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

>Osa01LNT0029900.2

CCCGTTTTAACTTACAACAGTGAGGTGCATACCCACAAACCCACTCATATCTTGGGTCAAAATATTCTACAAGCATGAGGGCTCGGGAATTGTCTAAATTTTAATCATAAACTCACTAAAGTTAAGGCCACTTTGTTCTGTAACAATGCTGGCCTGCAATTTTGTCAGGAGACCAGGAGAGCATCCGTCTTACATATTACCAGTATTGTGTATGATCTCATACAGTTGATCAGATCTATGGTATTATGATAAGATAAACTCAAAAAAAAAAAAGAGACATTTCCATATAAAGGAGTTATACAAAGCCATAATATAGTGTCATGGAATACAGGGTTCTTGAGAACAAAACAATGGACAAGATCGTCCACAAAAAGCGGCAAACCTTAAGAATATTGCGCTGCTGTCTCCGAGTAAACCAAGAAAAGTAGCTTAACATAGTCTCCAAAATCGCTTCCCCGTCAAGAAAGTACACTGGTAAGCAATTGACTACAGCCAATGCTGCAGACACACGAAATAAACAACTTAAACCATCTTGCAAGATACGAGGAACATCTGCAATGAAAAGCAAGAGAGGCCATCGAGGTCGGTAAGAGGATAACTTAATAGAATGTGCTGCTGATAACAGATCACCCGCATAAACAAAAGTTCCCTGGCAAGGACCCAATCCAGGGTTATTATTTCCATCATGCAGCAATGATGAGTTCCTTTCTTTCTGTAAGCACTCCAAAGAATAAGGTCTGGCATAAGAGATCTCTATCCATGAAATCCCAGGGCCTAGAACAGGCACCAAACAGTACTCATCCTCCAAACATGCAAAGTTGCTTCTGCCATCTTCGGCCCCCCGCCATCCATTTCCACATTTTTTAAGCTTGACAACATCTTTTGCAATCAAACAATATTTGTCTTCAACTTCCTTCTTGCCAATACCTTTCTCACTCATTCTTTGAAAGGCTACCAGATCATCTGGGCAAGATAGCTTGTCATTTATCTGCCAAAGATTCTTGCTTGCATCCATCCATGAGTTGGGAACACAGTAACCCTTTCTAGAACCAGTGGCACGATAGCCTTCAGAGCCTTCAAGGAGATCACGGCTGCTTATTTGTACTACATTGTCCTGAGTAAGCATTTTCATCCATTCATCAGCTCTTGTTATGTTCAATCCATCCACAGAAAGGATAAAATTGTGAGCAGACAAGTATCCTGACAGAGGAGATGCTTCTGGGACTCCTGTAATCATAAGACCACCAGTCACAAAGAGAGGATACAGCACCACAGGTAGTAATAATGCCATGATGACACATACTCCACATAACATAACATTATGCCAAATCCCTGCACAATAAATCCGAAGCATAGAAAAAAGAGGTAAATTTTGCAGCTGGTCACAGTTCAGAGCAATTAATGCCCCAGGAAAAAGTGCAGCTACGAATACCGCAACATACTCAATCTGTATGCCCTCGCTTCTGCAAATGAATGCAAACACATGCAGAACATCTCGTAGAAAATGTAGGTCAGCAAATAAGGACCTTGCAGCTGCAACAGCATGTCCAAATTCGTGAAAAGCAATAGAAAAAACTGTTGATGCTATGATTGCTGCGATGTCCATTATTGATATGCCAAAGCTGGAAGCCAGTAGATTTTGTAGCCAGGTACTAAATGACCGACCACTGAAATAAACTGCACCAATTGAGTCCCACAATAGCATCACTGATATTCCAACTAAAGCAACAACAGAGAAATAAACCCCTGCAGAAAACCATGCTCTCATGTATCTAGCATATCTCCATCCCAAATTAAATATGATGTCATTGAAGGAATATATTTTGCAGTCACAGTACCAGCAAGAGACGGAGTGCTCGGCGCGGCGGGCGGCGGCGCTCGAGGGCAGAACTGGCGGCGCACGGCCACGCCGCCTGCTGCGGCCGACGCCGCCGATCATTCCAGCGGCGACGGCGACGGCTTGG

Coding Potentia
Explanation CPC Score
noncoding -1.12229
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0029900.2 1 26523006 T C
Osa01LNT0029900.2 1 26523104 T A
Osa01LNT0029900.2 1 26523741 G A
Osa01LNT0029900.2 1 26524249 A G
Osa01LNT0029900.2 1 26524291 T A
Osa01LNT0029900.2 1 26525085 A G
Osa01LNT0029900.2 1 26526347 G A
Osa01LNT0029900.2 1 26527116 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
Osa01LNT0029900.2 osa-miR443 Translation 3.5 14.68 1 22
Osa01LNT0029900.2 osa-miR1435 Cleavage 4.5 13.51 1 20
Osa01LNT0029900.2 osa-miR1856 Cleavage 5.0 19.951 1 21
Osa01LNT0029900.2 osa-miR1876 Cleavage 3.5 17.59 1 24
Osa01LNT0029900.2 osa-miR2864.2 Cleavage 4.0 17.349 1 21
Osa01LNT0029900.2 osa-miR5507 Cleavage 5.0 18.645 1 21
Osa01LNT0029900.2 osa-miR5507 Translation 5.0 11.63 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0029900.2 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0029900.2 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0029900.2 1 QPh1b Resistance or Tolerance Submergency tolerance RZ527 RZ154
Osa01LNT0029900.2 1 nan Physiological trait Source activity RG532 RM472
Osa01LNT0029900.2 1 nan Morphological trait Seed CDO118 CDO455
Osa01LNT0029900.2 1 brt1d Resistance or Tolerance Drought tolerance C742 C904
Osa01LNT0029900.2 1 rfw1b Resistance or Tolerance Drought tolerance C813 C955
Osa01LNT0029900.2 1 yld1.1 Physiological trait Source activity RM5 RG462
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