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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgagaaatgtacctttgcaactgttagcttcaagtcctgctttctgattatgtattaaaacaatgctgacaagcattttatttcactttgttgctgcagGGACCTGAGATTCGAACTGGTTTTCTAAAGGATGCAAAGCCTATCCAACTTAAGGAAGGTGAGGAAATCACCATTAGTACTGATTACAGCATCAAGGGGG

Basic information

species Vitis vinifera
transcript Vv08s0056g00190.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0056g00190.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA19G00870.1 (Glycine max), 3'ss of exon 2
ttgagaaatgtacctttgca-actgttagcttcaagtcctgctttctgattatgtattaaaacaatgctgacaagcattttatttcactttgttgctgcagGGACCTGAGATTCGAACTGGTTTTCTAAAGGATGCAAAGCCTATCCAACTTAAGGAAGGTGAGGAAATCACCATTAGTACTGATTACAGCATCAAGGGGG
         |||  ||| |  ||||   || | | ||   |       ||  || ||    |      |   |  ||||  |     || | ||| ||||||||||||||||||| ||||||||||| || |||| ||| ||||| ||||||||||||||  | ||||||||||| | |||||||||   ||| |||||||
---------gtaggttttctcactgaatgccttatgtatggtg----aatggtgaatggtgatcgatttcttattcatta-acgcttctgttttg-tgcagGGACCTGAGATTCGGACTGGTTTTCTGAAAGATGGAAAACCTATTCAACTTAAGGAAGGACAAGAAATCACCATAACTACTGATTATGACATTAAGGGGG

upper sequence: Vv08s0056g00190.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA05G09310.1 (Glycine max), 3'ss of exon 1
ttgagaaatgtacctttgcaactgttagcttcaagtcctgctttctgattatg--tattaaaaca--atgctgacaagcattttattt-cactttgttgctgcagGGACCTGAGATTCGAACTGGTTTTCTAAAGGATGCAAAGCCTATCCAACTTAAGGAAGGTGAGGAAATCACCATTAGTACTGATTACAGCATCAAGGGGG
     |||| |    |||     | | |||    |||||| ||      ||||  | | ||      || |    ||   || | | | ||  |  ||  ||||||||||||||||||| ||||||||||| || |||| ||| ||||| |||||||| |||||  | ||| ||||||| | |||||||||   ||| |||||||
--cgtaaatatcttgttgaggaggatggctc---gtcctgtttctcttgtatggttgtcaatttcttattccattaacgtttctgtctacatctgctttgtgcagGGACCTGAGATTCGGACTGGTTTTCTGAAAGATGGAAAACCTATTCAACTTAAAGAAGGGCAAGAAGTCACCATAACTACTGATTATGACATTAAGGGGG
















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|161712102|gb|FC061474.1|FC061474
EST:     TTGCTATGCAGAACACTCAGATCCTCTGCGCTGTGATGCTTGATACCAAG                         GGACCTGAGATTCGAACTGGTTTTCTAAAGGATGCAAAGCCTATCCAACTT
genomic: TTGCTATGCAGAACACTCAGATCCTCTGCGCTGTGATGCTTGATACCAAGgtcactattc ... gttgctgcagGGACCTGAGATTCGAACTGGTTTTCTAAAGGATGCAAAGCCTATCCAACTT
EST: gi|110698076|gb|EE075678.1|EE075678
EST:     TTGCTATGCAGAACACTCAGATCCTCTGCGCTGTGATGCTTGATACCAAG                         GGACCTGAGATTCGAACTGGTTTTCTAAAGGATGCAAAGCCTATCCAACTT
genomic: TTGCTATGCAGAACACTCAGATCCTCTGCGCTGTGATGCTTGATACCAAGgtcactattc ... gttgctgcagGGACCTGAGATTCGAACTGGTTTTCTAAAGGATGCAAAGCCTATCCAACTT
EST: gi|71863653|gb|DT012708.1|DT012708
EST:     TTGCTATGCAGAACACTCAGATCCTCTGCGCTGTGATGCTTGATACCAAG                         GGACCTGAGATTCGAACTGGTTTTCTAAAGGATGCAAAGCCTATCCAACTT
genomic: TTGCTATGCAGAACACTCAGATCCTCTGCGCTGTGATGCTTGATACCAAGgtcactattc ... gttgctgcagGGACCTGAGATTCGAACTGGTTTTCTAAAGGATGCAAAGCCTATCCAACTT
EST: gi|161707202|gb|FC056407.1|FC056407
EST:     TTGCTATGCAGAACACTCAGATCCTCTGCGCTGTGATGCTTGATACCAAG                         GGACCTGAGATTCGAACTGGTTTTCTAAAGGATGCAAAGCCTATCCAACTT
genomic: TTGCTATGCAGAACACTCAGATCCTCTGCGCTGTGATGCTTGATACCAAGgtcactattc ... gttgctgcagGGACCTGAGATTCGAACTGGTTTTCTAAAGGATGCAAAGCCTATCCAACTT
EST: gi|110686726|gb|EE064694.1|EE064694
EST:     TTGCTATGCAGAACACTCAGATCCTCTGCGCTGTGATGCTTGATACCAAG                         GGACCTGAGATTCGAACTGGTTTTCTAAAGGATGCAAAGCCTATCCAACTT
genomic: TTGCTATGCAGAACACTCAGATCCTCTGCGCTGTGATGCTTGATACCAAGgtcactattc ... gttgctgcagGGACCTGAGATTCGAACTGGTTTTCTAAAGGATGCAAAGCCTATCCAACTT
EST: gi|161718515|gb|FC069292.1|FC069292
EST:     TTGCTATGCAGAACACTCAGATCCTCTGCGCTGTGATGCTTGATACCAAG                         GGACCTGAGATTCGAACTGGTTTTCTAAAGGATGCAAAGCCTATCCAACTT
genomic: TTGCTATGCAGAACACTCAGATCCTCTGCGCTGTGATGCTTGATACCAAGgtcactattc ... gttgctgcagGGACCTGAGATTCGAACTGGTTTTCTAAAGGATGCAAAGCCTATCCAACTT
EST: gi|161720977|gb|FC070692.1|FC070692
EST:     TTGCTATGCAGAACACTCAGATCCTCTGCGCTGTGATGCTTGATACCAAG                         GGACCTGAGATTCGAACTGGTTTTCTAAAGGATGCAAAGCCTATCCAACTT
genomic: TTGCTATGCAGAACACTCAGATCCTCTGCGCTGTGATGCTTGATACCAAGgtcactattc ... gttgctgcagGGACCTGAGATTCGAACTGGTTTTCTAAAGGATGCAAAGCCTATCCAACTT
EST: gi|110709558|gb|EE085123.1|EE085123
EST:     TTGCTATGCAGAACACTCAGATCCTCTGCGCTGTGATGCTTGATACCAAG                         GGACCTGAGATTCGAACTGGTTTTCTAAAGGATGCAAAGCCTATCCAACTT
genomic: TTGCTATGCAGAACACTCAGATCCTCTGCGCTGTGATGCTTGATACCAAGgtcactattc ... gttgctgcagGGACCTGAGATTCGAACTGGTTTTCTAAAGGATGCAAAGCCTATCCAACTT
EST: gi|110726242|gb|EE101850.1|EE101850
EST:     TTGCTATGCAGAACACTCAGATCCTCTGCGCTGTGATGCTTGATACCAAG                         GGACCTGAGATTCGAACTGGTTTTCTAAAGGATGCAAAGCCTATCCAACTT
genomic: TTGCTATGCAGAACACTCAGATCCTCTGCGCTGTGATGCTTGATACCAAGgtcactattc ... gttgctgcagGGACCTGAGATTCGAACTGGTTTTCTAAAGGATGCAAAGCCTATCCAACTT
EST: gi|71863537|gb|DT012592.1|DT012592
EST:     TTGCTATGCAGAACACTCAGATCCTCTGCGCTGTGATGCTTGATACCAAG                         GGACCTGAGATTCGAACTGGTTTTCTAAAGGATGCAAAGCCTATCCAACTT
genomic: TTGCTATGCAGAACACTCAGATCCTCTGCGCTGTGATGCTTGATACCAAGgtcactattc ... gttgctgcagGGACCTGAGATTCGAACTGGTTTTCTAAAGGATGCAAAGCCTATCCAACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattatgtattaaaacaatgctgacaagcattttatttcactttgttgctgcagGGACCTGAGATTCGAACTGGTTTTCTAAAGGATGCAAAGCCTATCCAACTTAAGGAAGGTGAGGAAATCACCATTAGTACTGATTACAGCATCAAGGGGG
                   tgctgac  putative branch site (score: 2)
                                         ctttgtt  putative PPT
     atgtattaaaacaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgagaaatgtacctttgcaactgttagcttcaagtcctgctttctgattatgtattaaaacaatgctgacaagcattttatttcactttgttgctgcagGGACCTGAGATTCGAACTGGTTTTCTAAAGGATGCAAAGCCTATCCAACTTAAGGAAGGTGAGGAAATCACCATTAGTACTGATTACAGCATCAAGGGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - cctttgc
- - - - - - - - - - -ctgttag
- - - - - - - - - - - - - - - - - - cctgctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acaagca