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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGTGGACTATCCACTAGAATTGGATGTTTATGATCTCTGTTCGGATGATCTTCGCAAAAAATTGGAAGCCCCTCGACAAgtatttgcttgcactttgctttgacaaacttataattacataatccatttatgtcttctctgccttgctgattttattttcaacatccaaccattag

Basic information

species Vitis vinifera
transcript Vv09s0002g02500.t01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g02500.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA08G20900.1 (Glycine max), 5'ss of exon 13
AAAGTGGACTATCCACTAGAATTGGATGTTTATGATCTCTGTTCGGATGATCTTCGCAAAAAATTGGAAGCCCCTCGACAAgtatttgcttgcactttgctttgacaaacttataatt-------------acataatccatttatgtcttctctgccttgctgattttattttcaacatccaaccattag
||||| || ||||| || || ||||||||||||||| | ||||| ||||||||||| ||||||||||| || ||| |||| ||||   |||     |||   ||| || |||||  ||             |  |  |   ||| |    | | ||  ||  |  | | | |||  | ||   ||| | ||
AAAGTAGATTATCCCCTGGAGTTGGATGTTTATGATTTTTGTTCAGATGATCTTCGTAAAAAATTGGATGCTCCTAGACAGgtatcctctt-tgtcttgacctgaaaatcttatggttgtttgtaagaaaaatgtgcttggtttgtaaaatgtgtgggtttatattctcactttggatattgtaccttcag

upper sequence: Vv09s0002g02500.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA07G01480.1 (Glycine max), 5'ss of exon 13
AAAGTGGACTATCCACTAGAATTGGATGTTTATGATCTCTGTTCGGATGATCTTCGCAAAAAATTGGAAGCCCCTCGACAAgtatttgcttgcactttgctttgacaaacttataattac--ataatccatttatgtcttctctgcc-----------ttgctgattttattttcaacatccaaccattag
||||| || ||||| || || ||||||||||||||| | ||||| || || ||||| |||||||||||||| ||| |||| ||||   |||     |||   ||| || |||||  ||     |||   |   |||| | || ||              |  |  | | |||||  | ||   ||| | ||
AAAGTAGATTATCCTCTGGAGTTGGATGTTTATGATTTTTGTTCTGACGAACTTCGTAAAAAATTGGAAGCTCCTAGACAGgtatactctt-tgtcttgacatgaaaatcttatggttgtttgtaagaaaaagatgtttgctttgtaaaatgtgtgggcttatattctcattttggatattgtaccttcag
















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|30296415|gb|CB973209.1|CB973209
EST:     ATGATCTCTGTTCGGATGATCTTCGCAAAAAATTGGAAGCCCCTCGACAA                         ATTTTAAGGGATGAGGAAGGTAAAAAGCTTGGTTTGAAGAACTCTGCTTCG
genomic: ATGATCTCTGTTCGGATGATCTTCGCAAAAAATTGGAAGCCCCTCGACAAgtatttgctt ... caaccattagATTCTAAGGGATGAGGAAGGTAAAAAGCTTGGTTTGAAGAACTCTGCTTCG
EST: gi|33404879|gb|CF210506.1|CF210506
EST:     ATGATCTCTGTTCGGATGATCTTCGCAAAAAATTGGAAGCCCCTCGACAA                         ATTCTAAGGGATGAGGAAGGTAAAAAGCTTGGTTTGAAGAACTCTGCTTCG
genomic: ATGATCTCTGTTCGGATGATCTTCGCAAAAAATTGGAAGCCCCTCGACAAgtatttgctt ... caaccattagATTCTAAGGGATGAGGAAGGTAAAAAGCTTGGTTTGAAGAACTCTGCTTCG
EST: gi|110422111|gb|EC988423.1|EC988423
EST:     ATGATCTCTGTTCGGATGATCTTCGCAAAAAATTGGAAGCCCCTCGACAA                         ATTCTAAGGGATGAGGAAGGTAAAAAGCTTGGTTTGAAGAACTCTGCTTCG
genomic: ATGATCTCTGTTCGGATGATCTTCGCAAAAAATTGGAAGCCCCTCGACAAgtatttgctt ... caaccattagATTCTAAGGGATGAGGAAGGTAAAAAGCTTGGTTTGAAGAACTCTGCTTCG
EST: gi|33405442|gb|CF211069.1|CF211069
EST:     ATGATCTCTGTTCGGATGATCTTCGCAAAAAATTGGAAGCCCCTCGACAA                         ATTCTAAGGGATGAGGAAGGTAAAAAGCTTGGTTTGAAGAACTCTGCTTCG
genomic: ATGATCTCTGTTCGGATGATCTTCGCAAAAAATTGGAAGCCCCTCGACAAgtatttgctt ... caaccattagATTCTAAGGGATGAGGAAGGTAAAAAGCTTGGTTTGAAGAACTCTGCTTCG
EST: gi|110701778|gb|EE079734.1|EE079734
EST:     ATGATCTCTGTTCGGATGATCTTCGCAAAAAATTGGAAGCCCCTCGACAA                         ATTCTAAGGGATGAGGAAGGTAAAAAGCTTGGTTTGAAGAACTCTGCTTCG
genomic: ATGATCTCTGTTCGGATGATCTTCGCAAAAAATTGGAAGCCCCTCGACAAgtatttgctt ... caaccattagATTCTAAGGGATGAGGAAGGTAAAAAGCTTGGTTTGAAGAACTCTGCTTCG
EST: gi|22009589|gb|BQ794623.1|BQ794623
EST:     ATGATCTCTGTTCGGATGATCTTCGCAAAAAATTGGAAGCCCCTCGACAA                         ATTCTAAGGGATGAGGAAGGTAAAAAGCTTGGTTTGAAGAACTCTGCTTCG
genomic: ATGATCTCTGTTCGGATGATCTTCGCAAAAAATTGGAAGCCCCTCGACAAgtatttgctt ... caaccattagATTCTAAGGGATGAGGAAGGTAAAAAGCTTGGTTTGAAGAACTCTGCTTCG
EST: gi|22012121|gb|BQ797155.1|BQ797155
EST:     ATGATCTCTGTTCGGATGATCTTCGCAAAAAATTGGAAGCCCCTCGACAA                         ATTCTAAGGGATGAGGAAGGTAAAAAGCTTGGTTTGAAGAACTCTGCTTCG
genomic: ATGATCTCTGTTCGGATGATCTTCGCAAAAAATTGGAAGCCCCTCGACAAgtatttgctt ... caaccattagATTCTAAGGGATGAGGAAGGTAAAAAGCTTGGTTTGAAGAACTCTGCTTCG
EST: gi|110428084|gb|EC994545.1|EC994545
EST:     ATGATCTCTGTTCGGATGATCTTCGCAAAAAATTGGAAGCCCCTCGACAA                         ATTCTAAGGGATGAGGAAGGTAAAAAGCTTGGTTTGAAGAACTCTGCTTCG
genomic: ATGATCTCTGTTCGGATGATCTTCGCAAAAAATTGGAAGCCCCTCGACAAgtatttgctt ... caaccattagATTCTAAGGGATGAGGAAGGTAAAAAGCTTGGTTTGAAGAACTCTGCTTCG
EST: gi|22009862|gb|BQ794896.1|BQ794896
EST:     ATGATCTCTGTTCGGATGATCTTCGCAAAAAATTGGAAGCCCCTCGACAA                         ATTCTAAGGGATGAGGAAGGTAAAAAGCTTGGTTTGAAGAACTCTGCTTCG
genomic: ATGATCTCTGTTCGGATGATCTTCGCAAAAAATTGGAAGCCCCTCGACAAgtatttgctt ... caaccattagATTCTAAGGGATGAGGAAGGTAAAAAGCTTGGTTTGAAGAACTCTGCTTCG
EST: gi|83275368|gb|DV939376.1|DV939376
EST:     AAAAA-TGGAAG-CCCTCGACAA                         A-TCTAAGGGA-GAGGAAGGT-AAAAGCTTGG-TTGAAGAACTCTGCTTCG
genomic: AAAAATTGGAAGCCCCTCGACAAgtatttgctt ... caaccattagATTCTAAGGGATGAGGAAGGTAAAAAGCTTGGTTTGAAGAACTCTGCTTCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGTGGACTATCCACTAGAATTGGATGTTTATGATCTCTGTTCGGATGATCTTCGCAAAAAATTGGAAGCCCCTCGACAAgtatttgcttgcactttgctttgacaaacttataattacataatccatttatgtcttctctgccttgctgattttattttcaacatccaaccattag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG