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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagggatgtgctctggtaggtctttttgtttgtttcatatttggttgctatgcaagcacatcattctaaacccttgtacaataccaacttgttcatgcagCTTGCAAATATCATGGGTCGTTTTCAGTGGCTAACATGTCCAAGGAAG

Basic information

species Vitis vinifera
transcript Vv00s0187g00380.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0187g00380.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA20G34940.1 (Glycine max), 3'ss of exon 6
tagggatgtgctctggtaggtctttttgtttgtttcatatttggttgctatgcaa----gcacatcattctaaacccttgtacaataccaacttgttcatgcagCTTGCAAATATCATGGGTCGTTTTCAGTGGCTAACATGTCCAAGGAAG
|    ||         |    || ||  ||   |   |||         | |  |    | ||   || ||||  | || | || |   ||||  ||  || ||||||| || ||||||||||||| |||||||||||| ||||||||||||
tcatcattcatggcaattaagctcttgcttaagtctttatacatcaatcaagttattctgaactagatgctaa--cattat-cattgaaaactcattt-tgtagCTTGCTAACATCATGGGTCGTTCTCAGTGGCTAACGTGTCCAAGGAAG

upper sequence: Vv00s0187g00380.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA10G32660.2 (Glycine max), 3'ss of exon 6
tagggatgtgctctggtaggtctttttgtttgtttcatatttggttgctatgcaagcacatcattctaaacc-----cttgta----caataccaacttgttcatgcagCTTGCAAATATCATGGGTCGTTTTCAGTGGCTAACATGTCCAAGGAAG
        |  ||    | | |  ||   || || | ||  |  ||      ||| ||  | ||||| |||      ||   |    || |   ||||  ||  || ||||||| || ||||||||||| | |||||||||||| ||||||||||||
--------tcatcattcatggcaattaagttcttgcttaagtctttatacatcaatcaagttattctgaactaaatactaacattatcattgaaaactcattt-tgtagCTTGCTAACATCATGGGTCGCTCTCAGTGGCTAACGTGTCCAAGGAAG

upper sequence: Vv00s0187g00380.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT4G22340.3 (Arabidopsis thaliana), 3'ss of exon 5
tagggatgtgctctggtaggtctttttgtttgtttcatatttggttgctatgcaagcacatcattctaaacccttgtacaataccaacttgttcatgcagCTTGCAAATATCATGGGTCGTTTTCAGTGGCTAACATGTCCAAGGAAG
               ||| |  | |||  | |  | |||  |   || | |   | |   |  |    ||    |  | ||| |   ||||||  || ||||||||||||| ||||||||||| | |||||| |||||||| ||  ||
---------------gtaagcttgttttatgggctaataagtatatgttttttga-cgagtagt----aattgattaataat-cttgcttgtttttgtagCTTGCAAATATAATGGGTCGTTTCCTGTGGCTGACATGTCCCAGAGAG

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|30327030|gb|CD010292.1|CD010292
EST:     GGGAAGGTTTCATTGGGGCATCTATTGCAACTATTATCTCTGCATTTGTG                         CTTGCAAATATCATGGGTCGTTTTCAGTGGCTAACATGTCCAAGGAAG
genomic: GGGAAGGTTTCATTGGGGCATCTATTGCAACTATTATCTCTGCATTTGTGgtagtctctc ... gttcatgcagCTTGCAAATATCATGGGTCGTTTTCAGTGGCTAACATGTCCAAGGAAG
EST: gi|32271292|gb|CD720451.1|CD720451
EST:     GGGAAGGTTTCATTGGGGCATCTATTGCAACTATTATCTCTGCATTTGTG                         CTTGCAAATATCATGGGTCGTTTTCAGTGGCTAACATGTCCAAGGAAG
genomic: GGGAAGGTTTCATTGGGGCATCTATTGCAACTATTATCTCTGCATTTGTGgtagtctctc ... gttcatgcagCTTGCAAATATCATGGGTCGTTTTCAGTGGCTAACATGTCCAAGGAAG
EST: gi|32249237|gb|CD715056.1|CD715056
EST:     GGGAAGGTTTCATTGGGGCATCTATTGCAACTATTATCTCTGCATTTGTG                         CTTGCAAATATCATGGGTCGTTTTCAGTGGCTAACATGTCCAAGGAAG
genomic: GGGAAGGTTTCATTGGGGCATCTATTGCAACTATTATCTCTGCATTTGTGgtagtctctc ... gttcatgcagCTTGCAAATATCATGGGTCGTTTTCAGTGGCTAACATGTCCAAGGAAG
EST: gi|32271411|gb|CD720570.1|CD720570
EST:     GGGAAGGTTTCATTGGGGCATCTATTGCAACTATTATCTCTGCATTTGTG                         CTTGCAAATATCATGGGTCGTTTTCAGTGGCTAACATGTCCAAGGAAG
genomic: GGGAAGGTTTCATTGGGGCATCTATTGCAACTATTATCTCTGCATTTGTGgtagtctctc ... gttcatgcagCTTGCAAATATCATGGGTCGTTTTCAGTGGCTAACATGTCCAAGGAAG
EST: gi|32249768|gb|CD715587.1|CD715587
EST:     GGGAAGGTTTCATTGGGGCATCTATTGCAACTATTATCTCTGCATTTGTG                         CTTGCAAATATCATGGGTCGTTTTCAGTGGCTAACATGTCCAAGGAAG
genomic: GGGAAGGTTTCATTGGGGCATCTATTGCAACTATTATCTCTGCATTTGTGgtagtctctc ... gttcatgcagCTTGCAAATATCATGGGTCGTTTTCAGTGGCTAACATGTCCAAGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctatgcaagcacatcattctaaacccttgtacaataccaacttgttcatgcagCTTGCAAATATCATGGGTCGTTTTCAGTGGCTAACATGTCCAAGGAAG
                  ttctaaa  putative branch site (score: 2)
                                          cttgttc  putative PPT
                 attctaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagggatgtgctctggtaggtctttttgtttgtttcatatttggttgctatgcaagcacatcattctaaacccttgtacaataccaacttgttcatgcagCTTGCAAATATCATGGGTCGTTTTCAGTGGCTAACATGTCCAAGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- -ggatgtg
- - - - - - -tggtagg
- - - - - - - - - - - - - - - - - - - - - - - -ctatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaccct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataccaa