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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagtcgatgaaactagagatcttctcagggtataatcatggtgcttatttctccctccttttttctttggaatgctaatgattaaaattcatggtgatagATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCGGAGCCGCAGCACCTGAGATACCACAGCCACTTATTGATCAGTTGAAGCC

Basic information

species Vitis vinifera
transcript Vv17s0000g09690.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g09690.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G18460.1 (Glycine max), 3'ss of exon 5
--------------------------------------aagtcgat-gaaactagagatcttctcagggtataatcatggtgcttatttctccctccttttttctttggaatgcta-atgattaaaattcatggtgatagATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCGGAGCCGCAGCACCTGAGATACCACAGCCACTTATTGATCAGTTGAAGCC
                                      |   | || ||| |||  |     ||    |  || | |  |     ||   ||| |  ||    || |||| |   | ||   |||   |  || ||| ||||||||||| ||||||||| |||| |||||| |||||||| |||||||| ||||| |||||||| || || || || ||||||||||| |||||||||||
gtcatctgaaatctttcaatctgtgtgatattgtatacatcacaattgaatctaatggatagctgcatgattattgaacggttaaatgaatccatagttggaactctggattagcatattgataattgttgtgttgacagATGGAAGGCAAGGTTGGCCAGAGTTTGCACCTTATGATGCCATTCACGTTGGAGCAGCAGCACCAGAAATTCCCCAACCACTTATTGACCAGTTGAAGCC

upper sequence: Vv17s0000g09690.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA04G36430.1 (Glycine max), 3'ss of exon 3
--------aagtcgatgaaactagagatcttctcagggtataatcatggtgcttatttctccctccttttttctttggaatgctaatgattaaaattcatggtgatagATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCGGAGCCGCAGCACCTGAGATACCACAGCCACTTATTGATCAGTTGAAGCC
        ||  | || | | |  | || | || |    | ||  |||   |  ||   |    || |   |     || || ||||  ||        || | | ||||||||||| ||||||||| |||| ||| || |||||||| |||||||| ||||| |||||||| || || || || ||||||||||| |||||||||||
tgctaacaaaaactataacaattaatatttgctgataaaaaaaaaatga-acccatagttggaaccctggattagcagattgataattgttg-------tgttaacagATGGAAGGCAAGGTTGGCCAGAGTTTGCCCCTTATGATGCCATTCACGTTGGAGCAGCAGCACCAGAAATTCCCCAACCACTTATTGACCAGTTGAAGCC

upper sequence: Vv17s0000g09690.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G02810.1 (Glycine max), 3'ss of exon 3
aagtcgatgaaactagagatcttctcagggtataatca--tggtgcttatttctccctccttttttctttggaatgctaatgattaaaattcatggtgatagATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCGGAGCCGCAGCACCTGAGATACCACAGCCACTTATTGATCAGTTGAAGCC
         | | ||  | |  |      ||| ||| |  || |   |     |      |    | |||  |||| |  ||| |||   |  || ||| ||||||||||| |||||||||||||| ||| || |||||||| |||||||| ||||| || ||||| || || || || ||||||||||| |||||||||||
tgcatagctatattaatgtttcttgagaagtaaaataatttgctatgtcaagttggtggatcaaatatttcaaatgtt--tgagtaattgttgtgttgacagATGGAAGGCAAGGTTGGCCTGAGTTTGCTCCTTATGATGCCATTCACGTTGGAGCAGCGGCACCCGAAATCCCCCAACCACTTATTGACCAGTTGAAGCC

upper sequence: Vv17s0000g09690.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT3G48330.1 (Arabidopsis thaliana), 3'ss of exon 3
aagtcgatgaaactagagatcttctcagggtataatcatggtgcttatttctccctccttttttctttggaatgctaatgattaaaattcatggtgatagATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCGGAGCCGCAGCACCTGAGATACCACAGCCACTTATTGATCAGTTGAAGCC
             |    |||   ||| | | |    ||     |  | | ||  |  ||   |   |||  |  | ||| ||  ||         |||||||| |||| ||| ||| |||||| ||| || |||||||| |||||||||||||| |||||||| ||||| ||| || |  | |||||||||||||||||
------------gtgagcatcagttcaagtttttgagatttctttggtgtttctgtttttacattgctggtttcttgatggttttaa--------aatagATGGGAGGCAAGGATGGGCTGAGTTTGCTCCGTATGATGCTATTCACGTCGGAGCAGCAGCACCGGAGATCCCAGAGGCGTTGATTGATCAGTTGAAGCC

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|110391868|gb|EC956879.1|EC956879
EST:     TGCAGCGGCTCCATTATTAAAAGAAGGTTCTCTCAAACTGCATGCTGGTG                         ATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCG
genomic: TGCAGCGGCTCCGTTATTAAAAGAAGGTTCTCTCAAACTGCATGCCGGTGgtatgtttct ... atggtgatagATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCG
EST: gi|30253100|gb|CB970651.1|CB970651
EST:     TGCAGCGGCTCCATTATTAAAAGAAGGTTCTCTCAAACTGCATGCTGGTG                         ATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCG
genomic: TGCAGCGGCTCCGTTATTAAAAGAAGGTTCTCTCAAACTGCATGCCGGTGgtatgtttct ... atggtgatagATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCG
EST: gi|110380339|gb|EC945595.1|EC945595
EST:     TGCAGCGGCTCCATTATTAAAAGAAGGTTCTCTCAAACTGCATGCTGGTG                         ATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCG
genomic: TGCAGCGGCTCCGTTATTAAAAGAAGGTTCTCTCAAACTGCATGCCGGTGgtatgtttct ... atggtgatagATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCG
EST: gi|22009919|gb|BQ794953.1|BQ794953
EST:     TGCAGCGGCTCCATTATTAAAAGAAGGTTCTCTCAAACTGCATGCTGGTG                         ATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCG
genomic: TGCAGCGGCTCCGTTATTAAAAGAAGGTTCTCTCAAACTGCATGCCGGTGgtatgtttct ... atggtgatagATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCG
EST: gi|110366911|gb|EC930830.1|EC930830
EST:     GCATGCTGGTG                         ATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCG
genomic: GCATGCCGGTGgtatgtttct ... atggtgatagATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCG
EST: gi|110726896|gb|EE103078.1|EE103078
EST:     TGCAGCGGCTCCGTTATTAAAAGAAAGTTCTCTCAAACTGCATGCCGGTG                         ATGGAAAGCTAGGTTGGCCTGAATGTGCACCATATGATGCAATTCACGTCG
genomic: TGCAGCGGCTCCGTTATTAAAAGAAGGTTCTCTCAAACTGCATGCCGGTGgtatgtttct ... atggtgatagATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCG
EST: gi|110688221|gb|EE066525.1|EE066525
EST:     TGCAACGGCTCCATTATTAAAAGAAGGTTCTCTCAAACTGCATGCTGGTG                         ATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCG
genomic: TGCAGCGGCTCCGTTATTAAAAGAAGGTTCTCTCAAACTGCATGCCGGTGgtatgtttct ... atggtgatagATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCG
EST: gi|33407775|gb|CF213402.1|CF213402
EST:     TGCAGCGGCTCCATTATTAAAAGAAGGTTCTCTCAAACTGCATGCTGGTG                         ATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCG
genomic: TGCAGCGGCTCCGTTATTAAAAGAAGGTTCTCTCAAACTGCATGCCGGTGgtatgtttct ... atggtgatagATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCG
EST: gi|33410468|gb|CF216095.1|CF216095
EST:     TGCAGCGGCTCCATTATTAAAAGAAGGTTCTCTCAAACTGCATGCTGGTG                         ATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCG
genomic: TGCAGCGGCTCCGTTATTAAAAGAAGGTTCTCTCAAACTGCATGCCGGTGgtatgtttct ... atggtgatagATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCG
EST: gi|14580339|gb|BG273781.1|BG273781
EST:     TGCAGCGGCTCCATTATTAAAAGAAGGTTCTCTCAAACTGCATGCTGGTG                         ATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCG
genomic: TGCAGCGGCTCCGTTATTAAAAGAAGGTTCTCTCAAACTGCATGCCGGTGgtatgtttct ... atggtgatagATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCG
EST: gi|110696639|gb|EE072934.1|EE072934
EST:     TGCAGCGGCTCCATTATTAAAAGAAGGTTCTCTCAAACTGCATGCTGGTG                         ATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCG
genomic: TGCAGCGGCTCCGTTATTAAAAGAAGGTTCTCTCAAACTGCATGCCGGTGgtatgtttct ... atggtgatagATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCG
EST: gi|110405103|gb|EC970636.1|EC970636
EST:     TGCAGCGGCTCCGTTATTAAAAGAAGGTTCTCTCAAACTGCATGCCGGTG                         ATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCG
genomic: TGCAGCGGCTCCGTTATTAAAAGAAGGTTCTCTCAAACTGCATGCCGGTGgtatgtttct ... atggtgatagATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCG
EST: gi|110413746|gb|EC979551.1|EC979551
EST:     TGCAGCGGCTCCGTTATTAAAAGAAGGTTCTCTCAAACTGCATGCCGGTG                         ATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCG
genomic: TGCAGCGGCTCCGTTATTAAAAGAAGGTTCTCTCAAACTGCATGCCGGTGgtatgtttct ... atggtgatagATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCG
EST: gi|161713127|gb|FC062485.1|FC062485
EST:     TGCAGCGGCTCCATTATTAAAAGAAGGTTCTCTCAAACTGCATGCTGGTG                         ATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCG
genomic: TGCAGCGGCTCCGTTATTAAAAGAAGGTTCTCTCAAACTGCATGCCGGTGgtatgtttct ... atggtgatagATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCG
EST: gi|34549921|gb|CF518153.1|CF518153
EST:     TGCAGCGGCTCCATTATTAAAAGAAGGTTCTCTCAAACTGCATGCTGGTG                         ATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCG
genomic: TGCAGCGGCTCCGTTATTAAAAGAAGGTTCTCTCAAACTGCATGCCGGTGgtatgtttct ... atggtgatagATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttctccctccttttttctttggaatgctaatgattaaaattcatggtgatagATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCGGAGCCGCAGCACCTGAGATACCACAGCCACTTATTGATCAGTTGAAGCC
                           tgctaat  putative branch site (score: 2)
                              taatgattaaaattca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagtcgatgaaactagagatcttctcagggtataatcatggtgcttatttctccctccttttttctttggaatgctaatgattaaaattcatggtgatagATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCGGAGCCGCAGCACCTGAGATACCACAGCCACTTATTGATCAGTTGAAGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - gaaacta
- - - - - - - - - - cttctca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attaaaa