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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacttaatgggaatgctctttaaaagtttccttttttgtcttgctttgtgttcatgcatatggttttagctaaccatttcattcttatgttctgatacagTATTGACTTATAGGCATGAGCTAGGAATGAATTACAACTTCATTCGTCCAGACTTGATTGTGGGGTCTTGCCTACAG

Basic information

species Vitis vinifera
transcript Vv00s0250g00020.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0250g00020.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g01750.2 (Oryza sativa), 3'ss of exon 4
aacttaatgggaatgctctttaaaagtttccttttttgtcttgctttgtgttcatgcatatggttttagctaaccatttcattcttatgt---tctgatacagTATTGACTTATAGGCATGAGCTAGGAATGAATTACAACTTCATTCGTCCAGACTTGATTGTGGGGTCTTGCCTACAG
   || ||||  | |||  |   |          |||  || | ||  |||  ||   |      |      | |||||| || || | |   ||   |  ||| ||||| ||||| |||||||| |||||||| ||||| ||||| || ||||||||||| ||||| || ||| |||||
---tttatggacaggcttgtactattcactaagcttttactggattactgtctatcattgatcactcctgagatcatttcctttttttctaaatcatttctagTGTTGACGTATAGACATGAGCTTGGAATGAACTACAATTTCATACGCCCAGACTTGATCGTGGGCTCCTGCTTACAG

upper sequence: Vv00s0250g00020.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G34370.1 (Glycine max), 3'ss of exon 4
-------aacttaatgggaatgctctttaaaagtttccttttttgtcttgctttgtgttcatgcatatggttttagctaaccatttcattcttatgttctgatacagTATTGACTTATAGGCATGAGCTAGGAATGAATTACAACTTCATTCGTCCAGACTTGATTGTGGGGTCTTGCCTACAG
          ||||    |       | ||  | |     | || | ||| | | ||   |     ||   | | | ||||| |||| |    | || ||   ||||| |||||||||||||||||  |||||||||| || || ||||| |||||||||||||||||||| || |||||||||
atagtttggattaactaaaggatcactcaattgctcatcctatttttttgttctttgaata-----attaatgttgttaaccctttc-taacgaagtgctt-cacagTTTTGACTTATAGGCATGAATTAGGAATGAACTATAATTTCATCCGTCCAGACTTGATTGTGGGATCATGCCTACAG

upper sequence: Vv00s0250g00020.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G33190.1 (Glycine max), 3'ss of exon 4
aacttaatgggaatgctctttaaaa--gtttccttttttgtcttgctttgtgttcatgcatatggttttagctaaccatttcattcttatgttctgat--acagTATTGACTTATAGGCATGAGCTAGGAATGAATTACAACTTCATTCGTCCAGACTTGATTGTGGGGTCTTGCCTACAG
    || |  | ||   ||  |  |    |   ||  |  || |  | | |  |  |    ||  ||   | |    |   | |||| | |   | ||  ||||| |||||||||||||||||  |||||||||| || || ||||| |||||||||||||||||||| || |||||||||
---atagtttggattaactaaaggatcactcaattgctcatcctattcttttgttctttgaataattaatgttg-ttaaccctttctaacgaagtaattcacagTTTTGACTTATAGGCATGAATTAGGAATGAACTATAATTTCATCCGTCCAGACTTGATTGTGGGATCATGCCTACAG

upper sequence: Vv00s0250g00020.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G52180.1 (Arabidopsis thaliana), 3'ss of exon 3
aacttaatgggaatgctctttaaaagtttccttttttgtcttgctttgtgttcatgcatatggttttagctaaccatttcattcttatgt----tctgatacagTATTGACTTATAGGCATGAGCTAGGAATGAATTACAACTTCATTCGTCCAGACTTGATTGTGGGGTCTTGCCTACAG
| ||||       ||||  || |  |      || |  ||||| | |     | |   ||||  |||   | ||   |||||||| ||||    |    | ||||  | ||||| ||||| ||| |||||||||| |||||||| |||||||||||  | ||||| || || ||| |||||
atcttatatcttttgcttgtttattgacaaacttatcttcttgttct----ccttaattatgtatttcagtcactgattcattctcatgtgtctttcatttcagTTCTAACTTACAGGCACGAGTTAGGAATGAACTACAACTTTATTCGTCCAGATCTAATTGTTGGATCCTGCTTACAG

upper sequence: Vv00s0250g00020.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ15444 (Selaginella moellendorffii), 3'ss of exon 1
aacttaatgggaatgctctttaaaagtttccttttttgtcttgctttgtgttcatgcatatggttttagctaaccatttcattcttatgttctgatacagTATTGACTTATAGGCATGAGCTAGGAATGAATTACAACTTCATTCGTCCAGACTTGATTGTGGGGTCTTGCCTACAG
                               | |   | |||| ||| |  ||  |    |  || |     |  |    | | || | |  |  | |||  |||||||||||||||||||| || |||||||||||     |||  ||  |  | || || || || ||| |||||
------------------------------gtatgaagccttgtttttttctctggtgcttttttctgatcgaagaacgaacttttgt-tattctttcagACTTGACTTATAGGCATGAGCTGGGGATGAATTACAATCGTGTTCTCCCGAATCTCATCGTTGGTTCCTGCTTACAG

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|71860017|gb|DT009072.1|DT009072
EST:     GGAAAAATCTGAGATCTACAGCAATAACATGACAGAAGCTATGGGGGCTG                         TATTGACTTATAGGCATGAGCTAGGAATGAATTACAACTTCATTCGTCCAG
genomic: GGAAAAATCTGAGATCTACAGCAATAACATGACAGAAGCTATGGGGGCTGgtaagctcat ... tctgatacagTATTGACTTATAGGCATGAGCTAGGAATGAATTACAACTTCATTCGTCCAG
EST: gi|110731715|gb|EE106367.1|EE106367
EST:     GGAAAAATCTGAGATCTACAGCAATAACATGACAGAAGCTATGGGGGCTG                         TATTGACTTATAGGCATGAGCTAGGAATGAATTACAACTTCATTCGTCCAG
genomic: GGAAAAATCTGAGATCTACAGCAATAACATGACAGAAGCTATGGGGGCTGgtaagctcat ... tctgatacagTATTGACTTATAGGCATGAGCTAGGAATGAATTACAACTTCATTCGTCCAG
EST: gi|110725728|gb|EE102561.1|EE102561
EST:     GGAAAAATCTGAGATCTACAGCAATAACATGACAGAAGCTATGGGGGCTG                         TATTGACTTATAGGCATGAGCTAGGAATGAATTACAACTTCATTCGTCCAG
genomic: GGAAAAATCTGAGATCTACAGCAATAACATGACAGAAGCTATGGGGGCTGgtaagctcat ... tctgatacagTATTGACTTATAGGCATGAGCTAGGAATGAATTACAACTTCATTCGTCCAG
EST: gi|110390476|gb|EC955386.1|EC955386
EST:     GGAAAAATCTGAGATCTACAGCAATAACATGACAGAAGCTATGGGGGCTG                         TATTGACTTATAGGCATGAGCTAGGAATGAATTACAACTTCATTCGTCCAG
genomic: GGAAAAATCTGAGATCTACAGCAATAACATGACAGAAGCTATGGGGGCTGgtaagctcat ... tctgatacagTATTGACTTATAGGCATGAGCTAGGAATGAATTACAACTTCATTCGTCCAG
EST: gi|110719002|gb|EE096483.1|EE096483
EST:     GGAAAAATCTGAGATCTACAGCAATAACATGACAGAAGCTATGGGGGCTG                         TATTGACTTATAGGCATGAGCTAGGAATGAATTACAACTTCATTCGTCCAG
genomic: GGAAAAATCTGAGATCTACAGCAATAACATGACAGAAGCTATGGGGGCTGgtaagctcat ... tctgatacagTATTGACTTATAGGCATGAGCTAGGAATGAATTACAACTTCATTCGTCCAG
EST: gi|71858350|gb|DT007405.1|DT007405
EST:     GGAAAAATCTGAGATCTACAGCAATAACATGACAGAAGCTATGGGGGCTG                         TATTGACTTATAGGCATGAGCTAGGAATGAATTACAACTTCATTCGTCCAG
genomic: GGAAAAATCTGAGATCTACAGCAATAACATGACAGAAGCTATGGGGGCTGgtaagctcat ... tctgatacagTATTGACTTATAGGCATGAGCTAGGAATGAATTACAACTTCATTCGTCCAG
EST: gi|110723499|gb|EE100881.1|EE100881
EST:     GGAAAAATCTGAGATCTACAGCAATAACATGACAGAAGCTATGGGGGCTG                         TATTGACTTATAGGCATGAGCTAGGAATGAATTACAACTTCATTCGTCCAG
genomic: GGAAAAATCTGAGATCTACAGCAATAACATGACAGAAGCTATGGGGGCTGgtaagctcat ... tctgatacagTATTGACTTATAGGCATGAGCTAGGAATGAATTACAACTTCATTCGTCCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgttcatgcatatggttttagctaaccatttcattcttatgttctgatacagTATTGACTTATAGGCATGAGCTAGGAATGAATTACAACTTCATTCGTCCAGACTTGATTGTGGGGTCTTGCCTACAG
                              atttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacttaatgggaatgctctttaaaagtttccttttttgtcttgctttgtgttcatgcatatggttttagctaaccatttcattcttatgttctgatacagTATTGACTTATAGGCATGAGCTAGGAATGAATTACAACTTCATTCGTCCAGACTTGATTGTGGGGTCTTGCCTACAG

- - - - - gaatgct
- - - - - - - - - - - - - - - - - - - - -tgctttg
- - - - - - - - - - - - - - - - - - - - - - - - - -tcatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaacca