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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaatgggtctgatgaattgtgttcctgcttggttatctgacaatgcccttagaatatagaaaccacggaagatgttttgacatacacatatacttgcagGCTTGTATAGGATCCAAGGTGATTGCTAGTGAAGCACTCTCAGCAATCAGAAAAGATGTTTTGGCAAAATGTTATG

Basic information

species Arabidopsis thaliana
transcript AT5G08650.1
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G08650.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: LOC_Os02g06300.1 (Oryza sativa), 3'ss of exon 19
caaatgggtctgatgaattgtgttcctgcttggttatct---gacaatgc--ccttagaatatagaaaccacggaagatgttttgacatacacatatacttgcagGCTTGTATAGGATCCAAGGTGATTGCTAGTGAAGCACTCTCAGCAATCAGAAAAGATGTTTTGGCAAAATGTTATG
  ||   ||  ||  |     ||  |    |  | ||     |||||  |  | | |  || |   ||  | | | ||| || | ||    || |    |  ||||| ||||||||  | ||||| ||||| ||||||||||| ||||| ||||| || ||||| ||| ||||||| ||||
-taacttgttggaaaacagaagtagccatctattcatgaggagacaaaactgcttaattatctcttaattaggaatgatattctaactaggactt----tgacagGCATGTATAGGTGCAAAGGTCATTGCAAGTGAAGCACTATCAGCCATCAGGAAGGATGTCTTGTCAAAATGCTATG
















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|124775102|gb|EH865231.1|EH865231
EST:     AGAAACTCAAAGAGCTTATTCCACGACAAATGTTTAAAGTGCCCATCCAG                         GCTTGTATAGGATCCAAGGTGATTGCTA
genomic: AGAAACTCAAAGAGCTTATTCCACGACAAATGTTTAAAGTGCCCATCCAGgtatatatct ... atacttgcagGCTTGTATAGGATCCAAGGTGATTGCTA
EST: gi|124783280|gb|EH873140.1|EH873140
EST:     TGCCCATCCAG                         GCTTGTATAGGATCCAAGGTGATTGCTAGTGAAGCACTCTCAGCAATCA
genomic: TGCCCATCCAGgtatatatct ... atacttgcagGCTTGTATAGGATCCAAGGTGATTGCTAGTGAAGCACTCTCAGCAATCA
EST: gi|125243955|gb|EL258040.1|EL258040
EST:     AGAAACTCAAAGAGCTTATTCCACGACAAATGTTTAAAGTGCCCATCCAG                         GCTTGTATAGGATCCAAGGTGATTGCTAGTGAAG
genomic: AGAAACTCAAAGAGCTTATTCCACGACAAATGTTTAAAGTGCCCATCCAGgtatatatct ... atacttgcagGCTTGTATAGGATCCAAGGTGATTGCTAGTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcccttagaatatagaaaccacggaagatgttttgacatacacatatacttgcagGCTTGTATAGGATCCAAGGTGATTGCTAGTGAAGCACTCTCAGCAATCAGAAAAGATGTTTTGGCAAAATGTTATG
                              ttttgac  putative branch site (score: 3)
        aatatagaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaatgggtctgatgaattgtgttcctgcttggttatctgacaatgcccttagaatatagaaaccacggaagatgttttgacatacacatatacttgcagGCTTGTATAGGATCCAAGGTGATTGCTAGTGAAGCACTCTCAGCAATCAGAAAAGATGTTTTGGCAAAATGTTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atacaca