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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattcccatgcttgatagtagattgaatttcatagtgaagcattagtaaaagttgcacaagttttttttaaaggaaaaacaaaatgatatactgttgcagGCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGAGGGGTTACCAGCTGCCCCGTGACTCCCGGGGATCACTCGAGGTGTTCAA

Basic information

species Oryza sativa
transcript LOC_Os11g01140.3
intron # 1
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|88827258|gb|CI777823.1|CI777823
EST:     TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAG                         GCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
genomic: TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAGgtatgtacta ... actgttgcagGCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
EST: gi|88824890|gb|CI775455.1|CI775455
EST:     TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAG                         GCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
genomic: TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAGgtatgtacta ... actgttgcagGCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
EST: gi|88387658|gb|CI585361.1|CI585361
EST:     TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAG                         GCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
genomic: TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAGgtatgtacta ... actgttgcagGCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
EST: gi|88571917|gb|CI663290.1|CI663290
EST:     TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAG                         GCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
genomic: TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAGgtatgtacta ... actgttgcagGCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
EST: gi|88385258|gb|CI630359.1|CI630359
EST:     TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAG                         GCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
genomic: TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAGgtatgtacta ... actgttgcagGCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
EST: gi|29635046|gb|CB640055.1|CB640055
EST:     TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAG                         GCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
genomic: TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAGgtatgtacta ... actgttgcagGCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
EST: gi|88733019|gb|CI756196.1|CI756196
EST:     TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAG                         GCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
genomic: TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAGgtatgtacta ... actgttgcagGCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
EST: gi|88316759|gb|CI624201.1|CI624201
EST:     TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAG                         GCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
genomic: TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAGgtatgtacta ... actgttgcagGCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
EST: gi|88311599|gb|CI574816.1|CI574816
EST:     TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAG                         GCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
genomic: TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAGgtatgtacta ... actgttgcagGCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
EST: gi|88397020|gb|CI593232.1|CI593232
EST:     TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCGATGGCTTCCAAAG                         GCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
genomic: TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAGgtatgtacta ... actgttgcagGCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
EST: gi|88327366|gb|CI645149.1|CI645149
EST:     TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAG                         GCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
genomic: TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAGgtatgtacta ... actgttgcagGCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
EST: gi|571767|gb|D41278.1|D41278
EST:     TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATNCATGGCTTCCAAAG                         GCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
genomic: TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAGgtatgtacta ... actgttgcagGCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
EST: gi|88305657|gb|CI632024.1|CI632024
EST:     TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAG                         GCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
genomic: TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAGgtatgtacta ... actgttgcagGCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
EST: gi|88412022|gb|CI566751.1|CI566751
EST:     TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAG                         GCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
genomic: TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAGgtatgtacta ... actgttgcagGCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
EST: gi|88572958|gb|CI664529.1|CI664529
EST:     TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAG                         GCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
genomic: TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAGgtatgtacta ... actgttgcagGCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
EST: gi|3759015|gb|C96714.1|C96714
EST:     TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAG                         GCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
genomic: TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAGgtatgtacta ... actgttgcagGCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
EST: gi|88311077|gb|CI657990.1|CI657990
EST:     TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAG                         GCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
genomic: TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAGgtatgtacta ... actgttgcagGCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
EST: gi|88337638|gb|CI632140.1|CI632140
EST:     TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAG                         GCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
genomic: TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAGgtatgtacta ... actgttgcagGCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
EST: gi|88724881|gb|CI748140.1|CI748140
EST:     TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAG                         GCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
genomic: TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAGgtatgtacta ... actgttgcagGCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
EST: gi|88403118|gb|CI570859.1|CI570859
EST:     TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAG                         GCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
genomic: TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAGgtatgtacta ... actgttgcagGCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
EST: gi|88363311|gb|CI643169.1|CI643169
EST:     TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAG                         GCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
genomic: TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAGgtatgtacta ... actgttgcagGCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
EST: gi|88376993|gb|CI597777.1|CI597777
EST:     TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAG                         GCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
genomic: TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAGgtatgtacta ... actgttgcagGCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
EST: gi|88733869|gb|CI755379.1|CI755379
EST:     TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAG                         GCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA
genomic: TAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAGgtatgtacta ... actgttgcagGCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGA

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: 45 (upstream exon), 52 (downstream exon)
Score: 8

ATTAATTTGAGTTGAGATCGACTTGAGAGCTAGCAGAGGCTCATCTCATCTAGGCCAGCAGAGGCTCTTCGCTCGCTTATTTCATCCATGGCTTCCAAAGgtatgtacta ... actgttgcagGCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGAGGGGTTACCAGCTGCCCCGTGACTCCCGGGGATCACTCGAGGTGTTCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaaagttgcacaagttttttttaaaggaaaaacaaaatgatatactgttgcagGCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGAGGGGTTACCAGCTGCCCCGTGACTCCCGGGGATCACTCGAGGTGTTCAA
                ttttttttaaaggaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattcccatgcttgatagtagattgaatttcatagtgaagcattagtaaaagttgcacaagttttttttaaaggaaaaacaaaatgatatactgttgcagGCACAGAAGGAGGCCATGGTGGCGTGGAGAGAAAGGAGCAGCAGCAGCAGAGGGGTTACCAGCTGCCCCGTGACTCCCGGGGATCACTCGAGGTGTTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - -atgcttg
- - - - - - - - - - - - - - - - - -tgaagca
- - - - - - - - - - - - - - - - - - - - - - agtaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - -gttgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacaaa