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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctagaaaaggcgaaaagagtacttaatcctttatgtgagcttttcaagtgatttctcattaagtctttcaaatattgcctctattttgttatttttccagTTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTGCAGAGAATGTTGAAAGTGTATTAGATGAGATCCGACCATATCTTATTTC

Basic information

species Vitis vinifera
transcript Vv12s0035g00770.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g00770.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G28900.2 (Glycine max), 3'ss of exon 2
ctagaaaaggcgaaaagagtacttaatcctttatgtgagcttttcaagtgatttctcattaagtctttcaaatattgcctctattttg---ttattt--ttccagTTGTCAAGGCTGTTGC--TACCCCGGATTCA--GCAGTGGAAT-TGCCACTAACTGCAGAGA--ATGTTGAAAGTGTATTAGATGAGATCCGACCATATCTTATTTC
      || | |    |        | ||    ||||   ||  ||  | | | || |  | ||        |||||  |  | || |    ||| |  || |||  |    |  ||| ||  |||  |  ||| |  ||| ||   |  ||    | || ||| |   |||| |    |||   || |  | | | |||||          
----ttaaagtgtgttgttactccgaacccagctgtggaattgccat-taactgctgaaaatgtagaaagtgtattggatgaaattcgaccctatctcattgcagACGGTGGGAATGTGGCTTTACATCAAATTGATGGCAATGTTGTGCGCTTGAAGCTACAGGGCGCATGTGGTTCCTGTCCAAGTTCTGTTACCACCATGAA-------

upper sequence: Vv12s0035g00770.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G28900.1 (Glycine max), 3'ss of exon 2
-ctagaaa--aggcgaaaagagtacttaatcctttatgtga----gcttttcaagtgattt-ctcattaagtct-ttcaaatattgcctctattttgttatttttccagTTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTGCAGAGAATGTTGAAAGTGTATTAGATGAGATCCGACCATATCTTATTTC
  ||| |   |  |  |||      | ||| | | |   |     ||||  |   |||  | ||   |   |   ||| |||   |   ||   |      || | ||| | | |||  ||||| ||| ||| |  |||| |||||||||||| ||||||| || ||||| ||||||||||| ||||| || ||||| ||||| ||| |
gttagtagttaccctcaaacttgtttcaatacataacacgcaaatgcttcccctatgacatgcttgctcctttaattccaattgggaaactgaatctcatcttctacagCTTTAAAGTGTGTTGTTACTCCGAACCCAGCTGTGGAATTGCCATTAACTGCTGAAAATGTAGAAAGTGTATTGGATGAAATTCGACCCTATCTCATTGC
















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|349812244|gb|FQ411839.1|FQ411839
EST:     CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAG                         TTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTTCCACTAACTG
genomic: CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAGgtagtcgatt ... atttttccagTTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
EST: gi|349816925|gb|FQ405051.1|FQ405051
EST:     CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGTG                         TTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
genomic: CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAGgtagtcgatt ... atttttccagTTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
EST: gi|351033002|gb|FQ461891.1|FQ461891
EST:     CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAG                         TTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
genomic: CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAGgtagtcgatt ... atttttccagTTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
EST: gi|351015380|gb|FQ447209.1|FQ447209
EST:     CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAG                         TTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
genomic: CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAGgtagtcgatt ... atttttccagTTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
EST: gi|351019291|gb|FQ429451.1|FQ429451
EST:     CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAG                         TTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
genomic: CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAGgtagtcgatt ... atttttccagTTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
EST: gi|110383835|gb|EC948236.1|EC948236
EST:     CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAG                         TTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
genomic: CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAGgtagtcgatt ... atttttccagTTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
EST: gi|349816960|gb|FQ405086.1|FQ405086
EST:     CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAG                         TTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTTCCACTAACTG
genomic: CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAGgtagtcgatt ... atttttccagTTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
EST: gi|110380986|gb|EC946293.1|EC946293
EST:     CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAG                         TTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
genomic: CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAGgtagtcgatt ... atttttccagTTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
EST: gi|349814109|gb|FQ414343.1|FQ414343
EST:     CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAG                         TTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAGTTGCCACTAACTG
genomic: CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAGgtagtcgatt ... atttttccagTTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
EST: gi|37190110|gb|CF609459.1|CF609459
EST:     CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAG                         TTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
genomic: CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAGgtagtcgatt ... atttttccagTTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
EST: gi|351015690|gb|FQ427175.1|FQ427175
EST:     CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAG                         TTGTCAAGGCTGTTGCTACCCCGGATTCGGCAGTGGAATTGCCACTAACTG
genomic: CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAGgtagtcgatt ... atttttccagTTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
EST: gi|26262230|gb|CA813293.1|CA813293
EST:     CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAG                         TTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
genomic: CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAGgtagtcgatt ... atttttccagTTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
EST: gi|110369819|gb|EC933988.1|EC933988
EST:     CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAG                         TTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
genomic: CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAGgtagtcgatt ... atttttccagTTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
EST: gi|110708505|gb|EE086122.1|EE086122
EST:     CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAG                         TTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
genomic: CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAGgtagtcgatt ... atttttccagTTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
EST: gi|349822331|gb|FQ412595.1|FQ412595
EST:     CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAG                         TTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAGTTGCCACTAACTG
genomic: CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAGgtagtcgatt ... atttttccagTTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
EST: gi|110390777|gb|EC955704.1|EC955704
EST:     CTCGTCGCGTTCCCTGCGGATTCGGAACCTTATTAGAACACGTAGCCGAG                         TTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
genomic: CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAGgtagtcgatt ... atttttccagTTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
EST: gi|349828646|gb|FQ418381.1|FQ418381
EST:     CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAG                         TTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
genomic: CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAGgtagtcgatt ... atttttccagTTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
EST: gi|351026904|gb|FQ436557.1|FQ436557
EST:     CTCGTTGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAG                         TTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
genomic: CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAGgtagtcgatt ... atttttccagTTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
EST: gi|351032469|gb|FQ458834.1|FQ458834
EST:     CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAG                         TTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTTCCACTAACTG
genomic: CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAGgtagtcgatt ... atttttccagTTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
EST: gi|349823025|gb|FQ400004.1|FQ400004
EST:     CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAG                         TTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAGTTGCCACTAACTG
genomic: CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAGgtagtcgatt ... atttttccagTTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
EST: gi|349823598|gb|FQ415008.1|FQ415008
EST:     CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAG                         TTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
genomic: CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAGgtagtcgatt ... atttttccagTTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
EST: gi|33407802|gb|CF213429.1|CF213429
EST:     CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAG                         TTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
genomic: CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAGgtagtcgatt ... atttttccagTTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
EST: gi|110713850|gb|EE090132.1|EE090132
EST:     CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAG                         TTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
genomic: CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAGgtagtcgatt ... atttttccagTTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
EST: gi|110407299|gb|EC972896.1|EC972896
EST:     CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAG                         TTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
genomic: CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAGgtagtcgatt ... atttttccagTTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG
EST: gi|351017333|gb|FQ435685.1|FQ435685
EST:     CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAG                         TTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTTCCACTAACTG
genomic: CTCGTCGCGTTCCCTGCGGATTCGGAACCCTATTAGAACACGTAGCCGAGgtagtcgatt ... atttttccagTTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtgatttctcattaagtctttcaaatattgcctctattttgttatttttccagTTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTGCAGAGAATGTTGAAAGTGTATTAGATGAGATCCGACCATATCTTATTTC
                                cctctattttgttatt  CT-rich tract
                                  tctattttgttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctagaaaaggcgaaaagagtacttaatcctttatgtgagcttttcaagtgatttctcattaagtctttcaaatattgcctctattttgttatttttccagTTGTCAAGGCTGTTGCTACCCCGGATTCAGCAGTGGAATTGCCACTAACTGCAGAGAATGTTGAAAGTGTATTAGATGAGATCCGACCATATCTTATTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
-tagaaaa
- - - - - -gaaaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaatat