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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcctgaagttcattcacaatttgaatgttttgatgtagggtattcagttttgcatgttccatatgctgttttcttcatcctcgttctctttttatggcagGATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATTACAAGTACAATGATGAGAATACTGTCTCATTTGTGACTTTGAACAAGGT

Basic information

species Vitis vinifera
transcript Vv18s0041g01900.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0041g01900.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S172_22V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------gcctgaagttca-ttcacaatttgaatgttttgatgtagggtattcagttttgc-----atgttcc-atatgctgttttcttcatcctcgttctcttttt----atggcagGATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATTACAAGTACAATGATGAGAATACTGTCTCATTTGTGACTTTGAACAAGGT
                || |    || | || | |   | |    | ||||   | | |  ||   ||       ||||    |    | | ||     | | | ||   |   ||    ||| ||||||| ||||| ||||  ||| ||||||| |  ||  | |||||||| |||||||||||||||||||||||    ||| | || |||||  |||| |||||
gtacgtcttctaatgagcatatgatttaatttagagcctcag---tctgatactgagcacccatgcttatggagaatgtcttgaccctcggcttgtgctaacgtggtggacgggttgaatatgccagGATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATTACAAGTACAATGATGAGAACCAAGTCACTTTCGTGACCATGAATAAGGT

upper sequence: Vv18s0041g01900.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S33_218V6.1 (Physcomitrella patens), 3'ss of exon 6
--gcctgaagttcattcacaatttgaatgttttgatgtagggtattca-gttttgcatgttccata-tgctgttttcttcatcctcgttctctttttatggcagGATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATTACAAGTACAATGATGAGAATACTGTCTCATTTGTGACTTTGAACAAGGT
   | |     ||||||  | | || |   |  || ||       ||| || | | | |||      || |  |    | ||  | | |   | | | |||||||||| ||||| ||||  ||  |||| || |||||| | |||||||| ||||||||||||||||| |||||    ||  | ||||||||| |||| || ||
gcactttttagtcattc-tagtctgcagagtcaga-gtgtttctctcatgtctcggacgtttggggctgatagtgagctaat--ttggtggttgtatgtggcagGATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATTACAAGTACAATGACGAGAACCAAGTAACCTTTGTGACTATGAATAAAGT

upper sequence: Vv18s0041g01900.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S132_188V6.1 (Physcomitrella patens), 3'ss of exon 6
--gcctgaagtt-cattcacaatttgaatgttttgatgtagggtattcagttttgcatgttccatatgctgttttcttcatcct--cgttctctttttatggcagGATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATTACAAGTACAATGATGAGAATACTGTCTCATTTGTGACTTTGAACAAGGT
     ||||  | || ||   ||||  |   |    | || | |  | |  |||  || |      ||| |     || ||  |   | |   |  || || |||| || ||||| ||||  ||| |||| || |||||  | |||||||| |||||||||||||||||||| ||    ||  | ||||||||  ||||||||||
gtttttgaatctgcactctggatttcgaaaatgccctctacgttcctgaaatttaaattt-----gtgccgacccattaatattgctgatgattgcttgtgacagGTTTCTGGGAGATGTTCGATGCTGAAGGTTACTCATTGTGGTTCTGTGATTACAAGTACAATGATGAAAACCAAGTTACGTTTGTGACCATGAACAAGGT

upper sequence: Vv18s0041g01900.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: EFJ14564 (Selaginella moellendorffii), 3'ss of exon 6
gcctgaagttcattcacaatttgaatgttttgatgtagggtattcagttttgcatgttccatatgctgttttcttcatcctcgttctctttttatggcagGATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATTACAAGTACAATGATGAGAATACTGTCTCATTTGTGACTTTGAACAAGGT
                             |  | || | || | ||  ||      ||  | |||||| ||  || ||||    ||| |       |||||||| ||||| |||||||| || ||||| ||||| || ||||||||||| ||||||||||| |||||||| || ||  | || |||||  ||||||||||
----------------------------gtacaagtggtgtttcca--ttgatcgcttgaaaatgctgatt--ttgatcccaaatcttt-------gcagGATTCTGGGAGATGTATGACCCCGAGGGATACTCCCTGTGGTTCTGCGACTACAAGTACAACGATGAGAACACGGTGCCTTTCGTGACGATGAACAAGGT

upper sequence: Vv18s0041g01900.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: EFJ26267 (Selaginella moellendorffii), 3'ss of exon 5
gcctgaagttcattcacaatttgaatgttttgatgtagggtattcagttttgcatgttccatatgctgttttcttcatcctcgttctctttttatggcagGATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATTACAAGTACAATGATGAGAATACTGTCTCATTTGTGACTTTGAACAAGGT
                             |  | || | || | ||  ||      ||  | |||||| ||           | ||||||    | |||||||| |||||||||||||| || ||||| ||||| || ||||||||||| ||||||||||| |||||||| || ||  | || |||||  ||||||||||
----------------------------gtacaagtggtgtttcca--ttgatcgcttgaaaatgctgattct---------gatctcttccc-ttgcagGATTCTGGGACATGTATGACCCCGAGGGATACTCCCTGTGGTTCTGCGACTACAAGTACAACGATGAGAACACGGTGCCTTTCGTGACGATGAACAAGGT

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|110360473|gb|EC923602.1|EC923602
EST:     GAGGCTTTATTCAAACACCAAGACCAACTTCCGTGAGGTTGCTATCAAAG                         GATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT
genomic: GAGGCTTTATTCAAACACCAAGACCAACTTCCGTGAGGTTGCTATCAAAGgtatttcctt ... tttatggcagGATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT
EST: gi|30130188|gb|CB915527.1|CB915527
EST:     GAGGCTTTATTCAAACACCAAGACCAACTTCCGTGAGGTTGCTATCAAAG                         GATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT
genomic: GAGGCTTTATTCAAACACCAAGACCAACTTCCGTGAGGTTGCTATCAAAGgtatttcctt ... tttatggcagGATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT
EST: gi|110705276|gb|EE081969.1|EE081969
EST:     GAGGCTTTATTCAAACACCAAGACCAACTTCCGTGAGGTTGCTATCAAAG                         GATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT
genomic: GAGGCTTTATTCAAACACCAAGACCAACTTCCGTGAGGTTGCTATCAAAGgtatttcctt ... tttatggcagGATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT
EST: gi|110373114|gb|EC937325.1|EC937325
EST:     GAGGCTTTATTCAAACACCAAGACCAACTTCCGCGAGGTTGCTATCAAAG                         GATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT
genomic: GAGGCTTTATTCAAACACCAAGACCAACTTCCGTGAGGTTGCTATCAAAGgtatttcctt ... tttatggcagGATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT
EST: gi|51052528|gb|CO819605.1|CO819605
EST:     AGGCTTTA-TCAAACACCAAGACCAACTTCCGCGAGGTTGCTATCAAAG                         GATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT
genomic: AGGCTTTATTCAAACACCAAGACCAACTTCCGTGAGGTTGCTATCAAAGgtatttcctt ... tttatggcagGATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT
EST: gi|110374183|gb|EC938782.1|EC938782
EST:     CAAACACCAAGACCAACTTCCGCGAGGTTGCTATCAAAG                         GATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT
genomic: CAAACACCAAGACCAACTTCCGTGAGGTTGCTATCAAAGgtatttcctt ... tttatggcagGATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT
EST: gi|110694831|gb|EE072292.1|EE072292
EST:     TTCAAACACCAAGACCAACTTCCGCGAGGTTGCTATCAAAG                         GATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT
genomic: TTCAAACACCAAGACCAACTTCCGTGAGGTTGCTATCAAAGgtatttcctt ... tttatggcagGATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT
EST: gi|33403349|gb|CF208976.1|CF208976
EST:     GAGGCTTTATTCAAACACCAAGACCAACTTCCGTGAGGTTGCTATCAAAG                         GATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT
genomic: GAGGCTTTATTCAAACACCAAGACCAACTTCCGTGAGGTTGCTATCAAAGgtatttcctt ... tttatggcagGATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT
EST: gi|110700467|gb|EE078543.1|EE078543
EST:     AACACCAAGACCAACTTCCGCGAGGTTGCTATCAAAG                         GATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT
genomic: AACACCAAGACCAACTTCCGTGAGGTTGCTATCAAAGgtatttcctt ... tttatggcagGATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT
EST: gi|34549717|gb|CF517949.1|CF517949
EST:     GAGGCTTTATTCAAACACCAAGACCAACTTCCGCGAGGTTGCTATCAAAG                         GATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT
genomic: GAGGCTTTATTCAAACACCAAGACCAACTTCCGTGAGGTTGCTATCAAAGgtatttcctt ... tttatggcagGATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT
EST: gi|34544800|gb|CF513032.1|CF513032
EST:     GAGGCTTTATTCAAACACCAAGACCAACTTCCGCGAGGTTGCTATCAAAG                         GATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT
genomic: GAGGCTTTATTCAAACACCAAGACCAACTTCCGTGAGGTTGCTATCAAAGgtatttcctt ... tttatggcagGATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT
EST: gi|110388506|gb|EC953264.1|EC953264
EST:     GAGGCTTTATTCAAACACCAAGACCAACTTCCGTGAGGTTGCTATCAAAG                         GATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT
genomic: GAGGCTTTATTCAAACACCAAGACCAACTTCCGTGAGGTTGCTATCAAAGgtatttcctt ... tttatggcagGATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT
EST: gi|110689238|gb|EE065287.1|EE065287
EST:     GAGGCTTTATTCAAACACCAAGACCAACTTCCGCGAGGTTGCTATCAAAG                         GATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT
genomic: GAGGCTTTATTCAAACACCAAGACCAACTTCCGTGAGGTTGCTATCAAAGgtatttcctt ... tttatggcagGATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT
EST: gi|110700590|gb|EE077380.1|EE077380
EST:     CTTCCGTGAGGTTGCTATCAAAA                         GATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT
genomic: CTTCCGTGAGGTTGCTATCAAAGgtatttcctt ... tttatggcagGATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT
EST: gi|110371700|gb|EC935822.1|EC935822
EST:     GAGGCTTTATTCAAACACCAAGACCAACTTCCGTGAGGTTGCTATCAAAG                         GATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT
genomic: GAGGCTTTATTCAAACACCAAGACCAACTTCCGTGAGGTTGCTATCAAAGgtatttcctt ... tttatggcagGATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT
EST: gi|110694572|gb|EE071796.1|EE071796
EST:     GAGGCTTTATTCAAACACCAAGACCAACTTCCGCGAGGTTGCTATCAAAG                         GATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT
genomic: GAGGCTTTATTCAAACACCAAGACCAACTTCCGTGAGGTTGCTATCAAAGgtatttcctt ... tttatggcagGATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT
EST: gi|110384296|gb|EC948724.1|EC948724
EST:     AACACCAAGACCAACTTCCGTGAGGTTGCTATCAAAG                         GATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT
genomic: AACACCAAGACCAACTTCCGTGAGGTTGCTATCAAAGgtatttcctt ... tttatggcagGATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttttgcatgttccatatgctgttttcttcatcctcgttctctttttatggcagGATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATTACAAGTACAATGATGAGAATACTGTCTCATTTGTGACTTTGAACAAGGT
                  tgctgttttcttcatc  CT-rich tract
                                         tctttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcctgaagttcattcacaatttgaatgttttgatgtagggtattcagttttgcatgttccatatgctgttttcttcatcctcgttctctttttatggcagGATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATTACAAGTACAATGATGAGAATACTGTCTCATTTGTGACTTTGAACAAGGT

gcctgaa
- - - - - cattcac
- - - - - - - - - - - - - - - - - - - - - - - - - - catgttc