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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAAATCAGGATCATTGTTCGACAATGTCTTGATCTGCGATGACCCAGACTATGCCAAGAAGTTGGCAGATGAAACATGGGGAAAGCTCAAGGATgtaggtgtttaaaatacccaatttcataacacagtttttttttttttgtttctggttactgatcagaatatccaatctaatatcacattgcag

Basic information

species Arabidopsis thaliana
transcript AT1G09210.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G09210.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv14s0060g01290.t01 (Vitis vinifera), 5'ss of exon 10
GTGAAATCAGGATCATTGTTCGACAATGTCTTGATCTGCGATGACCCAGACTATGCCAAGAAGTTGGCAGATGAAACATGGGGAAAGCTCAAGGATgtaggtgtttaaaatacccaattt---cataacacagtttttttttttttg--tttctggttactgatcagaatatccaatctaatat-cacattgcag
|||||||||||  | |||||||||||||||||||| || ||||| || || ||||| ||| | |||| ||| ||||||||||  |||  |||||||||| ||| |        |   |||   ||  | | ||    ||||   |    ||| |  |  |||    || | |  ||| |  | |     ||||||
GTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGATgtatgtgatgctgccttctgcttttgccaccatatagcgcattttccatcagatttttcatatctgggttgatt-tttaattttgtgtatgttttgcag
















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|164065146|gb|ES135752.1|ES135752
EST:     CAGACTATGCCAAGAAGTTGGCAGATGAAACATGGGGAAAGCTCAAGGAT                         GCGGAGAAAGCAGCTTTCGATGAGGCTGAGAAGAAGAATGAGGAA
genomic: CAGACTATGCCAAGAAGTTGGCAGATGAAACATGGGGAAAGCTCAAGGATgtaggtgttt ... cacattgcagGCGGAGAAAGCAGCTTTCGATGAGGCTGAGAAGAAGAATGAGGAA
EST: gi|116412926|gb|EG455518.1|EG455518
EST:     CAGACTATGCCAAGAAGTTGGCAGATGAAACATGGGGAAAGCTCAAGGAT                         GCGGAGAAAGCAGCTTTCGATGAGGCTGAGAAGAAGAATGAGGAAGAG
genomic: CAGACTATGCCAAGAAGTTGGCAGATGAAACATGGGGAAAGCTCAAGGATgtaggtgttt ... cacattgcagGCGGAGAAAGCAGCTTTCGATGAGGCTGAGAAGAAGAATGAGGAAGAG
EST: gi|164035205|gb|ES155213.1|ES155213
EST:     CTATGCCAAGAAGTTGGCAGATGAAACATGGGGAAAGCTCAAGGAT                         GCGGAGAAAGCAGCTTTCGATGAGGCTGAGAAGAAGAATGAGGAAGA
genomic: CTATGCCAAGAAGTTGGCAGATGAAACATGGGGAAAGCTCAAGGATgtaggtgttt ... cacattgcagGCGGAGAAAGCAGCTTTCGATGAGGCTGAGAAGAAGAATGAGGAAGA
EST: gi|125077249|gb|EL140106.1|EL140106
EST:     CAGACTATGCCAAGAAGTTGGCAGATGAAACATGGGGAAAGCTCAAGGAT                         GCGGAGAAAGCAG
genomic: CAGACTATGCCAAGAAGTTGGCAGATGAAACATGGGGAAAGCTCAAGGATgtaggtgttt ... cacattgcagGCGGAGAAAGCAG
EST: gi|124749901|gb|EH840031.1|EH840031
EST:     CAGACTATGCCAAGAAGTTGGCAGATGAAACATGGGGAAAGCTCAAGGAT                         GCGGAGAAAGCAG
genomic: CAGACTATGCCAAGAAGTTGGCAGATGAAACATGGGGAAAGCTCAAGGATgtaggtgttt ... cacattgcagGCGGAGAAAGCAG
EST: gi|86078431|gb|DR374188.1|DR374188
EST:     CAGACTATGCCAAGAAGTTGGCAGATGAAACATGGGGAAAGCTCAAGGAT                         GCGGAGAAAGCAGCTTTCGATGAGGCTGAGAAGAAGAATGAGGAAGAG
genomic: CAGACTATGCCAAGAAGTTGGCAGATGAAACATGGGGAAAGCTCAAGGATgtaggtgttt ... cacattgcagGCGGAGAAAGCAGCTTTCGATGAGGCTGAGAAGAAGAATGAGGAAGAG
EST: gi|116412928|gb|EG455520.1|EG455520
EST:     CAGACTATGCCAAGAAGTTGGCAGATGAAACATGGGGAAAGCTCAAGGAT                         GCGGAGAAAGCAGCTTTCGATGAGGCTGAGAAGAAGAATGAGGAAGAG
genomic: CAGACTATGCCAAGAAGTTGGCAGATGAAACATGGGGAAAGCTCAAGGATgtaggtgttt ... cacattgcagGCGGAGAAAGCAGCTTTCGATGAGGCTGAGAAGAAGAATGAGGAAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGAAATCAGGATCATTGTTCGACAATGTCTTGATCTGCGATGACCCAGACTATGCCAAGAAGTTGGCAGATGAAACATGGGGAAAGCTCAAGGATgtaggtgtttaaaatacccaatttcataacacagtttttttttttttgtttctggttactgatcagaatatccaatctaatatcacattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA