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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgatttattgtaaacaaaattgatgggtttgtttataattgatatttagattacctagtttttttttttttttaaatgtttaattgtttttttccacagATATACAGAGAGAAGAGAAAGGTGTGCAGAAAGCAATTAGGGAAGCAGCCAAGAGAAATGATATGGTGTCTGCTAAG

Basic information

species Vitis vinifera
transcript Vv06s0061g00540.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0061g00540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G21900.1 (Glycine max), 3'ss of exon 1
--gtgatttattgtaaacaaaattgatgggt--ttgtttataattgatatttagattacctagtttttttttttttttaaatgtttaattgtttttttccacagATATACAGAGAGAAGAGAAAGGTGTGCAGAAAGCAATTAGGGAAGCAGCCAAGAGAAATGATATGGTGTCTGCTAAG
   |   |   | | || ||   | ||   |   | ||| || ||  | ||    ||   | | || |  ||  ||||   ||||||   |||| | |    |||||||||||||||||| |||  ||||||||| |||||||| ||||| || ||||| ||||| ||||  ||||| |||
gtattcctctctctcaaaaaccctaattaatccctttttgtatttagttttggacttgttttggttatgcttgattttg--tgtttatgcgtttctatt---agATATACAGAGAGAAGAAAAAAATGTGCAGAAGGCAATTAGAGAAGCTGCAAAGAGGAATGACATGGGCTCTGCAAAG

upper sequence: Vv06s0061g00540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G08510.1 (Glycine max), 3'ss of exon 1
gtgatttattgtaaacaaaat-tgatgggtttgtttataattgatatttagattacctagtttttttttttttttaaatgtttaattgtttttttccacagATATACAGAGAGAAGAGAAAGGTGTGCAGAAAGCAATTAGGGAAGCAGCCAAGAGAAATGATATGGTGTCTGCTAAG
||  |    | |    |||   | ||   ||    | |  ||  | ||||| ||   | ||| |  ||  ||||    ||||||  ||||| | |    |||||||||||||||||| |||  ||||||||| || ||||| |||||||| ||||| ||||| ||||  ||||| |||
gtactcctctctctcaaaaccctaattaattccccttt--tttgtgtttagttt---tggttatgcttgatttt---gtgtttatgtgtttctgtt---agATATACAGAGAGAAGAAAAAAATGTGCAGAAGGCGATTAGAGAAGCAGCAAAGAGGAATGACATGGGCTCTGCAAAG

upper sequence: Vv06s0061g00540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G23570.2 (Glycine max), 3'ss of exon 2
gtgatttattgtaaacaaaattgatgggtttgtttataattgatatttagattacctagtttttttttttttttaaatgtttaattgtttttttccacagATATACAGAGAGAAGAGAAAGGTGTGCAGAAAGCAATTAGGGAAGCAGCCAAGAGAAATGATATGGTGTCTGCTAAG
||  |    | | || ||   | ||   ||    | |  ||  ||||||| ||   | ||| |  ||  ||||    ||||||   |||| | |    |||||||||||||||||| |||  ||||||||| || ||||| ||||| || ||||| ||||| ||||  ||||| |||
gtactcctctctcaa-aaccctaattaattccccttt--tttgtatttagttt---tggttatgcttgatttt---gtgtttatgggtttctatt---agATATACAGAGAGAAGAAAAAAATGTGCAGAAGGCTATTAGAGAAGCTGCAAAGAGGAATGACATGGGCTCTGCAAAG

upper sequence: Vv06s0061g00540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G19930.1 (Glycine max), 3'ss of exon 2
gtgatttattgtaaacaaaattgatgggtttgtttataattgatatttagattacctagtttttttttttttttaaatgtttaattgtttttttccacagATATACAGAGAGAAGAGAAAGG-TGTGCAGAAAGCAATTAGGGAAGCAGCCAAGAGAAATGATATGGTGTCTGCTAAG
                                                          ||| |  ||  ||||    ||||||   |||| | |    |||||||||||||||||| |||   ||||||||| || ||||| |||||||| ||||| ||||| ||||  || || |||
----------------------------------------------------------gttatgcttgatttt---gtgtttatgggtttctatt---agATATACAGAGAGAAGAAAAAAAATGTGCAGAAGGCGATTAGAGAAGCAGCAAAGAGGAATGACATGGGCTCCGCAAAG

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|30296312|gb|CB973106.1|CB973106
EST:     GCAACGGAAACTCCGGCAAGAGTGTCGCAACATCGAACGCCAAATTCGAG                         ATATACAGAGAGAAGAGAAAGGTGTGCAGAAAGCAATTAGGGAAGCAGCCA
genomic: GCAACGGAAACTCCGTCAAGAGTGTCGCAACATCGAACGCCAAATTCGAGgctagttttt ... ttttccacagATATACAGAGAGAAGAGAAAGGTGTGCAGAAAGCAATTAGGGAAGCAGCCA
EST: gi|110718482|gb|EE095363.1|EE095363
EST:     GCAACGGAAACTCCGTCAAGAGTGTCGCAACATCGAACGCCAAATTCGAG                         ATATACAGAGAGAAGAGAAAGGTGTGCAGAAAGCAATTAGGGAAGCAGCCA
genomic: GCAACGGAAACTCCGTCAAGAGTGTCGCAACATCGAACGCCAAATTCGAGgctagttttt ... ttttccacagATATACAGAGAGAAGAGAAAGGTGTGCAGAAAGCAATTAGGGAAGCAGCCA
EST: gi|110718154|gb|EE094659.1|EE094659
EST:     GCAACGGAAACTCCGTCAAGAGTGTCGCAACATCGAACGCCAAATTCGAG                         ATATACAGAGAGAAGAGAAAGGTGTGCAGAAAGCAATTAGGGAAGCAGCCA
genomic: GCAACGGAAACTCCGTCAAGAGTGTCGCAACATCGAACGCCAAATTCGAGgctagttttt ... ttttccacagATATACAGAGAGAAGAGAAAGGTGTGCAGAAAGCAATTAGGGAAGCAGCCA
EST: gi|26257618|gb|CA808681.1|CA808681
EST:     GCAACGGAAACTCCGTCAAGAGTGTCGCAACATCGAACGCCAAATTCGAG                         ATATACAGAGAGAAGAGAAAGGTGTGCAGAAAGCAATTAGGGAAGCAGCCA
genomic: GCAACGGAAACTCCGTCAAGAGTGTCGCAACATCGAACGCCAAATTCGAGgctagttttt ... ttttccacagATATACAGAGAGAAGAGAAAGGTGTGCAGAAAGCAATTAGGGAAGCAGCCA
EST: gi|351031409|gb|FQ445434.1|FQ445434
EST:     GCAACGGAAACTCCGTCAAGAGTGTCGCAACATCGAACGCCAAATTCGAG                         ATATACAGAGAGAAGAGAAAGGTGTGCAGAAAGCAATTAGGGAAGCAGCCA
genomic: GCAACGGAAACTCCGTCAAGAGTGTCGCAACATCGAACGCCAAATTCGAGgctagttttt ... ttttccacagATATACAGAGAGAAGAGAAAGGTGTGCAGAAAGCAATTAGGGAAGCAGCCA
EST: gi|110702630|gb|EE078767.1|EE078767
EST:     GCAACGGAAACTCCGTCAAGAGTGTCGCAACATCGAACGCCAAATTCGAG                         ATATACAGAGAGAAGAGAAAGGTGTGCAGAAAGCAATTAGGGAAGCAGCCA
genomic: GCAACGGAAACTCCGTCAAGAGTGTCGCAACATCGAACGCCAAATTCGAGgctagttttt ... ttttccacagATATACAGAGAGAAGAGAAAGGTGTGCAGAAAGCAATTAGGGAAGCAGCCA
EST: gi|110722756|gb|EE099290.1|EE099290
EST:     GCAACGGAAACTCCGTCAAGAGTGTCGCAACATCGAACGCCAAATTCGAG                         ATATACAGAGAGAAGAGAAAGGTGTGCAGAAAGCAATTAGGGAAGCAGCCA
genomic: GCAACGGAAACTCCGTCAAGAGTGTCGCAACATCGAACGCCAAATTCGAGgctagttttt ... ttttccacagATATACAGAGAGAAGAGAAAGGTGTGCAGAAAGCAATTAGGGAAGCAGCCA
EST: gi|110362725|gb|EC926275.1|EC926275
EST:     GCAACGGAAACTCCGTCAAGAGTGTCGCAACATCGAACGCCAAATTCGAG                         ATATACAGAGAGAAGAGAAAGGTGTGCAGAAAGCAATTAGGGAAGCAGCCA
genomic: GCAACGGAAACTCCGTCAAGAGTGTCGCAACATCGAACGCCAAATTCGAGgctagttttt ... ttttccacagATATACAGAGAGAAGAGAAAGGTGTGCAGAAAGCAATTAGGGAAGCAGCCA
EST: gi|351014990|gb|FQ444279.1|FQ444279
EST:     GCAACGGAAACTCCGTCAAGAGTGTCGCAGCATCGAACGCCAAATTCGAG                         ATATACAGAGAGAAGAGAAAGGTGTGCAGAAAGCAATTAGGGAAGCAGCCA
genomic: GCAACGGAAACTCCGTCAAGAGTGTCGCAACATCGAACGCCAAATTCGAGgctagttttt ... ttttccacagATATACAGAGAGAAGAGAAAGGTGTGCAGAAAGCAATTAGGGAAGCAGCCA
EST: gi|110396776|gb|EC962475.1|EC962475
EST:     GCAACGGAAACTCCGTCAAGAGTGTCGCAACATCGAACGCCAAATTCGAG                         ATATACAGAGAGAAGAGAAAGGTGTGCAGAAAGCAATTAGGGAAGCAGCCA
genomic: GCAACGGAAACTCCGTCAAGAGTGTCGCAACATCGAACGCCAAATTCGAGgctagttttt ... ttttccacagATATACAGAGAGAAGAGAAAGGTGTGCAGAAAGCAATTAGGGAAGCAGCCA
EST: gi|26257678|gb|CA808741.1|CA808741
EST:     GCAACGGAAACTCCGTCAAGAGTGTCGCAACATCGAACGCCAAATTCGAG                         ATATACAGAGAGAAGAGAAAGGTGTGCAGAAAGCAATTAGGGAAGCAGCCA
genomic: GCAACGGAAACTCCGTCAAGAGTGTCGCAACATCGAACGCCAAATTCGAGgctagttttt ... ttttccacagATATACAGAGAGAAGAGAAAGGTGTGCAGAAAGCAATTAGGGAAGCAGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagattacctagtttttttttttttttaaatgtttaattgtttttttccacagATATACAGAGAGAAGAGAAAGGTGTGCAGAAAGCAATTAGGGAAGCAGCCAAGAGAAATGATATGGTGTCTGCTAAG
                                 gtttaat  putative branch site (score: 4)
                                       ttgtttttttccac  CT-rich tract
           tagttttttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatttattgtaaacaaaattgatgggtttgtttataattgatatttagattacctagtttttttttttttttaaatgtttaattgtttttttccacagATATACAGAGAGAAGAGAAAGGTGTGCAGAAAGCAATTAGGGAAGCAGCCAAGAGAAATGATATGGTGTCTGCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - aaacaaa
- - - - - - - - - - - - -gggtttg