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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacagctatattagtataactcaagttgtatgaaagcgtattgttttcatatttatttgttaagttgatgaatcaaacccggaaaattgatcaattgcagCAAGCCTATTTCAAATGTGCATACGAGTGCTTTGACAGAAATAGGAAGCAAGAGGAGATAGCCAACTGTGTTGAGCACTGCAGTGTTCCAGTTGTCAATG

Basic information

species Arabidopsis thaliana
transcript AT1G05730.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G05730.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv05s0077g02200.t01 (Vitis vinifera), 3'ss of exon 1
tacagct---atattagtataactcaagttgtatgaaagcgtattgttttcatatttatttgt-taagttgatgaatcaaacccggaaaattgatcaattgcagCAAGCCTATTTCAAATGTGCATACGAGTGCTTTGACAGAAATAGGAAGCAAGAGGAGATAGCCAACTGTGTTGAGCACTGCAGTGTTCCAGTTGTCAATG
|||   |   ||||| |   |  |    |||| |       |    | ||  | || || ||| ||||||  ||  | ||| | | |  |  ||    ||||||||||| || |||||||| |||||||||||||| || || || || |||||||| || |||  |||||||||||| || ||||||||||||||||| ||||
tactttttgaatatttgaccacttgttattgtctcttgtgattccatattgttcttcatgtgtataagtt--tgtctgaaatctgaatga--gactgcttgcagCAAGCATACTTCAAATGCGCATACGAGTGCTTCGATAGGAAAAGAAAGCAAGAAGAAATAAGCAACTGTGTTGAACATTGCAGTGTTCCAGTTGTTAATG
















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|116377625|gb|EG420217.1|EG420217
EST:     CTCAATCGCAACTCTCTCCTATTCAAGATCACATCAATTTCACCCTTCAG                         CAAGCCTATTTCAAATGTGCATACGAGTGCTTTGACAGAAATAGGAAGCAA
genomic: CTCAATCGCAACTCTCTCCTATTCAAGATCACATCAATTTCACCCTTCAGgtatattaac ... tcaattgcagCAAGCCTATTTCAAATGTGCATACGAGTGCTTTGACAGAAATAGGAAGCAA
EST: gi|116377626|gb|EG420218.1|EG420218
EST:     CTCAATCGCAACTCTCTCCTATTCAAGATCACATCAATTTCACCCTTCAG                         CAAGCCTATTTCAAATGTGCATACGAGTGCTTTGACAGAAATAGGAAGCAA
genomic: CTCAATCGCAACTCTCTCCTATTCAAGATCACATCAATTTCACCCTTCAGgtatattaac ... tcaattgcagCAAGCCTATTTCAAATGTGCATACGAGTGCTTTGACAGAAATAGGAAGCAA
EST: gi|116428202|gb|EG470794.1|EG470794
EST:     AACTCTCTCCTATTCAAGATCACATCAATTTCACCCTTCAG                         CAAGCCTATTTCAAATGTGCATACGAGTGCTTTGACAGAAATAGGAAGCAA
genomic: AACTCTCTCCTATTCAAGATCACATCAATTTCACCCTTCAGgtatattaac ... tcaattgcagCAAGCCTATTTCAAATGTGCATACGAGTGCTTTGACAGAAATAGGAAGCAA
EST: gi|116377623|gb|EG420215.1|EG420215
EST:     CTCAATCGCAACTCTCTCCTATTCAAGATCACATCAATTTCACCCTTCAG                         CAAGCCTATTTCAAATGTGCATACGAGTGCTTTGACAGAAATAGGAAGCAA
genomic: CTCAATCGCAACTCTCTCCTATTCAAGATCACATCAATTTCACCCTTCAGgtatattaac ... tcaattgcagCAAGCCTATTTCAAATGTGCATACGAGTGCTTTGACAGAAATAGGAAGCAA
EST: gi|86060304|gb|DR356061.1|DR356061
EST:     CTCAATCGCAACTCTCTCCTATTCAAGATCACATCAATTTCACCCTTCAG                         CAAGCCTATTTCAAATGTGCATACGAGTGCTTTGACAGAAATAGGAAGCAA
genomic: CTCAATCGCAACTCTCTCCTATTCAAGATCACATCAATTTCACCCTTCAGgtatattaac ... tcaattgcagCAAGCCTATTTCAAATGTGCATACGAGTGCTTTGACAGAAATAGGAAGCAA
EST: gi|116377624|gb|EG420216.1|EG420216
EST:     CTCAATCGCAACTCTCTCCTATTCAAGATCACATCAATTTCACCCTTCAG                         CAAGCCTATTTCAAATGTGCATACGAGTGCTTTGACAGAAATAGGAAGCAA
genomic: CTCAATCGCAACTCTCTCCTATTCAAGATCACATCAATTTCACCCTTCAGgtatattaac ... tcaattgcagCAAGCCTATTTCAAATGTGCATACGAGTGCTTTGACAGAAATAGGAAGCAA
EST: gi|116428201|gb|EG470793.1|EG470793
EST:     CTCAATCGCAACTCTCTCCTATTCAAGATCACATCAATTTCACCCTTCAG                         CAAGCCTATTTCAAATGTGCATACGAGTGCTTTGACAGAAATAGGAAGCAA
genomic: CTCAATCGCAACTCTCTCCTATTCAAGATCACATCAATTTCACCCTTCAGgtatattaac ... tcaattgcagCAAGCCTATTTCAAATGTGCATACGAGTGCTTTGACAGAAATAGGAAGCAA
EST: gi|116377620|gb|EG420212.1|EG420212
EST:     CTCAATCGCAACTCTCTCCTATTCAAGATCACATCAATTTCACCCTTCAG                         CAAGCCTATTTCAAATGTGCATACGAGTGCTTTGACAGAAATAGGAAGCAA
genomic: CTCAATCGCAACTCTCTCCTATTCAAGATCACATCAATTTCACCCTTCAGgtatattaac ... tcaattgcagCAAGCCTATTTCAAATGTGCATACGAGTGCTTTGACAGAAATAGGAAGCAA
EST: gi|116377621|gb|EG420213.1|EG420213
EST:     CTCAATCGCAACTCTCTCCTATTCAAGATCACATCAATTTCACCCTTCAG                         CAAGCCTATTTCAAATGTGCATACGAGTGCTTTGACAGAAATAGGAAGCAA
genomic: CTCAATCGCAACTCTCTCCTATTCAAGATCACATCAATTTCACCCTTCAGgtatattaac ... tcaattgcagCAAGCCTATTTCAAATGTGCATACGAGTGCTTTGACAGAAATAGGAAGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatatttatttgttaagttgatgaatcaaacccggaaaattgatcaattgcagCAAGCCTATTTCAAATGTGCATACGAGTGCTTTGACAGAAATAGGAAGCAAGAGGAGATAGCCAACTGTGTTGAGCACTGCAGTGTTCCAGTTGTCAATG
                                       aattgat  putative branch site (score: 4)
     atttatttgttaagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacagctatattagtataactcaagttgtatgaaagcgtattgttttcatatttatttgttaagttgatgaatcaaacccggaaaattgatcaattgcagCAAGCCTATTTCAAATGTGCATACGAGTGCTTTGACAGAAATAGGAAGCAAGAGGAGATAGCCAACTGTGTTGAGCACTGCAGTGTTCCAGTTGTCAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - -aactcaa
- - - - - - - - - - - - - - - tgaaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaaccc