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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccaaccttaagtcatcgtaacatagcaagctccttattcaaaaaacaattatactgacttatttttacctttttctcctctcttacaatgaaaatgcagGTACCTGTGGGAGCCAGATTTGTGGGAATTCCAGGAACAGAGTCTGCAGAGAATCCCAGAGGAGTTATGGTAGAAGTACAATGGGAACAAGATGATACTG

Basic information

species Vitis vinifera
transcript Vv17s0000g05850.t01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g05850.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA06G20360.2 (Glycine max), 3'ss of exon 14
------------------------------------------------------------------------------tccaacctta--agtcatcgt----aacatagcaa----gctccttattcaaaaaacaattata-ctgacttatttt-tacctttttctcctctcttacaatgaaaatgcagGTACCTGTGGGAGCCAGATTTGTGGGAATTCCAGGAACAGAGTCTGCAGAGAATCCCAGAGGAGTTATGGTAGAAGTACAATGGGAACAAGATGATACTG
                                                                               || | |  |  |||||  ||     | ||| |      |||  | | |  || |  | ||  | || |   |  |  ||| |||||      |  |||||| || |||||| | ||| | ||||| || ||||||||||||||||||||||||||||| || || || |  ||  |||||||||||||| | |||||||||||||||||||
gtcagtgtaacagtattttgctttagatttttctacggtgacgtattaggtatatacctctaaaataccttatttatacccgatcacaatagtcaaagttgcagatataacccttctgcttttcagttcaatataagttgcaactaagacaactagtacatttttgctgattaatacaataaacatgcagATTCCTATAGGAGCTAGGTTTGTGGGAATTCCAGGAACAGAGTCTGCTGAAAACCCTACTGGGTTTATGGTAGAAGTATACTGGGAACAAGATGATACTG

upper sequence: Vv17s0000g05850.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA04G34140.1 (Glycine max), 3'ss of exon 15
---tccaaccttaagtcatcgtaacatagcaagctccttattcaaaaaacaattata-ctgacttatttt-tacctttttctcctctcttacaatgaaaatgcagGTACCTGTGGGAGCCAGATTTGTGGGAATTCCAGGAACAGAGTCTGCAGAGAATCCCAGAGGAGTTATGGTAGAAGTACAATGGGAACAAGATGATACTG
   || ||  |  ||  |   || | |     |||  | | |  || |  | || || || |   |  |  ||| |||||      |  |||||| ||||||||| | ||| | ||||| || ||||||||||||||||||||||||||||| || || || |   |  | |||||||||||| | |||||||||||||||||||
tggtcaaagttgcagatac--tacccttct--gcttttcagttcaatataagttgtaactaagacaactagtacatttttgctgattaatacaat-aaaatgcagATTCCTATAGGAGCTAGGTTTGTGGGAATTCCAGGAACAGAGTCTGCTGAAAACCCTACTTGGTTCATGGTAGAAGTATACTGGGAACAAGATGATACTG

upper sequence: Vv17s0000g05850.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: AT5G61730.1 (Arabidopsis thaliana), 3'ss of exon 15
----tccaaccttaagtcatcgtaacatagcaagctccttattcaaaaaacaattatactgactt------attttt--acctttttctcctctcttacaa-------tgaaaatgcagGTACCTGTGGGAGCCAGATTTGTGGGAATTCCAGGAACAGAGTCTGCAGAGAATCCCAGAGGAGTTATGGTAGAAGTACAATGGGAACAAGATGATACTG
    |    |   |||       || |||   || | |  ||  ||    | || | |   |||       |||  |  || |   | |       |||||       | ||  ||||| ||||||||||||| |||||||| || || || ||||||||    ||||||||||| |||||| | ||||| |||||  | ||| ||||||| |   | |
gtaattagtctacaaggtccatcaaaataatcagtttcacatgtaaccgtcgatgaaatgcactattgagaattaatgaacttgaatttaaatggatacaaactaacctcaatgtgcagATACCTGTGGGAGCAAGATTTGTAGGTATCCCTGGAACAGAAAACGCAGAGAATCCAAGAGGACTAATGGTGGAAGTGTACTGGCAACAAGACGGGTCAG

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|37184882|gb|CF604235.1|CF604235
EST:     CTGAAGGGAGCATGGAATCTCTGACTTTAACATCCGGCATAGTGGTTCAG                         GTACCTGTGGGAGCCAGATTTGTGGGAATTCCAGGAACAGAGTCTGCAGA
genomic: CTGAAGGGAGCATGGAATCTCTGACTTTAACATCCGGCATAGTGGTTCAGgtaggtaaag ... gaaaatgcagGTACCTGTGGGAGCCAGATTTGTGGGAATTCCAGGAACAGAGTCTGCAGA
EST: gi|110364066|gb|EC927708.1|EC927708
EST:     CTGAAGGGAGCATGGAATCTCTGACTTTAACATCCGGCATAGTGGTTCAG                         GTACCTGTGGGAGCCAGATTTGTGGGAATTCCAGGAACAGAGTCTGCAGAG
genomic: CTGAAGGGAGCATGGAATCTCTGACTTTAACATCCGGCATAGTGGTTCAGgtaggtaaag ... gaaaatgcagGTACCTGTGGGAGCCAGATTTGTGGGAATTCCAGGAACAGAGTCTGCAGAG
EST: gi|110380814|gb|EC946108.1|EC946108
EST:     CTGAAGGGAGCATGGAATCTCTGACTTTAACATCCGGCATAGTGGTTCAG                         GTACCTGTGGGAGCCAGATTTGTGGGAATTCCAGGAACAGAGTCTGCAGAG
genomic: CTGAAGGGAGCATGGAATCTCTGACTTTAACATCCGGCATAGTGGTTCAGgtaggtaaag ... gaaaatgcagGTACCTGTGGGAGCCAGATTTGTGGGAATTCCAGGAACAGAGTCTGCAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaattatactgacttatttttacctttttctcctctcttacaatgaaaatgcagGTACCTGTGGGAGCCAGATTTGTGGGAATTCCAGGAACAGAGTCTGCAGAGAATCCCAGAGGAGTTATGGTAGAAGTACAATGGGAACAAGATGATACTG
              ttatttttaccttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccaaccttaagtcatcgtaacatagcaagctccttattcaaaaaacaattatactgacttatttttacctttttctcctctcttacaatgaaaatgcagGTACCTGTGGGAGCCAGATTTGTGGGAATTCCAGGAACAGAGTCTGCAGAGAATCCCAGAGGAGTTATGGTAGAAGTACAATGGGAACAAGATGATACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
-ccaacct
- - - - - - - - - - -catagca
- - - - - - - - - - - - - - -gctcctt
- - - - - - - - - - - - - - - - - - - - - aaaacaa