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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattctcttgtaagttcctttaaactcggcattttaggtcttttctactctggttttcatggtcctccatatgcgtatgcgcttccttctgttgcaacagCGGGATACAATTCGGTTAACTACGCACCCAACGGTTCTGGAGGCAAGTATCAAAACCACAAG

Basic information

species Arabidopsis thaliana
transcript AT5G04430.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G04430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv13s0019g05360.t01 (Vitis vinifera), 3'ss of exon 6
-aattctcttgtaagttcctttaaactcggcattttaggtcttttctactctggttttcatggtcctccatatgcgtatgcgcttccttctgttgcaacagCGGGATACAATTCGGTTAACTACGCACCCAACGGTTCTGGAGGCAAGTATCAAAACCACAAG
    |  || |||||||   || || | |  ||||||||| |||||| ||| |||||||| |||  ||||||| | |||| ||||||||||||| ||||||| | |||||||||| | ||||| | ||| || ||  ||||||| |||| ||| ||  |||||
atgatgcctagtaagttttgttgaatttga-attttaggtgttttcttctccggttttcacggtattccatatacatatgtgcttccttctgttccaacagCAGCATACAATTCGATGAACTATGGACCAAATGGGGCTGGAGGAAAGTTTCAGAATAACAAG
















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|163988252|gb|ES195733.1|ES195733
EST:     TGAGGACGATCATTACTCCCAGGATGTGCATTCCCCATATTCATATGCAG                         CGGGATACAATTCGGTTAACTAC
genomic: TGAGGACGATCATTACTCCCAGAATGTGCATTCCCCATATTCATATGCAGgtatatcaac ... gttgcaacagCGGGATACAATTCGGTTAACTAC
EST: gi|125231316|gb|EL245401.1|EL245401
EST:     TGAGGACGATCATTACTCCCAGAATGTGCATTCCCCATATTCATATGCAG                         CGGGATACAATTCGGTTAACTACGCACCCAACG
genomic: TGAGGACGATCATTACTCCCAGAATGTGCATTCCCCATATTCATATGCAGgtatatcaac ... gttgcaacagCGGGATACAATTCGGTTAACTACGCACCCAACG
EST: gi|164172534|gb|EL996392.1|EL996392
EST:     TGAGGACGATCATTACTCCCAGGATGTGCATTCCCCATATTCATATGCAG                         CGGGATACAATTCGGTTAACTAC
genomic: TGAGGACGATCATTACTCCCAGAATGTGCATTCCCCATATTCATATGCAGgtatatcaac ... gttgcaacagCGGGATACAATTCGGTTAACTAC
EST: gi|86078249|gb|DR374006.1|DR374006
EST:     CTCCCAGAATGTGCATTCCCCATATTCATATGCAG                         C-GGATACAATTCGGTTAACTACGCACCCAACGGTTCTGGAGGCAAGTATC
genomic: CTCCCAGAATGTGCATTCCCCATATTCATATGCAGgtatatcaac ... gttgcaacagCGGGATACAATTCGGTTAACTACGCACCCAACGGTTCTGGAGGCAAGTATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactctggttttcatggtcctccatatgcgtatgcgcttccttctgttgcaacagCGGGATACAATTCGGTTAACTACGCACCCAACGGTTCTGGAGGCAAGTATCAAAACCACAAG
                                  cgcttccttctgtt  CT-rich tract
        ttttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattctcttgtaagttcctttaaactcggcattttaggtcttttctactctggttttcatggtcctccatatgcgtatgcgcttccttctgttgcaacagCGGGATACAATTCGGTTAACTACGCACCCAACGGTTCTGGAGGCAAGTATCAAAACCACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - taaactc