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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttataatccatagcagggtgcgctattttcaattttcaaaattattctgttgataatttccaatactatataatacaagtgtattctacttgtggatagGTGACTTCATGCAAACTGTGGCGGCAAGTGGGAGAGTCCTTTAAACCCCCAAA

Basic information

species Vitis vinifera
transcript Vv04s0044g01840.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0044g01840.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA11G09370.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------------------tttataatccatagcagggtgcgctatt--ttcaatttt--caaaattattctgttgataatttccaatactatataatacaagtgtattctacttgtggatagGTGACTTCATGCAAACTGTGGCGGCAAGTGGGAGAGTCCTTTAAACCCCCAAA
                                                            |||   |  ||  ||   |  ||||||  ||   || |  || |    || | |||||  ||||| | | | || |    || ||| || || || |  ||||||||||||||| ||| | |||||||||||||||||||| || ||||| || ||
gtattcaagtaattttacacttgatgagcaaaattttaaggggttgttatttgagccaaattaactttgattacactctcagctattagtttgtttatatcagatcccttgttttgattgtttccgaga-tgtacacc-taattgtcttgtaattataaatagGTGACTTCATGTAAATTATGGCGGCAAGTGGGAGAGTCTTTCAAACCTCCGAA

upper sequence: Vv04s0044g01840.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA01G36040.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------------------tttataatccatagcagggtgcgctatt--ttcaatttt--caaaattattctgttgataatttccaatactatataatacaagtgtattctacttgtggatagGTGACTTCATGCAAACTGTGGCGGCAAGTGGGAGAGTCCTTTAAACCCCCAAA
                                                            |||   |  ||  ||   |  ||||||  ||   || |  || |    || | || ||  ||||| | || ||| |    || ||  || || || |  ||||||||||||||| ||| | |||||||||||||||||||| || || || || ||
gtattcatgtaattttacacttgatgagcaaaattttaaggggttgttatttgagccaaattaactttgattacattctaagctattagtttgtttatatcagatcacttgtttttattttttccgagac-atacacc-taaatggcttatatttataaatagGTGACTTCATGTAAATTATGGCGGCAAGTGGGAGAGTCTTTCAAGCCTCCGAA

upper sequence: Vv04s0044g01840.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA16G21840.1 (Glycine max), 3'ss of exon 4
tttataatccatagcagggtgcgctat-tttcaattttcaa-aattattct---gttgataatttccaatactatataatacaagtgtattctacttgtggatagGTGACTTCATGCAAACTGTGGCGGCAAGTGGGAGAGTCCTTTAAACCCCCAAA
      ||| ||  ||   |||   |  ||| | ||  ||  | || || |   ||||  |||| | | |  |||||     |   |  || ||  | || |||||| || ||||| ||| | |||||||||||||||||||| || ||||| |||||
----acatcaattacactatgcttcaagttttagttcacagcagttgttttcatgttgccaattgcta-tgatatatgcctaattggggttatatatatgaatagGTTACCTCATGTAAATTCTGGCGGCAAGTGGGAGAGTCTTTCAAACCTCCAAA

upper sequence: Vv04s0044g01840.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G32820.1 (Glycine max), 3'ss of exon 2
tttataatccatagcagggtgcgctattttcaattttcaa-aattattct----gttgataatttccaatactatataatacaagtgtattctacttgtggatagGTGACTTCATGCAAACTGTGGCGGCAAGTGGGAGAGTCCTTTAAACCCCCAAA
   || |   | |  | | | |   | ||| | ||  ||  | || || |    ||||  |||| |||  |  ||||     |   |  || ||  | |  |||||| || ||||  ||| |||||||||||||||||||||| || ||||| |||||
--catcaattacactaagctcca--agttttagttcacatcagttgttttcattgttgccaattgccatgataatatgcctaactggggttatatatata-atagGTTACCTCATATAAATTGTGGCGGCAAGTGGGAGAGTCTTTCAAACCTCCAAA

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|110703600|gb|EE080590.1|EE080590
EST:     AGAGCGGTGACTAGATTGGGTGGCTATGACAAG                         GTGACTTCATGCAAACTGTGGCGGCAAGTGGGAGAGTCCTTTAAACCCCCA
genomic: AGAGCGGTGACTAGATTGGGTGGCTATGACAAGgtataactga ... ttgtggatagGTGACTTCATGCAAACTGTGGCGGCAAGTGGGAGAGTCCTTTAAACCCCCA
EST: gi|32248497|gb|CD714316.1|CD714316
EST:     ATTATGGAGAGCGGTGACTAGATTGGGTGGCTATGACAAG                         GTGACTTCATGCAAACTGTGGCGGCAAGTGGGAGAGTCCTTTAAACCCCCA
genomic: ATTATGGAGAGCGGTGACTAGATTGGGTGGCTATGACAAGgtataactga ... ttgtggatagGTGACTTCATGCAAACTGTGGCGGCAAGTGGGAGAGTCCTTTAAACCCCCA
EST: gi|32249759|gb|CD715578.1|CD715578
EST:     ATTATGGAGAGCGGTGACTAGATTGGGTGGCTATGACAAG                         GTGACTTCATGCAAACTGTGGCGGCAAGTGGGAGAGTCCTTTAAACCCCCA
genomic: ATTATGGAGAGCGGTGACTAGATTGGGTGGCTATGACAAGgtataactga ... ttgtggatagGTGACTTCATGCAAACTGTGGCGGCAAGTGGGAGAGTCCTTTAAACCCCCA
EST: gi|32247711|gb|CD713530.1|CD713530
EST:     ATTATGGAGAGCGGTGACTAGATTGGGTGGCTATGACAAG                         GTGACTTCATGCAAACTGTGGCGGCAAGTGGGAGAGTCCTTTAAACCCCCA
genomic: ATTATGGAGAGCGGTGACTAGATTGGGTGGCTATGACAAGgtataactga ... ttgtggatagGTGACTTCATGCAAACTGTGGCGGCAAGTGGGAGAGTCCTTTAAACCCCCA
EST: gi|110688872|gb|EE067920.1|EE067920
EST:     ATTATGGAGAGCGGTGACTAGATTGGGTGGCTATGACAAG                         GTGACTTCATGCAAACTGTGGCGGCAAGTGGGAGAGTCCTTTAAACCCCCA
genomic: ATTATGGAGAGCGGTGACTAGATTGGGTGGCTATGACAAGgtataactga ... ttgtggatagGTGACTTCATGCAAACTGTGGCGGCAAGTGGGAGAGTCCTTTAAACCCCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgttgataatttccaatactatataatacaagtgtattctacttgtggatagGTGACTTCATGCAAACTGTGGCGGCAAGTGGGAGAGTCCTTTAAACCCCCAAA
   tgttgat  putative branch site (score: 4)
                                       ttctactt  putative PPT
        ataatttccaatacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttataatccatagcagggtgcgctattttcaattttcaaaattattctgttgataatttccaatactatataatacaagtgtattctacttgtggatagGTGACTTCATGCAAACTGTGGCGGCAAGTGGGAGAGTCCTTTAAACCCCCAAA

- - - - -catagca
- - - - - - - - gggtgcg
- - - - - - - - - - - - - - - - - -ttcaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatacaa