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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttttgtcttgctgacattggctgtcatttatacatgaatcttctttttggttcccaaatcatagtgctttatgctctttatcgtgcagGGAGTTCTTCACTGGGTTGCTGAAGCTTCCCCTGGACTCGATCCACTTACAGTGGAAGTCAGATTGTTTGACAAACTGTTCCTCTCTGAG

Basic information

species Vitis vinifera
transcript Vv15s0021g01230.t01
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0021g01230.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA20G25120.1 (Glycine max), 3'ss of exon 20
gttttt--gtcttgctgacattggctgtcatttatacatgaatcttctttttggttcccaaatcatagtgctt-tatgctctttatcgtgcagGGAGTTCTTCACTGGGTTGCTGAAGCTTCCCCTGGACTCGATCCACTTACAGTGGAAGTCAGATTGTTTGACAAACTGTTCCTCTCTGAG
||||       ||||  |   ||   || |   |||    |      ||  |      | | |  |  |  ||  |   | ||| |  |  |||| ||||| || ||||||||| || |||| |||||| | |||||| | |  |||||||||||||||||||| |  || ||||| || |||
gtttgccaactttgccaattctgctggttaaaaatagtctacaagagttggtaagattcgattggtgatctttgcaaaatttttgtttt-tagGGGGTTCTCCATTGGGTTGCTCAACCTTCTCCTGGAGTTGATCCATTGAAGGTGGAAGTCAGATTGTTTGAGAGGCTATTCCTATCAGAG

upper sequence: Vv15s0021g01230.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA10G41920.1 (Glycine max), 3'ss of exon 20
gttttt--gtcttgctgacattggctgtcatttat-----acatgaatct-tctttttggttcccaaatcatagtgctttatgctctttatcgtgcagGGAGTTCTTCACTGGGTTGCTGAAGCTTCCCCTGGACTCGATCCACTTACAGTGGAAGTCAGATTGTTTGACAAACTGTTCCTCTCTGAG
||||       |||||||   ||   || |   ||     ||| || |   |    |  | |     |||   |   ||| || | ||| |  |  |||| ||||| || ||||||||| || |||| |||||| | |||||| | |  |||||||||||||||||||| |  |||||||| |  |||
gtttgccaactttgctgattctgctggttaaaaatagtctacaagagttggtaagatcagattggtgatctatgcaattt-tgttttttgtttt-tagGGGGTTCTCCATTGGGTTGCTCAACCTTCTCCTGGAGTTGATCCATTAAAGGTGGAAGTCAGATTGTTTGAGAGGCTGTTCCTATTAGAG
















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|22009286|gb|BQ794320.1|BQ794320
EST:     AAGACAAAGCCAAAG                         GGAGTTCTTCACTGGGTTGCTGAAGCTTCCCCTGGACTCAATCCACTTACA
genomic: AAGACAAAGCCAAAGgtttttgtct ... tatcgtgcagGGAGTTCTTCACTGGGTTGCTGAAGCTTCCCCTGGACTCGATCCACTTACA
EST: gi|46918000|gb|CN547329.1|CN547329
EST:     CTTCGAAGAAGACAAAGCCAAAG                         GGAGTTCTTCACTGGGTTGCTGAAGCTTCCCCTGGACTCAATCCACTTACA
genomic: CTTCGAAGAAGACAAAGCCAAAGgtttttgtct ... tatcgtgcagGGAGTTCTTCACTGGGTTGCTGAAGCTTCCCCTGGACTCGATCCACTTACA
EST: gi|22008319|gb|BQ793353.1|BQ793353
EST:     CTTCGAAGAAGACAAAGCCAAAG                         GGAGTTCTTCACTGGGTTGCTGAAGCTTCCCCTGGACTCAATCCACTTACA
genomic: CTTCGAAGAAGACAAAGCCAAAGgtttttgtct ... tatcgtgcagGGAGTTCTTCACTGGGTTGCTGAAGCTTCCCCTGGACTCGATCCACTTACA
EST: gi|30330123|gb|CD013385.1|CD013385
EST:     TGGTTGAGGTCCGGGCAGAGTATGATTCTTCGAAGAAGACAAAGCCAAAG                         GGAGTTCTTCACTGGGTTGCTGAAGCTTCCCCTGGACTCAATCCACTTACA
genomic: TGGTTGAGGTCCGGGCAGAGTATGATTCTTCGAAGAAGACAAAGCCAAAGgtttttgtct ... tatcgtgcagGGAGTTCTTCACTGGGTTGCTGAAGCTTCCCCTGGACTCGATCCACTTACA
EST: gi|30329220|gb|CD012482.1|CD012482
EST:     TGGTTGAGGTCCGGGCAGAGTATGATTCTTCGAAGAAGACAAAGCCAAAG                         GGAGTTCTTCACTGGGTTGCTGAAGCTTCCCCTGGACTCAATCCACTTACA
genomic: TGGTTGAGGTCCGGGCAGAGTATGATTCTTCGAAGAAGACAAAGCCAAAGgtttttgtct ... tatcgtgcagGGAGTTCTTCACTGGGTTGCTGAAGCTTCCCCTGGACTCGATCCACTTACA
EST: gi|22009340|gb|BQ794374.1|BQ794374
EST:     CTTCGAAGAAGACAAAGCCAAAG                         GGAGTTCTTCACTGGGTTGCTGAAGCTTCCCCTGGACTCAATCCACTTACA
genomic: CTTCGAAGAAGACAAAGCCAAAGgtttttgtct ... tatcgtgcagGGAGTTCTTCACTGGGTTGCTGAAGCTTCCCCTGGACTCGATCCACTTACA
EST: gi|33404073|gb|CF209700.1|CF209700
EST:     TGGTTGAGGACCGGACAGAGTATGATTCTTCGAAGAAGACAAAGCCAAAG                         GGAGTTCTTCACTGGGTTGCTGAA
genomic: TGGTTGAGGTCCGGGCAGAGTATGATTCTTCGAAGAAGACAAAGCCAAAGgtttttgtct ... tatcgtgcagGGAGTTCTTCACTGGGTTGCTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaatcttctttttggttcccaaatcatagtgctttatgctctttatcgtgcagGGAGTTCTTCACTGGGTTGCTGAAGCTTCCCCTGGACTCGATCCACTTACAGTGGAAGTCAGATTGTTTGACAAACTGTTCCTCTCTGAG
                                        ctctttatc  CT-rich tract
       ttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttttgtcttgctgacattggctgtcatttatacatgaatcttctttttggttcccaaatcatagtgctttatgctctttatcgtgcagGGAGTTCTTCACTGGGTTGCTGAAGCTTCCCCTGGACTCGATCCACTTACAGTGGAAGTCAGATTGTTTGACAAACTGTTCCTCTCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG