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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACATCAAGCGACCTAAATATCTCCAAGCTCAAGCAGCCATTGACTATGGAATTGCAGACAAGATAGCTGACTCGCAGGACAGTTCTTTCGAGAAACGGgtaactttcaaaattatacttttatattcacccaaaaccaagtgatctttttgttgacttcattcatgcttaaatggaaaatatatctgggtttag

Basic information

species Arabidopsis thaliana
transcript AT1G49970.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G49970.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: Vv03s0091g00700.t01 (Vitis vinifera), 5'ss of exon 8
GGACATCAAGCGACCTAAATATCTCCAAGCTCAAGCAGCCATTGACTATGGAATTGCAGACAAGATAGCTGACTCGCAGGACAGTTCTTTCGAGAAACGGgtaa----ctttcaaaattatacttttatattcacccaaaaccaagtgatctttttgttgacttcattcatgcttaaatggaaaatatatctgggtttag
 ||  || | || || |||||| | ||||| |||| |||||||||||||||  ||||||||||||||  |  |||   |||     | |  |||||||||||||    |||   ||||| | || |    ||     || | ||  || | |   |||  | |  |    |  ||   |    |  |             
AGATGTCGAACGCCCAAAATATTTGCAAGCACAAGAAGCCATTGACTATGGCCTTGCAGACAAGATAATTAGCTCAATGGATCCAGCATATGAGAAACGGgtaaaactcttattaaatttttctctcccgttttgttaacatcacttgctttccatgtctattctaacagtattttgttactgatcag------------
















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|86082322|gb|DR378081.1|DR378081
EST:     GAATTGCAGACAAGATAGCTGACTCGCAGGACAGTTCTTTCGAGAAACGG                         GATTACGATGGGACCCTTGCCCAGAGAGCTATGAGACCTGGAGGAGGCAGT
genomic: GAATTGCAGACAAGATAGCTGACTCGCAGGACAGTTCTTTCGAGAAACGGgtaactttca ... ctgggtttagGATTACGATGGGACCCTTGCCCAGAGAGCTATGAGACCTGGAGGAGGCAGT
EST: gi|86080505|gb|DR376262.1|DR376262
EST:     GAATTGCAGACAAGATAGCTGACTCGCAGGACAGTTCTTTCGAGAAACGG                         GATTACGATGGGACCCTTGCCCAGAGAGCTATGAGACCTGGAGGAGGCAGT
genomic: GAATTGCAGACAAGATAGCTGACTCGCAGGACAGTTCTTTCGAGAAACGGgtaactttca ... ctgggtttagGATTACGATGGGACCCTTGCCCAGAGAGCTATGAGACCTGGAGGAGGCAGT
EST: gi|125185729|gb|EL200683.1|EL200683
EST:     GAATTGCAGACAAGATAGCTGACTCGCAGGACAGTTCTTTCGAGAAACGG                         GATTACGATGGGACCCTTGCCCAGAGAGCTATGAGA
genomic: GAATTGCAGACAAGATAGCTGACTCGCAGGACAGTTCTTTCGAGAAACGGgtaactttca ... ctgggtttagGATTACGATGGGACCCTTGCCCAGAGAGCTATGAGA
EST: gi|86078722|gb|DR374479.1|DR374479
EST:     GAATTGCAGACAAGATAGCTGACTCGCAGGACAGTTCTTTCGAGAAACGG                         GATTACGATGGGACCCTTGCCCAGAGAGCTATGAGACCTGGATGAGGCAGT
genomic: GAATTGCAGACAAGATAGCTGACTCGCAGGACAGTTCTTTCGAGAAACGGgtaactttca ... ctgggtttagGATTACGATGGGACCCTTGCCCAGAGAGCTATGAGACCTGGAGGAGGCAGT

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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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGACATCAAGCGACCTAAATATCTCCAAGCTCAAGCAGCCATTGACTATGGAATTGCAGACAAGATAGCTGACTCGCAGGACAGTTCTTTCGAGAAACGGgtaactttcaaaattatacttttatattcacccaaaaccaagtgatctttttgttgacttcattcatgcttaaatggaaaatatatctgggtttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA