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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATTGATCTCAAAAAGGTGGACAAGTGTATCGGAGACCCTGAAGCAGATGTGGAGAACCCAGTTCTTAAAGCAGAGCAGGAGTCACAGgtttgcctttttgtaactaattggctcttacacgtcttcccaagatcttgttggttttaagttgccatatattctccattcctcgaggtgttcttaaaatgagtctacttcaatttcag

Basic information

species Arabidopsis thaliana
transcript AT3G52850.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G52850.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv08s0058g01360.t01 (Vitis vinifera), 5'ss of exon 3
GCATTGATCTCAAAAAGGTGGACAAGTGTATCGGAGACCCTGAAGCAGATGTGGAGAACCCAGTTCTTAAAGCAGAGCAGGAGTCACAGgttt----gcctttttgtaactaattggctcttacacgtcttcccaagatcttgttggttttaagttgccatatattctccattcctcgaggtgttcttaaaatgagtctacttcaatttcag
|  ||||| |||| ||| | ||| | ||||| ||||||||||| ||||||||||| || |||||||||||||| || |||||  |||||||      | || | | | ||||||   ||  || |     | |  |||| ||| || ||     |||   | |||| |   |   |     | |||||  | |   |   |||||       
GTGTTGATGTCAAGAAGATAGACCAATGTATTGGAGACCCTGAGGCAGATGTGGATAATCCAGTTCTTAAAGCTGAACAGGATGCACAGgtgaaagagactatctatgactaatactcttgtatattgtcttctcagattttgctgctt---gcttgtattttattgtttgtgattttccattttctttgagt--tttggcttcag------
















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|125264348|gb|EL278433.1|EL278433
EST:     GATGTGGAGAACCCAGTTCTTAAAGCAGAGCAGGAGTCACAG                         ATAGGCAAAGGTTCCCGTGGAGACGTGACTATACTCCCAACTCTTGTCGCG
genomic: GATGTGGAGAACCCAGTTCTTAAAGCAGAGCAGGAGTCACAGgtttgccttt ... tcaatttcagATAGGCAAAGGTTCCCGTGGAGACGTGACTATACTCCCAACTCTTGTCGTG
EST: gi|124723100|gb|EH814502.1|EH814502
EST:     CTGAAGCAGATGTGGAGAACCCAGTTCTTAAAGCAGAGCAGGAGTCACAG                         ATAGGCAAAGGTTCCCGTGGAGACGTGACTATACTCCCAACTCT
genomic: CTGAAGCAGATGTGGAGAACCCAGTTCTTAAAGCAGAGCAGGAGTCACAGgtttgccttt ... tcaatttcagATAGGCAAAGGTTCCCGTGGAGACGTGACTATACTCCCAACTCT
EST: gi|164054780|gb|ES112207.1|ES112207
EST:     CCCAGTTCTTAAAGCAGAGCAGGAGTCACAG                         ATAGGCAAAGGTTCCCGTGGAGACGTGACTATACTCCCAACTCTTGTCGTG
genomic: CCCAGTTCTTAAAGCAGAGCAGGAGTCACAGgtttgccttt ... tcaatttcagATAGGCAAAGGTTCCCGTGGAGACGTGACTATACTCCCAACTCTTGTCGTG
EST: gi|125101831|gb|EL156824.1|EL156824
EST:     CTGAAGCAGATGTGGAGAACCCAGTTCTTAAAGCAGAGCAGGAGTCACAG                         ATAGGCAAAGGTTCCCGTGGAGACGTGACTATACTCCCAA
genomic: CTGAAGCAGATGTGGAGAACCCAGTTCTTAAAGCAGAGCAGGAGTCACAGgtttgccttt ... tcaatttcagATAGGCAAAGGTTCCCGTGGAGACGTGACTATACTCCCAA
EST: gi|86037689|gb|DR333444.1|DR333444
EST:     CTGAAGCAGATGTGGAGAACCCAGTTCTTAAAGCAGAGCAGGAGTCACAG                         ATAGGCAAAGGTTCCCGTGGAGACGTGACTATACTCCCAACTCTTGTCGTG
genomic: CTGAAGCAGATGTGGAGAACCCAGTTCTTAAAGCAGAGCAGGAGTCACAGgtttgccttt ... tcaatttcagATAGGCAAAGGTTCCCGTGGAGACGTGACTATACTCCCAACTCTTGTCGTG
EST: gi|86037688|gb|DR333443.1|DR333443
EST:     CTGAAGCAGATGTGGAGAACCCAGTTCTTAAAGCAGAGCAGGAGTCACAG                         ATAGGCAAAGGTTCCCGTGGAGACGTGACTATACTCCCAACTCTTGTCGTG
genomic: CTGAAGCAGATGTGGAGAACCCAGTTCTTAAAGCAGAGCAGGAGTCACAGgtttgccttt ... tcaatttcagATAGGCAAAGGTTCCCGTGGAGACGTGACTATACTCCCAACTCTTGTCGTG
EST: gi|86037687|gb|DR333442.1|DR333442
EST:     CTGAAGCAGATGTGGAGAACCCAGTTCTTAAAGCAGAGCAGGAGTCACAG                         ATAGGCAAAGGTTCCCGTGGAGACGTGACTATACTCCCAACTCTTGTCGTG
genomic: CTGAAGCAGATGTGGAGAACCCAGTTCTTAAAGCAGAGCAGGAGTCACAGgtttgccttt ... tcaatttcagATAGGCAAAGGTTCCCGTGGAGACGTGACTATACTCCCAACTCTTGTCGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATTGATCTCAAAAAGGTGGACAAGTGTATCGGAGACCCTGAAGCAGATGTGGAGAACCCAGTTCTTAAAGCAGAGCAGGAGTCACAGgtttgcctttttgtaactaattggctcttacacgtcttcccaagatcttgttggttttaagttgccatatattctccattcctcgaggtgttcttaaaatgagtctacttcaatttcag

- - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG