGTATACAGAAGGGAAAAAAAAAGGAGCAAAGCATCAGTCCTCCATAAGGTAGGTAGTGTCCAAAACCAAAACTATGTTGTTTTTTAGCAGAGCCGTGACAATTTAAAATGTCGAGGGGGAAGGGAACGCAACAAACAAAAAACAAGTTGTATGAAAGGGAAAAGGGCTGGCGCTATTCCAACTAGTGAAAATGATACGGCAGTTCCAACTATCCCATATCGCTTGTTGTTCAACAGATGATCACATGAGAGAAGAAACTTAAAAGTTCTACAACCTACGTTCAATAGCCTCTTCTACATTTCACATTTGCACATAATAGATACACGCAAAAAAAATGCAGCAAAAAACAAATATGATCACAGGGACATTATTGTGAATGAATATTACTCACGATGATAGTCAACATGTTGGTGTCTTCATCAATCATGATGTTGCCATACTGAAGATCGTTGTGGCAAAAACCAATCCCGTGGTAATCCCCTGAAAATTCTTTCTCCAATGCAGCAATCTCGTTCTCCAGGCTACCCAGCCGAAATTTCTTGGATTCATCAGATGAGCACAGGTTCCTTGCAGTTTTGAGCCAGTTTTTCAGTCGGTCCCAAATGAGTACAGATTTCGGGCCAGGCATGTCAAGGTTGTGGAATTCCCTCAGTTTTGACGCCACCAGAGCTGAAATTTCAGGATCACGAAGGTCTGCTGCAGATAGTGTCCTTGCGTGGATGAACTCCTCGACGCGGCCGTTGGTGAACCGGCCGAGGAGGCGGGGGCCTTGGCCATGGCGAGACATGCACTCGAAGGTGCGCACCTCGTCCTCGCGGTCGAAGAAGAGCTCCACGCCGTCGCCGTATATCCGCACGAGGACCTTCCTCACCTCCCTCTCCCTTGCGGCCGCCTCCGCCTCCACCTCGCCGCCGTCGGCGGTGGCCGGGGCGCCGTTGAGCCAGCGCACCTGGTACACCTCGTTGGTCATGGCGCCCTTGAGCGGAATCACCTGCAGCGCCCGGCAGTCGGCAACGTCCGCCCACGACGCCGCCATCTCGTGCAGTAGCCGCCGCGCCTCCCTGGGGATCCGTGGCTGCGCCGCCGCCTCCGCCGCCCGCTGGCCCTGGCTCTGGTTCTCGATCGCCACCATCCTTGCTAATCACGTCCTTTTACCGTTTTTTTTTCTCTCTCCCTTTTTGCTCGCGATCAAGAAAGAAGAAAAGCTGAAGCGAAGTGGCTAGAGATGAGAAGAGGAATGGCTAATCACGCTTTCTAATTTTTTTTTCTTTTTCTTCGATTTGGATATCTTTCCGAAGCAAGATTAGAGAAAGAGTTGCAAGTAACAAGCGTACTAGCGAGTTTTCCTCCAATCTGATCCGCTATCGCTACGATTCACCCTC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.980189
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0035000.2 1 29843495 A C
Osa01LNT0035000.2 1 29843814 T C
Osa01LNT0035000.2 1 29844148 T C
Osa01LNT0035000.2 1 29844417 T G
Osa01LNT0035000.2 1 29845208 G C
Osa01LNT0035000.2 1 29845796 A C
Osa01LNT0035000.2 1 29846056 G A
Osa01LNT0035000.2 1 29846614 A T
Osa01LNT0035000.2 1 29842922 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
Osa01LNT0035000.2 osa-miR5337b Cleavage 5.0 18.539 1 21
Osa01LNT0035000.2 osa-miR156a Translation 4.5 13.109 1 20
Osa01LNT0035000.2 osa-miR156b-5p Translation 4.5 13.109 1 20
Osa01LNT0035000.2 osa-miR156c-5p Translation 4.5 13.109 1 20
Osa01LNT0035000.2 osa-miR156d Translation 4.5 13.109 1 20
Osa01LNT0035000.2 osa-miR156e Translation 4.5 13.109 1 20
Osa01LNT0035000.2 osa-miR156f-5p Translation 4.5 13.109 1 20
Osa01LNT0035000.2 osa-miR156g-5p Translation 4.5 13.109 1 20
Osa01LNT0035000.2 osa-miR156h-5p Translation 4.5 13.109 1 20
Osa01LNT0035000.2 osa-miR156i Translation 4.5 13.109 1 20
Osa01LNT0035000.2 osa-miR156j-5p Translation 4.5 13.109 1 20
Osa01LNT0035000.2 osa-miR167a-5p Cleavage 5.0 19.356 1 21
Osa01LNT0035000.2 osa-miR167b Cleavage 5.0 19.356 1 21
Osa01LNT0035000.2 osa-miR167c-5p Cleavage 5.0 19.356 1 21
Osa01LNT0035000.2 osa-miR167d-5p Cleavage 5.0 19.356 1 21
Osa01LNT0035000.2 osa-miR167e-5p Cleavage 5.0 19.356 1 21
Osa01LNT0035000.2 osa-miR167f Cleavage 5.0 19.356 1 21
Osa01LNT0035000.2 osa-miR167g Cleavage 5.0 19.356 1 21
Osa01LNT0035000.2 osa-miR167h-5p Cleavage 5.0 19.356 1 21
Osa01LNT0035000.2 osa-miR167i-5p Cleavage 5.0 19.356 1 21
Osa01LNT0035000.2 osa-miR167j Cleavage 5.0 19.356 1 21
Osa01LNT0035000.2 osa-miR820a Cleavage 5.0 20.506 1 21
Osa01LNT0035000.2 osa-miR820b Cleavage 5.0 20.506 1 21
Osa01LNT0035000.2 osa-miR820c Cleavage 5.0 20.506 1 21
Osa01LNT0035000.2 osa-miR1871 Translation 4.5 17.719 1 24
Osa01LNT0035000.2 osa-miR2864.1 Translation 3.0 10.855 1 21
Osa01LNT0035000.2 osa-miR2907a Translation 5.0 12.58 1 22
Osa01LNT0035000.2 osa-miR2907b Translation 5.0 12.58 1 22
Osa01LNT0035000.2 osa-miR2907c Translation 5.0 12.58 1 22
Osa01LNT0035000.2 osa-miR2907d Translation 5.0 12.58 1 22
Osa01LNT0035000.2 osa-miR2919 Cleavage 3.5 12.714 1 19
Osa01LNT0035000.2 osa-miR2919 Cleavage 4.5 19.892 1 19
Osa01LNT0035000.2 osa-miR5338 Cleavage 5.0 14.782 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0035000.2 1 nan Physiological trait Source activity RG532 RM472
Osa01LNT0035000.2 1 An10 Morphological trait Panicle/flower nan nan
Osa01LNT0035000.2 1 brt1d Resistance or Tolerance Drought tolerance C742 C904
Osa01LNT0035000.2 1 rfw1b Resistance or Tolerance Drought tolerance C813 C955
Osa01LNT0035000.2 1 qHUS-1-2 Others Others RM246 RG101
Osa01LNT0035000.2 1 dgl1 Morphological trait Dwarf nan nan
Osa01LNT0035000.2 1 qLRC-1 Resistance or Tolerance Drought tolerance RM237 RM302
Osa01LNT0035000.2 1 yld1.1 Physiological trait Source activity RM5 RG462
Osa01LNT0035000.2 1 nan Morphological trait Root RM3475 RM3494
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