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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaagaaacccgtctttcttttgaaatttatgttacatgagctccagtagcattcttatcatccgagtttctggcttccaaccttttgctctacgtccagGAACTGCACAATTTGTGCTCAAAGAAAGGAGTTCTTCTAGTTCTTCATGGAGCTTCTGGGTTGTCAGAGAAACTCATCAAG

Basic information

species Vitis vinifera
transcript Vv17s0000g02140.t01
intron # 38
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g02140.t01 (Vitis vinifera), 3'ss of exon 38
lower sequence: AT1G18270.3 (Arabidopsis thaliana), 3'ss of exon 40
gaaagaaacccgtctttcttttgaaatttatg-ttacatgagctccagtagcattcttatcatccgagtt-tctggcttccaaccttttgctctacgtccagGAACTGCACAATTTGTGCTCAAAGAAAGGAGTTCTTCTAGTTCTTCATGGAGCTTCTGGGTTGTCAGAGAAACTCATCAAG
                     |||| | |||  ||       ||  ||||   ||||     |  | ||  |     ||| |||   |  |  |   |  |||||||||||   ||  |||| |||||||| ||| |||| |||||||| ||||||||||| ||||| ||||| || ||||||
--------------------gtgaattatattcttgtgctgactgaagtaa-gttctatgagtttgtgtcattcttattctaactgatcaccatgtatgtagGAACTGCACGCCTTAAGCTCGAAGAAAGGCGTTTTTCTTGTTCTTCACGGAGCTTCTGGTTTGTCTGAGAACCTTATCAAG
















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|349820359|gb|FQ403975.1|FQ403975
EST:     ATGGAAAATACACTGCAACTGGCCCAAATCTCAGACTTGATTTACTTAAG                         A
genomic: ATGGAAAATACCCTGCAACTGGCCCAAATCTCAGACTTGATTTACTTAAGgttaagtata ... ctacgtccag-
EST: gi|349820359|gb|FQ403975.1|FQ403975
EST:     ATGGAAAATACACTGCAACTGGCCCAAATCTCAGACTTGATTTACTTAAG                         A
genomic: ATGGAAAATACCCTGCAACTGGCCCAAATCTCAGACTTGATTTACTTAAGgttaagtata ... ctacgtccag-
EST: gi|349808649|gb|FQ405793.1|FQ405793
EST:     ATGGAAAATACCCTGCAACTGGCCCCAATCTCAGACTTGATTTACTTAAG                         GAACTGCACAAT
genomic: ATGGAAAATACCCTGCAACTGGCCCAAATCTCAGACTTGATTTACTTAAGgttaagtata ... ctacgtccagGAACTGCACAAT
EST: gi|30125587|gb|CB910926.1|CB910926
EST:     ATGGAAAATACCCTGCAACTGGCCCAAATCTCAGACTTGATTTACTTAAG                         GAACTGCACAATTTGTGCTCAAAGAAAGGAGTTCTTCTAGTTCTTCATGGA
genomic: ATGGAAAATACCCTGCAACTGGCCCAAATCTCAGACTTGATTTACTTAAGgttaagtata ... ctacgtccagGAACTGCACAATTTGTGCTCAAAGAAAGGAGTTCTTCTAGTTCTTCATGGA
EST: gi|349826605|gb|FQ418696.1|FQ418696
EST:     ATGGAAAATACCCTGCAACTGGCCCAAATCTCAGACTTGATTTACTTAAG                         GAACTGCACAATTTGTGCTCAAAGAAAGGAGTTCTTCTAGTTCTTCATGGA
genomic: ATGGAAAATACCCTGCAACTGGCCCAAATCTCAGACTTGATTTACTTAAGgttaagtata ... ctacgtccagGAACTGCACAATTTGTGCTCAAAGAAAGGAGTTCTTCTAGTTCTTCATGGA
EST: gi|349824745|gb|FQ414603.1|FQ414603
EST:     ATGGAAAATACCCTGCAACTGGCCCAAATCTCAAACTTGAATTACTTAAG                         GAACTGCACAATTTG
genomic: ATGGAAAATACCCTGCAACTGGCCCAAATCTCAGACTTGATTTACTTAAGgttaagtata ... ctacgtccagGAACTGCACAATTTG
EST: gi|349820676|gb|FQ408505.1|FQ408505
EST:     ATGGAAAATACCCTGCAACTGGCCCAAATCTCAGACTTGATTTACTTAAG                         GAACTGCACAATTTGT
genomic: ATGGAAAATACCCTGCAACTGGCCCAAATCTCAGACTTGATTTACTTAAGgttaagtata ... ctacgtccagGAACTGCACAATTTGT
EST: gi|349808888|gb|FQ406738.1|FQ406738
EST:     ATGGAAAATACCCTGCTACTGGCCCAAATCTCAGACTTGATTTACTTAAG                         GAACTGCACAATTTGTGCTCAAAGAAAGGAGTTCTTCTAGTTCTTCATGGA
genomic: ATGGAAAATACCCTGCAACTGGCCCAAATCTCAGACTTGATTTACTTAAGgttaagtata ... ctacgtccagGAACTGCACAATTTGTGCTCAAAGAAAGGAGTTCTTCTAGTTCTTCATGGA
EST: gi|27582127|gb|CB004822.1|CB004822
EST:     ATGGAAAATATCCTGCAACTGGCCCAAATCTCAGACTTGATTTACTTAAG                         GAACTGCACAATTTGTGCTCAAAGAAAGGAGTTCTTCTAGTTCTTCATGGA
genomic: ATGGAAAATACCCTGCAACTGGCCCAAATCTCAGACTTGATTTACTTAAGgttaagtata ... ctacgtccagGAACTGCACAATTTGTGCTCAAAGAAAGGAGTTCTTCTAGTTCTTCATGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtagcattcttatcatccgagtttctggcttccaaccttttgctctacgtccagGAACTGCACAATTTGTGCTCAAAGAAAGGAGTTCTTCTAGTTCTTCATGGAGCTTCTGGGTTGTCAGAGAAACTCATCAAG
                                    ccttttgctct  CT-rich tract
      attcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaagaaacccgtctttcttttgaaatttatgttacatgagctccagtagcattcttatcatccgagtttctggcttccaaccttttgctctacgtccagGAACTGCACAATTTGTGCTCAAAGAAAGGAGTTCTTCTAGTTCTTCATGGAGCTTCTGGGTTGTCAGAGAAACTCATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
-aaagaaa
- - - - - - - - - - - - - - - - - -catgagc
- - - - - - - - - - - - - - - - - - - - - - - - -gcattct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttcca