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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaaatcatagattatggaggaagaaaagaaaagaagttgttcacgtaattgtaattggggtggtttctgaagctgtgttccccgttttcatgtacacagACAGGTGTTCTTGTGGAGAAATTGAACCAAGTGAACGCAGAAAACAGGAAGCTAACGGAAATGCTAACAGTGATGTGTGAGAATTACAACGCTTTGAGAA

Basic information

species Vitis vinifera
transcript Vv09s0018g00240.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0018g00240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G44730.1 (Glycine max), 3'ss of exon 2
---tcaaatcatagattatggaggaagaaaagaaaagaagttgttcacgtaattgtaattggggtggtttctgaagctgtgt-tccccgttttcatgtacacagACAGGTGTTCTTGTGGAGAAATTGAACCAAGTGAACGCAGAAAACAGGAAGCTAACGGAAATGCTAACAGTGATGTGTGAGAATTACAACGCTTTGAGAA
   ||    |||  ||||||||  |  |     ||  |  || ||    |     || |    |  |  |         | | |    | |  ||| |       | ||||   | | |||| |  |||| |  ||||  |||||||||| |||| |||| |||||||| |||| ||||||||||||||||||| |||||    
tagtctgtccatccattatggat-attagttataagcatctttttttttttcccttattaaaagctgcataaatgatgatatatatgtgctgccatttcagTCTGCTGGTGCCTTGGCGGAGGAGCTGAAGCGGGTGAGTGCAGAAAACAAGAAGTTAACCGAAATGCTCACAGAGATGTGTGAGAATTACAACACTTTGC---

upper sequence: Vv09s0018g00240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA15G00570.1 (Glycine max), 3'ss of exon 2
----tcaaatcatagattatggaggaagaaaagaaaagaagttgttcacgtaattgtaattggggtggtttctgaagctgtgttccccgttttcatgtacacagACAGGTGTTCTTGTGGAGAAATTGAACCAAGTGAACGCAGAAAACAGGAAGCTAACGGAAATGCTAACAGTGATGTGTGAGAATTACAACGCTTTGAGAA
    | | ||    | || |||    |        ||  | |   |    |  || |||      |   |  |||  |     |    | |  ||| |       ||||||   | | |||| || |||| |  ||||  |||||||||| |||| |||| |||||||| |||| |||||||||||| |||||| |||||    
gatttgatattgctgcttgtggcaccatttggttgaatgattctcttgtttt-ttataagctacatcaatgatgatacatatatatgtgctgccatttcagTCAGCAGGTGCCTTGGCGGAGGAACTGAAGCGGGTGAGTGCAGAAAACAAGAAGTTAACCGAAATGCTCACAGAGATGTGTGAGAACTACAACACTTTGC---

upper sequence: Vv09s0018g00240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G23380.3 (Glycine max), 3'ss of exon 2
tcaaatcatagattatggaggaagaaaagaaaagaagttgttcacgtaattgtaattggggt---ggtttctga-----agctgtgttccccgttttcatgtacacagACAGGTGTTCTTGTGGAGAAATTGAACCAAGTGAACGCAGAAAACAGGAAGCTAACGGAAATGCTAACAGTGATGTGTGAGAATTACAACGCTTTGAGAA
  ||| |||  |  ||| |  || | ||| | |  | |  ||    |||   ||   | | |   || | || |      | ||   |    | |  ||| |      ||  |||   | | |||| || |||| |  ||||  |||||||||| |||| |  | ||||||||  ||||| ||||||||||||||||| ||||||   
-aaaaacatgaa--atgaa--aacagaagtatatgattcttttggctaaaaatatacgagataaagggtcctaatatatggatggtattgttggtggcatttcagTCTACTAGTGACTTGGAGGAGGAACTGAAGCGGGTGAGTGCAGAAAACAAGAAGTTGGCCGAAATGCTCTCAGTGGTGTGTGAGAATTACAACACTTTGA---

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|349818243|gb|FQ409018.1|FQ409018
EST:     A-GATTTTACAGGGTTGGGGTTGAAGGTCGTCTCATTGAAAGAAGAAGAG                         ACAGGTGTTCTTGTGGAGAAATTGAACCAAGTGAACGCAGAAAACAGGAAG
genomic: ATGATTTTACAGGGTTGGGGTTGAAGGTCGTCTCATTGAAAGAAGAAGAGgtgagtctat ... atgtacacagACAGGTGTTCTTGTGGAGAAATTGAACCAAGTGAACGCAGAAAACAGGAAG
EST: gi|349810369|gb|FQ401815.1|FQ401815
EST:     A-GATTTTACAGGGTTGGGGTTGAAGGTCGTCTCATTGAAAGAAGAAGAG                         ACAGGTGTTCTTGTGGAGAAATTGTACCAAGTGAACGCAGAAAACAGGAAG
genomic: ATGATTTTACAGGGTTGGGGTTGAAGGTCGTCTCATTGAAAGAAGAAGAGgtgagtctat ... atgtacacagACAGGTGTTCTTGTGGAGAAATTGAACCAAGTGAACGCAGAAAACAGGAAG
EST: gi|294967229|gb|GW840104.1|GW840104
EST:     ATGATTTTACAGGGTTGGGGTTGAAGGTCGTCTCATTGAAAGAAGAAGAG                         ACAGGTGTTCTTGTGGAGAAATTGAACCAAGTGAACGCAGAAAACAGGAAG
genomic: ATGATTTTACAGGGTTGGGGTTGAAGGTCGTCTCATTGAAAGAAGAAGAGgtgagtctat ... atgtacacagACAGGTGTTCTTGTGGAGAAATTGAACCAAGTGAACGCAGAAAACAGGAAG
EST: gi|161712086|gb|FC061458.1|FC061458
EST:     ATGATTTTACAGGGTTGGGGTTGAAGGTCGTCTCATTGAAAGAAGAAGAG                         ACAGGTGTTCTTGTGGAGAAATTGAACCAAGTGAACGCAGAAAACAGGAAG
genomic: ATGATTTTACAGGGTTGGGGTTGAAGGTCGTCTCATTGAAAGAAGAAGAGgtgagtctat ... atgtacacagACAGGTGTTCTTGTGGAGAAATTGAACCAAGTGAACGCAGAAAACAGGAAG
EST: gi|161706799|gb|FC055509.1|FC055509
EST:     ATGATTTTACAGGGTTGGGGTTGAAGGTCGTCTCATTGAAAGAAGAAGAG                         ACAGGTGTTCTTGTGGAGAAATTGAACCAAGTGAACGCAGAAAACAGGAAG
genomic: ATGATTTTACAGGGTTGGGGTTGAAGGTCGTCTCATTGAAAGAAGAAGAGgtgagtctat ... atgtacacagACAGGTGTTCTTGTGGAGAAATTGAACCAAGTGAACGCAGAAAACAGGAAG
EST: gi|351054947|gb|FQ440286.1|FQ440286
EST:     ATGATTTTACAGGGTTGGGGTTGAAGGTCGTCTCATTGAAAGAAGAAGAG                         GCAGGTGTTCTTGTGGAGAAATTGAACCAAGTGAACGCAGAAAACAGGAAG
genomic: ATGATTTTACAGGGTTGGGGTTGAAGGTCGTCTCATTGAAAGAAGAAGAGgtgagtctat ... atgtacacagACAGGTGTTCTTGTGGAGAAATTGAACCAAGTGAACGCAGAAAACAGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaattgtaattggggtggtttctgaagctgtgttccccgttttcatgtacacagACAGGTGTTCTTGTGGAGAAATTGAACCAAGTGAACGCAGAAAACAGGAAGCTAACGGAAATGCTAACAGTGATGTGTGAGAATTACAACGCTTTGAGAA
                                 ttccccgttttcat  CT-rich tract
     tgtaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaaatcatagattatggaggaagaaaagaaaagaagttgttcacgtaattgtaattggggtggtttctgaagctgtgttccccgttttcatgtacacagACAGGTGTTCTTGTGGAGAAATTGAACCAAGTGAACGCAGAAAACAGGAAGCTAACGGAAATGCTAACAGTGATGTGTGAGAATTACAACGCTTTGAGAA

- aaatcat
- - - - - - - - - -ggaagaa
- - - - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggggtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaagct