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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTAGTTACCCTTTGTCTCGGTTCTTGGTGCGTGGTCAATCGGGACTACAGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCACTTCGAGGTGAAAGgttcgttgaatggtaaagttaggtgttcttatgctgtcttggtgttgggctcagtgatttgatttgatttgcttctgtttgatcacag

Basic information

species Oryza sativa
transcript LOC_Os12g40490.1
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|29634158|gb|CB639167.1|CB639167
EST:     TTATAATTGGAGTTTCTTGTGGTATTTTCAGGGTCACTTCGAGGTGAAAG                         CGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTG
genomic: AGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCACTTCGAGGTGAAAGgttcgttgaa ... ttgatcacagCGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTG
EST: gi|88322002|gb|CI673152.1|CI673152
EST:     AGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCACTTCGAGGTGAAAG                         CGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTG
genomic: AGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCACTTCGAGGTGAAAGgttcgttgaa ... ttgatcacagCGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTG
EST: gi|88391277|gb|CI595531.1|CI595531
EST:     AGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCAATTCGAGGTGAAAG                         CGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTG
genomic: AGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCACTTCGAGGTGAAAGgttcgttgaa ... ttgatcacagCGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTG
EST: gi|29632389|gb|CB637398.1|CB637398
EST:     AGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCACTTCGAGGTGAAAG                         CGGACTGAGCGGGAGGCGAGGCGATCGACTGCGAACTGAATTCCTAGTTTG
genomic: AGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCACTTCGAGGTGAAAGgttcgttgaa ... ttgatcacagCGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTG
EST: gi|88733513|gb|CI756690.1|CI756690
EST:     AGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCACTTCGAGGTGAAAG                         CGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTG
genomic: AGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCACTTCGAGGTGAAAGgttcgttgaa ... ttgatcacagCGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTG
EST: gi|88593039|gb|CI711188.1|CI711188
EST:     AGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCACTTCGAGGTGAAAG                         CGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTG
genomic: AGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCACTTCGAGGTGAAAGgttcgttgaa ... ttgatcacagCGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTG
EST: gi|88737536|gb|CI759417.1|CI759417
EST:     AGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCACTTCGAGGTGAAAG                         CGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTG
genomic: AGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCACTTCGAGGTGAAAGgttcgttgaa ... ttgatcacagCGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTG
EST: gi|88367909|gb|CI572630.1|CI572630
EST:     AGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCACTTCGAGGTGAAAG                         CGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTG
genomic: AGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCACTTCGAGGTGAAAGgttcgttgaa ... ttgatcacagCGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTG
EST: gi|88581980|gb|CI699200.1|CI699200
EST:     AGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCACTTCGAGGTGAAAG                         CGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTG
genomic: AGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCACTTCGAGGTGAAAGgttcgttgaa ... ttgatcacagCGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTG
EST: gi|33678894|gb|CF307133.1|CF307133
EST:     AGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCACTTCGAGGTGAAAG                         CGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTG
genomic: AGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCACTTCGAGGTGAAAGgttcgttgaa ... ttgatcacagCGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTG
EST: gi|88826328|gb|CI776893.1|CI776893
EST:     AGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCACTTCGAGGTGAAAG                         CGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTG
genomic: AGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCACTTCGAGGTGAAAGgttcgttgaa ... ttgatcacagCGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTG
EST: gi|88317739|gb|CI672328.1|CI672328
EST:     AGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCACTTCGAGGTGAAAG                         CGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTG
genomic: AGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCACTTCGAGGTGAAAGgttcgttgaa ... ttgatcacagCGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTG
EST: gi|29635157|gb|CB640166.1|CB640166
EST:     AGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCACTTCGAGGTGAAAG                         CGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTG
genomic: AGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCACTTCGAGGTGAAAGgttcgttgaa ... ttgatcacagCGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTG
EST: gi|29630464|gb|CB635473.1|CB635473
EST:     AGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCACTTCGAGGTGAAAG                         CGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTG
genomic: AGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCACTTCGAGGTGAAAGgttcgttgaa ... ttgatcacagCGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTG
EST: gi|29627991|gb|CB633002.1|CB633002
EST:     AGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCACTTCGAGGTGAAAG                         CGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTG
genomic: AGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCACTTCGAGGTGAAAGgttcgttgaa ... ttgatcacagCGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTG
EST: gi|88412122|gb|CI566851.1|CI566851
EST:     AGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCACTTCGAGGTGAAAG                         CGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTG
genomic: AGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCACTTCGAGGTGAAAGgttcgttgaa ... ttgatcacagCGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTG

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: 72 (upstream exon), 51 (downstream exon)
Score: 11

GATTAGTTACCCTTTGTCTCGGTTCTTGGTGCGTGGTCAATCGGGACTACAGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCACTTCGAGGTGAAAGgttcgttgaa ... ttgatcacagCGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAG




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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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTAGTTACCCTTTGTCTCGGTTCTTGGTGCGTGGTCAATCGGGACTACAGAGAATTGGAGTTTCTTGTGGGAGTTTCAGGGTCACTTCGAGGTGAAAGgttcgttgaatggtaaagttaggtgttcttatgctgtcttggtgttgggctcagtgatttgatttgatttgcttctgtttgatcacag

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