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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCCGCCGCCACCAGGCTGCTAGGGTTTTCGGCACCGAGCTCGCGCCGCCGCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATGgtcagaatccccgtgtctcgtccttctctcctcctactctttgccctgtttagattttgcttgtttcttgccatttctgtagttgcctagatcgtgcacg...

Basic information

species Oryza sativa
transcript LOC_Os07g26740.1
intron # 1
splice site 5'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|58599599|gb|CK010127.1|CK010127
EST:     GCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATG                         GTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
genomic: GCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATGgtcagaatcc ... tgttttttagGTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
EST: gi|88330761|gb|CI636769.1|CI636769
EST:     GCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATG                         GTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
genomic: GCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATGgtcagaatcc ... tgttttttagGTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
EST: gi|88742622|gb|CI766130.1|CI766130
EST:     GCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATG                         GTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
genomic: GCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATGgtcagaatcc ... tgttttttagGTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
EST: gi|88310008|gb|CI657432.1|CI657432
EST:     GCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATG                         GTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
genomic: GCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATGgtcagaatcc ... tgttttttagGTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
EST: gi|88575814|gb|CI669959.1|CI669959
EST:     GCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATG                         GTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
genomic: GCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATGgtcagaatcc ... tgttttttagGTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
EST: gi|2311208|gb|C27363.1|C27363
EST:     GGGAGAGGAACCCAAAGCTCGGCGCCATG                         GTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
genomic: GGGAGAGGAACCCAAAGCTCGGCGCCATGgtcagaatcc ... tgttttttagGTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
EST: gi|88330344|gb|CI633550.1|CI633550
EST:     GCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATG                         GTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
genomic: GCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATGgtcagaatcc ... tgttttttagGTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
EST: gi|88336818|gb|CI644245.1|CI644245
EST:     GCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATG                         GTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
genomic: GCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATGgtcagaatcc ... tgttttttagGTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
EST: gi|88349588|gb|CI653867.1|CI653867
EST:     GCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATG                         GTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
genomic: GCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATGgtcagaatcc ... tgttttttagGTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
EST: gi|425966|gb|D22649.1|D22649
EST:     GCCATCGCACCCACCGAA-GAGGGAGAGGAACCCAAAGCTCGGCGCCATG                         GTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
genomic: GCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATGgtcagaatcc ... tgttttttagGTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
EST: gi|88575707|gb|CI669852.1|CI669852
EST:     GCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATG                         GTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
genomic: GCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATGgtcagaatcc ... tgttttttagGTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
EST: gi|88423189|gb|CI613490.1|CI613490
EST:     GCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATG                         GTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
genomic: GCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATGgtcagaatcc ... tgttttttagGTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
EST: gi|88427254|gb|CI586802.1|CI586802
EST:     GCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATG                         GTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
genomic: GCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATGgtcagaatcc ... tgttttttagGTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
EST: gi|286577|gb|D15384.1|D15384
EST:     GCCATCGCACCCACCGAA-GAGGGAGAGGAACCCAAAGCTCGGCGCCATG                         GTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
genomic: GCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATGgtcagaatcc ... tgttttttagGTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
EST: gi|88332629|gb|CI651789.1|CI651789
EST:     GCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATG                         GTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
genomic: GCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATGgtcagaatcc ... tgttttttagGTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
EST: gi|88364533|gb|CI644611.1|CI644611
EST:     GCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATG                         GTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
genomic: GCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATGgtcagaatcc ... tgttttttagGTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
EST: gi|88382288|gb|CI633146.1|CI633146
EST:     GCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATG                         GTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
genomic: GCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATGgtcagaatcc ... tgttttttagGTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
EST: gi|87012754|gb|CI295198.1|CI295198
EST:     GCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATG                         GTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG
genomic: GCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATGgtcagaatcc ... tgttttttagGTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 57 (upstream exon), 70 (downstream exon)
Score: 21

AGCCGCCGCCACCAGGCTGCTAGGGTTTTCGGCACCGAGCTCGCGCCGCCGCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATGgtcagaatcc ... tgttttttagGTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGGAAGCACACCCTACACAAGGTTACCCAGTACAAGAAAGGAAAGGATAGCC




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCCGCCGCCACCAGGCTGCTAGGGTTTTCGGCACCGAGCTCGCGCCGCCGCCATCGCACCCACCGAAGGAGGGAGAGGAACCCAAAGCTCGGCGCCATGgtcagaatccccgtgtctcgtccttctctcctcctactctttgccctgtttagattttgcttgtttcttgccatttctgtagttgcctagatcgtgcacg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcctcc