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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attaccccacgctaggaaacatagaaaagaaatgaaagtaacagtattttatgttctctctttcttccttctctatctaaatgatatgtctctcatgtagCTGATAGTTCAAAAAAGGCTGACCCAAAGGCACAAGCCGCAAAGGCTGCTAAAGCAGTCAAATTGGGTGCATCAACTTTCAAGAAGAAAGCGAAGAAGAT

Basic information

species Vitis vinifera
transcript Vv06s0004g04090.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g04090.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G40780.2 (Glycine max), 3'ss of exon 1
attaccccacgctaggaaacatagaaaagaaatgaaagtaacagt---attttatgttctctctttcttccttctctatctaaat-gatatgtctctcatgtagCTGATAGTTCAAAAAAGGCTGACCCAAAGGCACAAGCCGCAAAGGCTGCTAAAGCAGTCAAATTGGGTGCATCAACTTTCAAGAAGAAAGCGAAGAAGAT---
    |     | |    |  ||       ||| |  ||| |   |   ||||  | || | | |    |  |    | | | | | ||  |   | | ||| ||||||||||||||| |||||||| ||||||||||| |||   ||  |||| || ||||| || |  |||||   |||||| ||||||||  | ||||||||   
----cattgtgatgaagattatgctgtttaaagggtagttatctttcgatttatttttgtatgtaatgtaatgtgatgtgtgactagagctagttttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCAAGGCAGTTAAGTCCGGTGC--TAACTTT-AAGAAGAAGACCAAGAAGATCCG

upper sequence: Vv06s0004g04090.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA15G04670.2 (Glycine max), 3'ss of exon 2
--attaccccacgctaggaaacatagaaaagaaatgaaagtaacagtattttatgttctctctttcttccttctctatctaaatgatatgtctctcatgtagCTGATAGTTCAAAAAAGGCTGACCCAAAGGCACAAGCCGCAAAGGCTGCTAAAGCAGTCAAATTGGGTGCATCAACTTTCAAGAAGAAAGCGAAGAAGAT---
    | |     | |    |  ||       |||    |||   ||  ||| ||  | |    |      |  | | |    |    | || | | ||| ||||||||||| ||| |||||||| |||||||||||||||   ||  ||||||| || || || |  |||||    ||||| ||||| ||  | ||||||||   
tatctgcattgtgttgaagattatgctgtttaaaaagtagt--tagcttttgattattttgtatggagtgtgatgtgtgactagagcaagtgtttaatgcagCTGATAGTTTAAAGAAGGCTGATCCAAAGGCACAAGCCTTGAAAACTGCTAAGGCTGTTAAGTCAGGTGCT---ACTTTAAAGAAAAAGACCAAGAAGATCCG
















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|110693591|gb|EE069954.1|EE069954
EST:     AGCAATCAATGGCTCCTGCTAAAG                         CTGATAGTTCAAAAAAGGCTGACCCAAAGGCACAAGCCGCAAAGGCTGCTA
genomic: AGCAATCAATGGCTCCTGCTAAAGgtagtcgttc ... tctcatgtagCTGATAGTTCAAAAAAGGCTGACCCAAAGGCACAAGCCGCAAAGGCTGCTA
EST: gi|110723721|gb|EE101359.1|EE101359
EST:     TTGATTGAAAGGGTGACAGTTTGTTCAGCAATCAATGGCTCCTGCTAAAG                         CTGATAGTTCAAAAAAGGCTGACCCAAAGGCACAAGCCGCAAAGGCTGCTA
genomic: TTGATTGAAAGGGTGACAGTTTGTTCAGCAATCAATGGCTCCTGCTAAAGgtagtcgttc ... tctcatgtagCTGATAGTTCAAAAAAGGCTGACCCAAAGGCACAAGCCGCAAAGGCTGCTA
EST: gi|110383279|gb|EC947641.1|EC947641
EST:     TTGATTGAAAGGGTGACAGTTTGTTCAGCAATCAATGGCTCCTGCTAAAG                         CTGATAGTTCAAAAAAGGCTGACCCAAAGGCACAAGCCGCAAAGGCTGCTA
genomic: TTGATTGAAAGGGTGACAGTTTGTTCAGCAATCAATGGCTCCTGCTAAAGgtagtcgttc ... tctcatgtagCTGATAGTTCAAAAAAGGCTGACCCAAAGGCACAAGCCGCAAAGGCTGCTA
EST: gi|110689147|gb|EE065119.1|EE065119
EST:     TTGATTGAAAGGGTGACAGTTTGTTCAGCAATCAATGGCTCCTGCTAAAG                         CTGATAGTTCAAAAAAGGCTGACCCAAAGGCACAAGCCGCAAAGGCTGCTA
genomic: TTGATTGAAAGGGTGACAGTTTGTTCAGCAATCAATGGCTCCTGCTAAAGgtagtcgttc ... tctcatgtagCTGATAGTTCAAAAAAGGCTGACCCAAAGGCACAAGCCGCAAAGGCTGCTA
EST: gi|110708203|gb|EE085476.1|EE085476
EST:     ATTGAAAGGGTGACAGTTTGTTCAGCAATCAATGGCTCCTGCTAAAG                         CTGATAGTTCAAAAAAGGCTGACCCAAAGGCACAAGCCGCAAAGGCTGCTA
genomic: ATTGAAAGGGTGACAGTTTGTTCAGCAATCAATGGCTCCTGCTAAAGgtagtcgttc ... tctcatgtagCTGATAGTTCAAAAAAGGCTGACCCAAAGGCACAAGCCGCAAAGGCTGCTA
EST: gi|110377848|gb|EC942944.1|EC942944
EST:     TGATTGAAAGGGGTGACAGTTTGTTCAGCAATCAATGGCTCCTGCTAAAG                         CTGATAGTTCAAAAAAGGCTGACCCAAAGGCACAAGCCGCAAAGGCTGCTA
genomic: TGATTGAAA-GGGTGACAGTTTGTTCAGCAATCAATGGCTCCTGCTAAAGgtagtcgttc ... tctcatgtagCTGATAGTTCAAAAAAGGCTGACCCAAAGGCACAAGCCGCAAAGGCTGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttatgttctctctttcttccttctctatctaaatgatatgtctctcatgtagCTGATAGTTCAAAAAAGGCTGACCCAAAGGCACAAGCCGCAAAGGCTGCTAAAGCAGTCAAATTGGGTGCATCAACTTTCAAGAAGAAAGCGAAGAAGAT
                             atctaaa  putative branch site (score: 3)
                                         tgtctctc  putative PPT
                            tatctaaatgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attaccccacgctaggaaacatagaaaagaaatgaaagtaacagtattttatgttctctctttcttccttctctatctaaatgatatgtctctcatgtagCTGATAGTTCAAAAAAGGCTGACCCAAAGGCACAAGCCGCAAAGGCTGCTAAAGCAGTCAAATTGGGTGCATCAACTTTCAAGAAGAAAGCGAAGAAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
-ttacccc
- - - - - - - ggaaaca
- - - - - - - - - - - - -aaagaaa
- - - - - - - - - - - - - - - - - aaagtaa