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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttggtgattaaaacatattgggttattaagagcagagaaatggaactttgttctagcctttttatgtgataattaatacattttcttttctctagttcagTGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAATGGTCCATCTGTAAAATTTATGGTTGATGCTG

Basic information

species Vitis vinifera
transcript Vv07s0005g04550.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g04550.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA18G51310.1 (Glycine max), 3'ss of exon 2
ttggtgattaaaacatattgggttattaagagcagagaaatggaactttgttctagcctttttatgtgataattaatacattttcttttctctagttcagTGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAATGGTCCATCTGTAAAATTTATGGTTGATGCTG
    ||| |      ||| |   ||||     |    |          |   | || | | | || | ||| |        | |||| || |   |  |||||||||| || |||||||| ||| | |||||||| |||||||||||||| ||||||||||||||| | |||  |||||
acaatgactgttgagtatagtaatatttgacactctaattctttgtcatcaccgagtcctgtcatcttatattctgatttgtgtcttctcccctttcaagTGCAGGAAGCATAAAGATCTTTATCTCTGGATGGCAAAATGCCCCAATGGCCCATCTGTAAAATTTCTAGTTAGTGCTG

upper sequence: Vv07s0005g04550.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G28320.2 (Glycine max), 3'ss of exon 3
ttggtgattaaaacatattgggttattaagagcagagaaatggaactttgttctagcctttttatgtgataattaatacattttcttttctctagttcagTGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAATGGTCCATCTGTAAAATTTATGGTTGATGCTG
 || |  ||  ||  | ||   |||||            ||   |     |  ||     | |  |   |  |     | |||   | | |  | ||||||||||||| || |||||||| ||| | |||||||| |||||||||||||| ||||||||||| ||| | |||  ||| |
atgattgttttaaatttttattttattttattttattttattttatagattcatatttcatatcggccttcttctccccttttctatatatgaatttcagTGCAGGAAGCATAAAGATCTTTATCTCTGGATGGCAAAATGCCCCAATGGCCCATCTGTAAAGTTTCTAGTTAGTGCCG

upper sequence: Vv07s0005g04550.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G12700.1 (Glycine max), 3'ss of exon 3
ttggtgattaaaacatattgggttattaagagcagagaaatggaactttgttctagcctttttat-gtgataattaatacattttcttttctctagttcagTGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAATGGTCCATCTGTAAAATTTATGGTTGATGCTG
 |  |  || | ||  |||       |   |   | |       |  |||||  |  ||  |||| ||  |        | |||   | | |  | ||||||||||||| || |||||||| ||| | ||||| || |||||||||||||| ||||||||||||||| | |||  |||||
-taatatttgacactaattcttagtctgccaattgggtctgatcaacttgttacattctgattattgtcttgtcctccccttttatatatatgaatttcagTGCAGGAAGCAAAAAGATCTTTATCTCTGGATAGCAAAATGCCCCAATGGCCCATCTGTAAAATTTTTAGTTAGTGCTG

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|161716827|gb|FC068099.1|FC068099
EST:     TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAG                         TGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAATGGT
genomic: TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAGgtcagttttt ... tctagttcagTGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAATGGT
EST: gi|34544827|gb|CF513059.1|CF513059
EST:     TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAG                         TGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAATGGT
genomic: TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAGgtcagttttt ... tctagttcagTGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAATGGT
EST: gi|294967323|gb|GW836677.1|GW836677
EST:     TGAACGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAG                         TGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAATGGT
genomic: TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAGgtcagttttt ... tctagttcagTGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAATGGT
EST: gi|110417096|gb|EC983122.1|EC983122
EST:     TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAG                         TGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAGTGGT
genomic: TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAGgtcagttttt ... tctagttcagTGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAATGGT
EST: gi|110723555|gb|EE101001.1|EE101001
EST:     TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAG                         TGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAGTGGT
genomic: TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAGgtcagttttt ... tctagttcagTGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAATGGT
EST: gi|34549744|gb|CF517976.1|CF517976
EST:     TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAG                         TGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAATGGT
genomic: TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAGgtcagttttt ... tctagttcagTGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAATGGT
EST: gi|110731138|gb|EE109014.1|EE109014
EST:     TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAG                         TGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAGTGGT
genomic: TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAGgtcagttttt ... tctagttcagTGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAATGGT
EST: gi|30252907|gb|CB970458.1|CB970458
EST:     TGAATGAGCTCGTTGAGCTCAAGAATTGTTCTTCCTGTTTGTTTTTTGAG                         TGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAGTGGT
genomic: TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAGgtcagttttt ... tctagttcagTGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAATGGT
EST: gi|71854618|gb|DT003673.1|DT003673
EST:     TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAG                         TGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAATGGT
genomic: TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAGgtcagttttt ... tctagttcagTGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAATGGT
EST: gi|110702082|gb|EE080390.1|EE080390
EST:     TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAG                         TGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAGTGGT
genomic: TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAGgtcagttttt ... tctagttcagTGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAATGGT
EST: gi|110720764|gb|EE096972.1|EE096972
EST:     TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAG                         TGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAGTGGT
genomic: TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAGgtcagttttt ... tctagttcagTGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAATGGT
EST: gi|37187733|gb|CF607086.1|CF607086
EST:     TGAATGAGCTCGTTGAGCTCAAGAATTGTTCTTCCTGTTTGTTTTTTGAG                         TGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAGTGGT
genomic: TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAGgtcagttttt ... tctagttcagTGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAATGGT
EST: gi|110719294|gb|EE097103.1|EE097103
EST:     TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAG                         TGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAGTGGT
genomic: TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAGgtcagttttt ... tctagttcagTGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAATGGT
EST: gi|110685809|gb|EE062855.1|EE062855
EST:     TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAG                         TGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAATGGT
genomic: TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAGgtcagttttt ... tctagttcagTGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAATGGT
EST: gi|110732371|gb|EE107597.1|EE107597
EST:     TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAG                         TGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAGTGGT
genomic: TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAGgtcagttttt ... tctagttcagTGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAATGGT
EST: gi|110373531|gb|EC937775.1|EC937775
EST:     TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAG                         TGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAATGGT
genomic: TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAGgtcagttttt ... tctagttcagTGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAATGGT
EST: gi|27585576|gb|CB008271.1|CB008271
EST:     TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAG                         TGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAGTGGT
genomic: TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAGgtcagttttt ... tctagttcagTGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAATGGT
EST: gi|110718547|gb|EE095508.1|EE095508
EST:     TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAG                         TGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAGTGGT
genomic: TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAGgtcagttttt ... tctagttcagTGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAATGGT
EST: gi|294965135|gb|GW836966.1|GW836966
EST:     TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAG                         TGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAGTGGT
genomic: TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAGgtcagttttt ... tctagttcagTGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAATGGT
EST: gi|110685111|gb|EE063162.1|EE063162
EST:     TGAATGAGCTCGTTGAGCTCAAGAATTGTTCTTCCTGTTTGTTTTTTGAG                         TGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAGTGGT
genomic: TGAATGAGCTCGTTGAGCTCAAGAACTGTTCTTCCTGTTTGTTTTTTGAGgtcagttttt ... tctagttcagTGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgttctagcctttttatgtgataattaatacattttcttttctctagttcagTGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAATGGTCCATCTGTAAAATTTATGGTTGATGCTG
                         aattaat  putative branch site (score: 3)
                                   ttttcttttctctagt  putative PPT
             tttttatgtgataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttggtgattaaaacatattgggttattaagagcagagaaatggaactttgttctagcctttttatgtgataattaatacattttcttttctctagttcagTGCAGGAAACAGAAAGATCTATATTTATGGATGGCCAAATGCCCCAATGGTCCATCTGTAAAATTTATGGTTGATGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
-tggtgat
- - - - -aaaacat
- - - - - - - - - - - - - - - - -agagaaa