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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtgtcaacttattcaatctttttttttcaagtattcatcgtgcaatacccaagcaggaaattcattgctttgagtttctcctattcttacaacaatcctgtgatcgtagcaattattaacctttacatgagaatgcttgttaaatttctgttcttttttttctttcacaacagAGAGCTTTGGCCCTTCACAAGAATCAGACAGCAAAGATTGTTTCTCCTACCCACTCGATTCTCGAGACTGACAGGAAGACATACTTACCAGAAGATAATC

Basic information

species Oryza sativa
transcript LOC_Os01g46710.1
intron # 4
splice site 3'
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|88578643|gb|CI687585.1|CI687585
EST:     TGTTGGGTTCACATAACCTTAAAAACAAGAGTGATATCTTTCAG                         AGAGCTTTGGCCCTTCACAAGAATCAGACAGCAAAGATTGTTTCTCCTACC
genomic: TGTTGGGTTCACATAACCTTAAAAACAAGAGTGATATCTTTCAGgcaagtgtca ... ttcacaacagAGAGCTTTGGCCCTTCACAAGAATCAGACAGCAAAGATTGTTTCTCCTACC
EST: gi|88588631|gb|CI706464.1|CI706464
EST:     TGTTGGGTTCACATAACCTTAAAAACAAGAGTGATATCTTTCAG                         AGAGCTTTGGCCCTTCACAAGAATCAGACAGCAAAGATTGTTTCTCCTACC
genomic: TGTTGGGTTCACATAACCTTAAAAACAAGAGTGATATCTTTCAGgcaagtgtca ... ttcacaacagAGAGCTTTGGCCCTTCACAAGAATCAGACAGCAAAGATTGTTTCTCCTACC
EST: gi|88436662|gb|CI691394.1|CI691394
EST:     TGTTGGGTTCACATAACCTTAAAAACAAGAGTGATATCTTTCAG                         AGAGCTTTGGCCCTTCACAAGAATCAGACAGCAAAGATTGTTTCTCCTACC
genomic: TGTTGGGTTCACATAACCTTAAAAACAAGAGTGATATCTTTCAGgcaagtgtca ... ttcacaacagAGAGCTTTGGCCCTTCACAAGAATCAGACAGCAAAGATTGTTTCTCCTACC
EST: gi|88852018|gb|CI683536.1|CI683536
EST:     TGTTGGGTTCACATAACCTTAAAAACAAGAGTGATATCTTTCAG                         AGAGCTTTGGCCCTTCACAAGAATCAGACAGCAAAGATTGTTTCTCCTACC
genomic: TGTTGGGTTCACATAACCTTAAAAACAAGAGTGATATCTTTCAGgcaagtgtca ... ttcacaacagAGAGCTTTGGCCCTTCACAAGAATCAGACAGCAAAGATTGTTTCTCCTACC
EST: gi|88852047|gb|CI683565.1|CI683565
EST:     TGTTGGGTTCACATAACCTTAAAAACAAGAGTGATATCTTTCAG                         AGAGCTTTGGCCCTTCACAAGAATCAGACAGCAAAGATTGTTTCTCCTACC
genomic: TGTTGGGTTCACATAACCTTAAAAACAAGAGTGATATCTTTCAGgcaagtgtca ... ttcacaacagAGAGCTTTGGCCCTTCACAAGAATCAGACAGCAAAGATTGTTTCTCCTACC
EST: gi|568900|gb|D39749.1|D39749
EST:     CCAATCTGTTGGGTTCACATAACCTTAAAAACAAGAGTGATATCTTTCAG                         AGAGCTTTGGCCCTTCACAAGAATCAGACAGCAAAGATTGTTTCTCCTACC
genomic: CCAATCTGTTGGGTTCACATAACCTTAAAAACAAGAGTGATATCTTTCAGgcaagtgtca ... ttcacaacagAGAGCTTTGGCCCTTCACAAGAATCAGACAGCAAAGATTGTTTCTCCTACC
EST: gi|29658224|gb|CB654499.1|CB654499
EST:     CCAATCTGTTGGGTTCACATAACCTTAAAAACAAGAGTGATATCTTTCAG                         AGAGCTTTGGCCCTTCACAAGAATCAGACAGCAAAGATTGTTTCTCCTACC
genomic: CCAATCTGTTGGGTTCACATAACCTTAAAAACAAGAGTGATATCTTTCAGgcaagtgtca ... ttcacaacagAGAGCTTTGGCCCTTCACAAGAATCAGACAGCAAAGATTGTTTCTCCTACC

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: 58 (upstream exon), 73 (downstream exon)
Score: 29

AACAATGGAAGCTTTGGGAAGATAAATAGAAAACTTGGAACCCCCAATCTGTTGGGTTCACATAACCTTAAAAACAAGAGTGATATCTTTCAGgcaagtgtca ... ttcacaacagAGAGCTTTGGCCCTTCACAAGAATCAGACAGCAAAGATTGTTTCTCCTACCCACTCGATTCTCGAGACTGACAGGAAGACATACTTACCAGAAGATAATC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctttacatgagaatgcttgttaaatttctgttcttttttttctttcacaacagAGAGCTTTGGCCCTTCACAAGAATCAGACAGCAAAGATTGTTTCTCCTACCCACTCGATTCTCGAGACTGACAGGAAGACATACTTACCAGAAGATAATC
 tattaac  putative branch site (score: 29)
                     ttaaatttctgttctt  putative PPT
                     ttaaatttctgttctt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagtgtcaacttattcaatctttttttttcaagtattcatcgtgcaatacccaagcaggaaattcattgctttgagtttctcctattcttacaacaatcctgtgatcgtagcaattattaacctttacatgagaatgcttgttaaatttctgttcttttttttctttcacaacagAGAGCTTTGGCCCTTCACAAGAATCAGACAGCAAAGATTGTTTCTCCTACCCACTCGATTCTCGAGACTGACAGGAAGACATACTTACCAGAAGATAATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA