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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttaggagaatattacttgacctcatgttttaattttgggtttgaaacacaggtttattttttattttttatttattattcatctgttttgactcgctagGAAGTGGAAAAAGATGTGAAAGCAAGGACAAAGGGCGAGACAGGAGCAGCTAAAACTCTTTGTGCTCCTTTTGATCAGCCAGACCTTGAAG

Basic information

species Vitis vinifera
transcript Vv07s0005g02620.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g02620.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA19G40930.1 (Glycine max), 3'ss of exon 11
---gttaggagaatattacttg-acctcatgttttaattttgggtttgaaacacaggtttattttttattttttatttattattcatctgttttgactcgctagGAAGTGGAAAAAGATGTGAAAGCAAGGACAAAGGGCGAGACAGGAGCAGCTAAAACTCTTTGTGCTCCTTTTGATCAGCCAGACCTTGAAG---
    ||  || | |    | || |    || ||||  ||||     ||  |||     | | | | |  | | || |  || ||  ||| |  ||  |   ||||| || ||    ||||| ||||| ||||||||||| ||||  ||||||||||| ||||||||   ||| |||||||||||||| ||   ||   
tacttttagaaactccatcgtgtaatgtatattttctttttat-catgggacattacataactgtattatgtgtaatagtttttggtctataatgctt---tagGAGGTTGAGGCTGATGTCAAAGCGAGGACAAAGGGTGAGATGGGAGCAGCTAAGACTCTTTGCAGTCCCTTTGATCAGCCAGAACTCCCAGAAG

upper sequence: Vv07s0005g02620.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA03G38340.1 (Glycine max), 3'ss of exon 11
---gttaggagaatattacttgacctcatgttttaattttgggtttgaaacacaggtttattttttattttttatttattattcatctgttttgactcgctagGAAGTGGAAAAAGATGTGAAAGCAAGGACAAAGGGCGAGACAGGAGCAGCTAAAACTCTTTGTGCTCCTTTTGATCAGCCAGACCTTGAAG---
    |       | | | | |    | |||| |   ||||     ||  |||     |   | | |    | || |  || ||  ||| |  ||  |   ||||| |||||    ||||| ||||| ||||||||||| ||||  ||||||||||| ||||||||    || |||||||||||||| ||   ||   
ttgatattttagaaactccatcgtgtaatgtatatttttttatcatgggacattacatagctgtattacgtgtaatagtttttggtctataatgctt---tagGAGGTGGAGGCTGATGTCAAAGCCAGGACAAAGGGTGAGATGGGAGCAGCTAAGACTCTTTGCAGCCCCTTTGATCAGCCAGAACTCCCAGAAG

upper sequence: Vv07s0005g02620.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT3G62120.2 (Arabidopsis thaliana), 3'ss of exon 10
gttaggagaatattacttga-cctcatgttttaattt-tgggtttgaaacacaggtttattttttattttttatttattattcatctgttttgactcgctagGAAGTGGAAAAAGATGTGAAAGCAAGGACAAAGGGCGAGACAGGAGCAGCTAAAACTCTTTGTGCTCCTTTTGATCAGCCAGA---CCTTGAAG
    | |   ||   |   | | || | ||  |  || | |  || |||| || |   ||     |||||   ||  |||  | |   ||    ||   ||||||||||||| |||||| || ||| | || || || || ||||||||||||||||| |||||| |||| ||||||||||| ||   || |||||
----gtatgttacagcaaaaacttcttattccagcttatagaattaaaactcaagaagataaca-attttaagttccttaaacttaaatt----ctttgtagGAAGTGGAAAGAGATGTTAAGGCACGTACGAAAGGTGAAACAGGAGCAGCTAAAACCCTTTGTTCTCCATTTGATCAGCCTGAACTCCCTGAAG

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|349830341|gb|FQ420601.1|FQ420601
EST:     AAGCGCTTGGCCAGAAGAAAATGATCCTTGCTCCTTGGTGTGATGAGATG                         GAAGTGGAAAAAGATGTGAAAGCAAGGACAAAGGGCGAGACAGGAGCAGCT
genomic: AAGCGCTTGGCCAGAAGAAAATGATCCTTGCTCCTTGGTGTGATGAGATGgtatggaaac ... gactcgctagGAAGTGGAAAAAGATGTGAAAGCAAGGACAAAGGGCGAGACAGGAGCAGCT
EST: gi|30306346|gb|CB983140.1|CB983140
EST:     AAGCGCTTGGCCAGAAGAAAATGATCCTTGCTCCTTGGTGTGATGAGATG                         GAAGTGGAAAAAGATGTGGAAGCAAGGACAAAGGGCGAGACAGGAGCAGCT
genomic: AAGCGCTTGGCCAGAAGAAAATGATCCTTGCTCCTTGGTGTGATGAGATGgtatggaaac ... gactcgctagGAAGTGGAAAAAGATGTGAAAGCAAGGACAAAGGGCGAGACAGGAGCAGCT
EST: gi|110427116|gb|EC993547.1|EC993547
EST:     AAGCGCTTGGCCAGAAGAAAATGATCCTTGCTCCTTGGTGTGATGAGATG                         GAAGTGGAAAAAGATGTGAAAGCAAGGACAAAGGGCGAGACAGGAGCAGCT
genomic: AAGCGCTTGGCCAGAAGAAAATGATCCTTGCTCCTTGGTGTGATGAGATGgtatggaaac ... gactcgctagGAAGTGGAAAAAGATGTGAAAGCAAGGACAAAGGGCGAGACAGGAGCAGCT
EST: gi|349826601|gb|FQ418692.1|FQ418692
EST:     AAGCGCTTGGCCAGAAGAAAATGATCCTTGCTCCTTGGTGTGATGAGATG                         GAAGTGGAAAAAGATGTGAAAGCAAGGACAAAGGGCGAGACAGGAGCAGCT
genomic: AAGCGCTTGGCCAGAAGAAAATGATCCTTGCTCCTTGGTGTGATGAGATGgtatggaaac ... gactcgctagGAAGTGGAAAAAGATGTGAAAGCAAGGACAAAGGGCGAGACAGGAGCAGCT
EST: gi|110361565|gb|EC925047.1|EC925047
EST:     AAGCGCTTGGTCAGAAGAAAATGATCCTTGCTCCTTGGTGTGATGAGATG                         GAAGTGGAAAAAGATGTGAAAGCAAGGACAAAGGGCGAGACAGGAGCAGCT
genomic: AAGCGCTTGGCCAGAAGAAAATGATCCTTGCTCCTTGGTGTGATGAGATGgtatggaaac ... gactcgctagGAAGTGGAAAAAGATGTGAAAGCAAGGACAAAGGGCGAGACAGGAGCAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacacaggtttattttttattttttatttattattcatctgttttgactcgctagGAAGTGGAAAAAGATGTGAAAGCAAGGACAAAGGGCGAGACAGGAGCAGCTAAAACTCTTTGTGCTCCTTTTGATCAGCCAGACCTTGAAG
                                         ttttgac  putative branch site (score: 3)
        tttattttttattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaggagaatattacttgacctcatgttttaattttgggtttgaaacacaggtttattttttattttttatttattattcatctgttttgactcgctagGAAGTGGAAAAAGATGTGAAAGCAAGGACAAAGGGCGAGACAGGAGCAGCTAAAACTCTTTGTGCTCCTTTTGATCAGCCAGACCTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- -aggagaa
- - - - - - - - - - cctcatg
- - - - - - - - - - - - - - - - -ttttggg
- - - - - - - - - - - - - - - - - - - - - -gaaacac