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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agattcaccattttaattcacatttgatatgccatccaatttgtttgataaccattctcttttcctgattttgatttcaagagtagttatttacttgcagGGTTCTTGCTGTTCCTCGCACTGATGATAGATAGACTTCACCATTACATTCGAGAGCTTCGTTTACTCAGGAAGGCCATGGAGGCTGAAAAGAAGCAAAA

Basic information

species Vitis vinifera
transcript Vv12s0059g00810.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0059g00810.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA13G38590.1 (Glycine max), 3'ss of exon 1
agattcaccattttaattcacatttgatatgccatccaatttgtttga--taaccattctcttttcctgattttgatttcaagagtag--ttatttactt------------gcagGGTTCTTGCTGTTCCTCGCACTGATGATAGATAGACTTCACCATTACATTCGAGAGCTTCGTTTACTCAGGAAGGCCATGGAGGCTGAAAAGAAGCAAAA
                | |||  |  ||||     |||||||||||||  | |    | |||||     ||  |  ||     | | |  || || || |            ||||||||  |||||||| |  | ||||||||||||||| | |||||||||||  |||||||||| ||||| |||||||||||||||||||  ||||| || | 
----------------tgcacgctaaatatatggaccaatttgtttgatttgaagggtttctttcttgtataatagttgtggcatttgatttgttgacatatgaagatgtgagcagGGTTTGTGCTGTTCTTGTCTCTGATGATAGATAGATTGCACCATTACATAAGAGAGCTTCGGTTACTGAGGAAGGCCATGGAGGCTGCTAAGAAACAGAG

upper sequence: Vv12s0059g00810.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA12G10400.1 (Glycine max), 3'ss of exon 1
---agattcaccattttaattcacatt-tgatatgccatccaatttgtttgata-accattctcttttcctgattttgatttcaagagtagttatttacttgcagGGTTCTTGCTGTTCCTCGCACTGATGATAGATAGACTTCACCATTACATTCGAGAGCTTCGTTTACTCAGGAAGGCCATGGAGGCTGAAAAGAAGCAAAA
      ||    ||||   | |  ||| |  | |    | |   ||  | |||| |  |||   ||||  |||  ||||| |   |  |  | || |   |||||||||  ||||||||||| | |||||||| |||||| | |||||||||||  |||||||||| | |||||||||| ||||||| |||   ||||| |||| 
cgtgagttggatatttctttacttattgtagtttttttttcctattaatagatatattatttagtttt--tgaacttgatcttttgcatc-taatgtg--tgcagGGTTTCTGCTGTTCCTCTCTCTGATGATTGATAGATTGCACCATTACATAAGAGAGCTTCGGTCACTCAGGAAGACCATGGAAGCTATTAAGAAACAAAG

upper sequence: Vv12s0059g00810.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA12G31900.1 (Glycine max), 3'ss of exon 1
----agattcaccattttaattca--catttgatatgccatccaatttgtttgataaccattctcttttcctgattttgatttcaagagtagttatttacttgcagGGTTCTTGCTGTTCCTCGCACTGATGATAGATAGACTTCACCATTACATTCGAGAGCTTCGTTTACTCAGGAAGGCCATGGAGGCTGAAAAGAAGCAAAA
    | | |   | | | ||   |   ||||||| ||        ||| |||  |    | |     || | || ||||||||      ||      |    ||||||||  ||||||||||  |  |||||||||||||| | ||||||||||| ||||| ||| | ||||| |||||||||||||||||||  ||||| || | 
ttaaaaaattgtcttgtgaaccaagttatttgatttgaag---ggtttctttcttgtgtaatag---ttgcggaatttgatttttgacatatgatgatgtgggcagGGTTTGTGCTGTTCCTGTCTTTGATGATAGATAGATTGCACCATTACATCCGAGAACTTAGGTTACTAAGGAAGGCCATGGAGGCTGCTAAGAAACAGAG

upper sequence: Vv12s0059g00810.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA06G46370.1 (Glycine max), 3'ss of exon 1
agattcaccattttaattcacatttgatatgccatccaatttgt-ttgataaccattctcttt---tcctgattttgatttcaagagtagttatttacttgcagGGTTCTTGCTGTTCCTCGCACTGATGATAGATAGACTTCACCATTACATTCGAGAGCTTCGTTTACTCAGGAAGGCCATGGAGGCTGAAAAGAAGCAAAA
 | ||      ||   |    | |  |  |   ||  | ||| | || ||||  ||  | |||   || ||| |||||| |      || | || |   |||||||||  | ||||||||| | |||||||| |||||||| |||||||||||  |||||||||| | |||||||||| ||||||| ||    ||||| |||| 
-ggttggatgattctttatttagtgcagtttttatttattttttattaataaatatattatttagttcttgaatttgatctttcacata-taatgtg--tgcagGGTTTGTACTGTTCCTCTCTCTGATGATTGATAGACTGCACCATTACATAAGAGAGCTTCGGTCACTCAGGAAGACCATGGAAGCCATTAAGAAACAAAG

upper sequence: Vv12s0059g00810.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G42570.1 (Arabidopsis thaliana), 3'ss of exon 1
--agattcacca---ttttaattcacatttgatatgccatccaatttgtttgataaccattctcttttcctgattttgatttcaagagtagttatttacttgcagGGTTCTTGCTGTTCCTCGCACTGATGATAGATAGACTTCACCATTACATTCGAGAGCTTCGTTTACTCAGGAAGGCCATGGAGGCTGAAAAGAAGCAAAA
    ||| |  |    ||||   || |||   |   || |   | || | |       ||| | |    ||||| ||| ||     | |  || | || || |||||||  || |||| ||| | || ||||| |||||||| |||||||||||| |||||||||||||  | |||||| | |||||| ||| ||||||||| ||
agtaattaaggaggtatttagagcaaatt--gtgatccttattagttatgtagatctgattatatgaatctgatattggttattgaatt--ttgtata-ttacagGGTTTGTGTTGTTTCTCTCGCTTATGATTGATAGACTACACCATTACATTAGAGAGCTTCGTTTGTTGAGGAAGACAATGGAGACTGCAAAGAAGCAGAA

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|110688807|gb|EE067783.1|EE067783
EST:     CACCGATCAGGTTCTTATGGCCAGGCATCTGCTCGAAGCCTCTCTCATGG                         GGTTCTTGCTGTTCCTCGCACTGATGATAGATAGACTTCACCATTACATTC
genomic: CACCGATCAGGTTCTTATGGCCAGGCATCTGCTCGAAGCCTCTCTCATGGgtatttccga ... ttacttgcagGGTTCTTGCTGTTCCTCGCACTGATGATAGATAGACTTCACCATTACATTC
EST: gi|33111285|gb|CF074629.1|CF074629
EST:     CACCGATCAGGTTCTTATGGCCAGGCATCTGCTCGAAGCCTCTCTCATGG                         GGTTCTTGCTGTTCCTCGCACTGATGATAGATAGACTTCACCATTACATTC
genomic: CACCGATCAGGTTCTTATGGCCAGGCATCTGCTCGAAGCCTCTCTCATGGgtatttccga ... ttacttgcagGGTTCTTGCTGTTCCTCGCACTGATGATAGATAGACTTCACCATTACATTC
EST: gi|351016858|gb|FQ424285.1|FQ424285
EST:     CACCGATCAGGTTCTTATGGCCAGGCATCTGCTCGAAGCCTCTCTCATGG                         GGTTCTTGCTGTTCCTCGCACTGATGATAGATAGACTTCACCATTACATTC
genomic: CACCGATCAGGTTCTTATGGCCAGGCATCTGCTCGAAGCCTCTCTCATGGgtatttccga ... ttacttgcagGGTTCTTGCTGTTCCTCGCACTGATGATAGATAGACTTCACCATTACATTC
EST: gi|349830984|gb|FQ418268.1|FQ418268
EST:     CACCGATCAGGTTCTTATGGCCAGGCATCTGCTCGAAGCCTCTCTCATGG                         GGTTCTTGCTGTTCCTCGCACTGATGATAGATAGACTTCACCATTACATTC
genomic: CACCGATCAGGTTCTTATGGCCAGGCATCTGCTCGAAGCCTCTCTCATGGgtatttccga ... ttacttgcagGGTTCTTGCTGTTCCTCGCACTGATGATAGATAGACTTCACCATTACATTC
EST: gi|110697166|gb|EE073914.1|EE073914
EST:     CACCGATCAGGTTCTTATGGCCAGGCATCTGCTCGAAGCCTCTCTCATGG                         GGTTCTTGCTGTTCCTCGCACTGATGATAGATAGACTTCACCATTACATTC
genomic: CACCGATCAGGTTCTTATGGCCAGGCATCTGCTCGAAGCCTCTCTCATGGgtatttccga ... ttacttgcagGGTTCTTGCTGTTCCTCGCACTGATGATAGATAGACTTCACCATTACATTC
EST: gi|351042568|gb|FQ431166.1|FQ431166
EST:     CACCGATCAGGTTCTTATGGCCAGGCATCTGCTCGAAGCCTCTCTCATGG                         GGTTCTTGCTGTTCCTCGCACTGATGATAGATAGACTTCACCATTACATTC
genomic: CACCGATCAGGTTCTTATGGCCAGGCATCTGCTCGAAGCCTCTCTCATGGgtatttccga ... ttacttgcagGGTTCTTGCTGTTCCTCGCACTGATGATAGATAGACTTCACCATTACATTC
EST: gi|34550063|gb|CF518295.1|CF518295
EST:     CACCGATCAGGTTCTTATGGCCAGGCATCTGCTCGAAGCCTCTCTCATGG                         GGTTCTTGCTGTTCCTCGCACTGATGATAGATAGACTTCACCATTACATTC
genomic: CACCGATCAGGTTCTTATGGCCAGGCATCTGCTCGAAGCCTCTCTCATGGgtatttccga ... ttacttgcagGGTTCTTGCTGTTCCTCGCACTGATGATAGATAGACTTCACCATTACATTC
EST: gi|110366979|gb|EC930899.1|EC930899
EST:     CACCGATCAGGTTCTTATGGCCAGGCATCTGCTCGAAGCCTCTCTCATGG                         GGTTCTTGCTGTTCCTCGCACTGATGATAGATAGACTTCACCATTACATTC
genomic: CACCGATCAGGTTCTTATGGCCAGGCATCTGCTCGAAGCCTCTCTCATGGgtatttccga ... ttacttgcagGGTTCTTGCTGTTCCTCGCACTGATGATAGATAGACTTCACCATTACATTC
EST: gi|351036222|gb|FQ464067.1|FQ464067
EST:     CACCGATCAGGTTCTTATGGCCAGGCATCTGCTCGAAGCCTCTCTCATGG                         GGTTCTTGCTGTTCCTCGCACTGATGATAGATAGACTTCACCATTACATTC
genomic: CACCGATCAGGTTCTTATGGCCAGGCATCTGCTCGAAGCCTCTCTCATGGgtatttccga ... ttacttgcagGGTTCTTGCTGTTCCTCGCACTGATGATAGATAGACTTCACCATTACATTC
EST: gi|110408374|gb|EC974009.1|EC974009
EST:     CACCGATCAGGTTCTTATGGCCAGGCATCTGCTCGAAGCCTCTCTCATGGTTATTTACTTGCAG            
genomic: CACCGATCAGGTTCTTATGGCCAGGCATCTGCTCGAAGCCTCTCTC----------A--TG--Ggtatttccga .
EST: gi|30136618|gb|CB921956.1|CB921956
EST:     CACCGATCAGGTTCTTATGGCCAGGCATCTGCTCGAAGCCTCTCTCATGG                         GGTTCTTGCTGTTCCTCGCACTGATGATAGATAGACTTCACCATTACATTC
genomic: CACCGATCAGGTTCTTATGGCCAGGCATCTGCTCGAAGCCTCTCTCATGGgtatttccga ... ttacttgcagGGTTCTTGCTGTTCCTCGCACTGATGATAGATAGACTTCACCATTACATTC
EST: gi|351036368|gb|FQ458743.1|FQ458743
EST:     CACCGATCAGGTTCTTATGGCCAGGCATCTGCTCGAAGCCTCTCTCATGG                         GGTTCTTGCTGTTCCTCGCACTGATGATAGATAGACTTCACCATTACATTC
genomic: CACCGATCAGGTTCTTATGGCCAGGCATCTGCTCGAAGCCTCTCTCATGGgtatttccga ... ttacttgcagGGTTCTTGCTGTTCCTCGCACTGATGATAGATAGACTTCACCATTACATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgataaccattctcttttcctgattttgatttcaagagtagttatttacttgcagGGTTCTTGCTGTTCCTCGCACTGATGATAGATAGACTTCACCATTACATTCGAGAGCTTCGTTTACTCAGGAAGGCCATGGAGGCTGAAAAGAAGCAAAA
                                            tttactt  CT-rich tract
                      attttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agattcaccattttaattcacatttgatatgccatccaatttgtttgataaccattctcttttcctgattttgatttcaagagtagttatttacttgcagGGTTCTTGCTGTTCCTCGCACTGATGATAGATAGACTTCACCATTACATTCGAGAGCTTCGTTTACTCAGGAAGGCCATGGAGGCTGAAAAGAAGCAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - -caccatt
- - - - - - - - - - - - - - - -ccatcca