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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAATGCTACCGCTCTGTTCCTCTTCTTGGCTCCACTgtaagtagagaaggctctctctctctctctctcttcctgtgattcttgttcttttgcgttttcaaaagttgggctcaaaggggctctagttcatcaagaa...

Basic information

species Vitis vinifera
transcript Vv18s0001g15330.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g15330.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA06G12740.2 (Glycine max), 5'ss of exon 2
GAAATGCTACCGCTCTGTTCCTCTTCTTGGCTCCACTgtaagtag-agaaggctctctctctctctctctcttcctgtgattcttgttcttttgcgttttcaaaagttgggctcaaaggggctctagttcatcaagaa--
| |||||| |||||||||||||||||||||||||| |||| | |  | |  |||   ||  || |||| | ||        ||||    | ||| |  || |    ||     ||       |   |   ||  ||    
GGAATGCTTCCGCTCTGTTCCTCTTCTTGGCTCCAGTgtatgcattacatagctgcttccttccctctttgttagctc---tcttaaattgttgtggctttatcctttttttccattcttttttgtgggtatggagggtt

upper sequence: Vv18s0001g15330.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA06G12740.1 (Glycine max), 5'ss of exon 2
GAAATGCTACCGCTCTGTTCCTCTTCTTGGCTCCACTgtaagtag-agaaggctctctctctctctctct-----cttcctgtgattcttgt--tcttttgcgttttcaaaagttgggctcaaaggggctctagttcatcaagaa-------------------------
| |||||| |||||||||||||||||||||||||| |||| | |  | |  |||   ||  || |||| |     ||  ||   ||| ||||    || | | ||||    | |     |    ||       | |   || |                           
GGAATGCTTCCGCTCTGTTCCTCTTCTTGGCTCCAGTGTATGCATTACATAGCTGCTTCCTTCCCTCTTTgttagctctcttaaattgttgtggctttatcctttttttccattcttttttgtgggtatggagggtttccatgggccctgttaaaatttgttcgagatat

upper sequence: Vv18s0001g15330.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA04G42040.1 (Glycine max), 5'ss of exon 2
GAAATGCTACCGCTCTGTTCCTCTTCTTGGCTCCACTgtaagtag-agaaggctctctctctctctctctcttcctgtgattcttgttcttttgcgttttcaaaagttgggctcaaaggggctctagttcatcaagaa
| |||||| ||||||||||||| |||||||||||| |||| | |  | |  |||   || ||| |||||| ||    |   ||||   |||||| |  || |     |    |       | | | ||  ||   || 
GGAATGCTTCCGCTCTGTTCCTATTCTTGGCTCCAGTgtatgcattacatagctgcttccctccctctctgttatc-tccctcttaaacttttgtggctttaccttctttttttttttatgtttttgtggatatggag

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|110731976|gb|EE106858.1|EE106858
EST:     GAAATGCTACCGCTCTGTTCCTCTTCTTGGCTCCACT                         GATTACTTTCAAGAGAATCATTAAAAGCAAATCTACGGAGCAGTTCTCAGG
genomic: GAAATGCTACCGCTCTGTTCCTCTTCTTGGCTCCACTgtaagtagag ... ctttttttagGATTACTTTCAAGAGAATCATTAAAAGCAAATCTACGGAGCAGTTCTCAGG
EST: gi|110387851|gb|EC952549.1|EC952549
EST:     GAAATGCTACCGCTCTGTTCCTCTTCTTGGCTCCACT                         GATTACTTTCAAGAGAATCATTAAAAGCAAATCTACGGAGCAGTTCTCAGG
genomic: GAAATGCTACCGCTCTGTTCCTCTTCTTGGCTCCACTgtaagtagag ... ctttttttagGATTACTTTCAAGAGAATCATTAAAAGCAAATCTACGGAGCAGTTCTCAGG
EST: gi|33403642|gb|CF209269.1|CF209269
EST:     GAAATGCTACCGCTCTGTTCCTCTTCTTGGCTCTACT                         GATTACTTTCAAGAGAATCATTAAAAGCAAATCTACGGAGCAGTTCTCAGG
genomic: GAAATGCTACCGCTCTGTTCCTCTTCTTGGCTCCACTgtaagtagag ... ctttttttagGATTACTTTCAAGAGAATCATTAAAAGCAAATCTACGGAGCAGTTCTCAGG
EST: gi|294966391|gb|GW839498.1|GW839498
EST:     GAAATGCTACCGCTCTGTTCCTCTTCTTGGCTCCACT                         GATTACTTTCAAGAGAATCATTAAAAGCAAATCTACGGAGCAGTTCTCAGG
genomic: GAAATGCTACCGCTCTGTTCCTCTTCTTGGCTCCACTgtaagtagag ... ctttttttagGATTACTTTCAAGAGAATCATTAAAAGCAAATCTACGGAGCAGTTCTCAGG
EST: gi|27755280|gb|CB036035.1|CB036035
EST:     GAAATGCTACCGCTCTGTTCCTCTTCTTGGCTCCACT                         GATTACTTTCAAGAGAATCATTAAAAGCAAATCTACGGAGCAGTTCTCAGG
genomic: GAAATGCTACCGCTCTGTTCCTCTTCTTGGCTCCACTgtaagtagag ... ctttttttagGATTACTTTCAAGAGAATCATTAAAAGCAAATCTACGGAGCAGTTCTCAGG
EST: gi|110374121|gb|EC938672.1|EC938672
EST:     GAAATGCTACCGCTCTGTTCCTCTTCTTGGCTCCACT                         GATTACTTTCAAGAGAATCATTAAAAGCAAATCTACGGAGCAGTTCTCAGG
genomic: GAAATGCTACCGCTCTGTTCCTCTTCTTGGCTCCACTgtaagtagag ... ctttttttagGATTACTTTCAAGAGAATCATTAAAAGCAAATCTACGGAGCAGTTCTCAGG
EST: gi|110699794|gb|EE077102.1|EE077102
EST:     GAAATGCTACCGCTCTGTTCCTCTTCTTGGCTCCACT                         GATTACTTTCAAGAGAATCATTAAAAGCAAATCTACGGAGCAGTTCTCAGG
genomic: GAAATGCTACCGCTCTGTTCCTCTTCTTGGCTCCACTgtaagtagag ... ctttttttagGATTACTTTCAAGAGAATCATTAAAAGCAAATCTACGGAGCAGTTCTCAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAATGCTACCGCTCTGTTCCTCTTCTTGGCTCCACTgtaagtagagaaggctctctctctctctctctcttcctgtgattcttgttcttttgcgttttcaaaagttgggctcaaaggggctctagttcatcaagaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agagaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctctc