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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACCACTGGATGAAATGTCTATAGCTTGCATTTTACGTGATCTACTCCATGCAATTGAGTATCTCCATAATGAAGGAAAAATTCACAGAGATATCAAAGgtattgtcatcaaatggaccctttgttaactcaagtatctttgcttgaaatagtgtcttttgatttgctgtttttaataatttctctaattagagcttttctttcttcttgtaaactattttggtggaatgacaacattgatattataaatttgcag

Basic information

species Vitis vinifera
transcript Vv19s0014g02310.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0014g02310.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA12G27300.1 (Glycine max), 5'ss of exon 6
CAACCACTGGATGAAATGTCTATAGCTTGCATTTTACGTGATCTACTCCATGCAATTGAGTATCTCCATAATGAAGGAAAAATTCACAGAGATATCAAAGgtattgtcatcaaatggaccctttgttaactcaagtatctttgcttgaaatagtgtcttttgatttgctgtttttaataatttctctaattagagcttttctttcttcttgtaaactattttggtggaatgacaacattgatattataaatttgcag
|  ||||| ||||||||||| |||||||||||| |||||||| | || ||||||||||| || || |||||||||||||||||||| ||||| || ||||||||   ||   |    || ||   ||  ||    |  || |||||  ||  |   |||      | |  |  |||  ||||| | ||||    |  ||   || || || | | || |        | | |||  |||   ||   || |||||||
CCTCCACTTGATGAAATGTCAATAGCTTGCATTCTACGTGATTTGCTTCATGCAATTGATTACCTTCATAATGAAGGAAAAATTCATAGAGACATTAAAGgtatcaacagtgac---actctccattgtct----ttcctgtgctttgaa--gctgcttcccccctcccataattag-aatttttataatcgtggacttcaattttt-ttattagctct------aaattcacagaatttgcatatcaattttgcag

upper sequence: Vv19s0014g02310.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA06G36130.2 (Glycine max), 5'ss of exon 5
CAACCACTGGATGAAATGTCTATAGCTTGCATTTTACGTGATCTACTCCATGCAATTGAGTATCTCCATAATGAAGGAAAAATTCACAGAGATATCAAAGgtattgtcatcaaatggaccctttgttaactcaagtatctttgcttgaaatagtgtcttttgatttgctgtttttaataatttctctaattagagcttttctttcttcttgtaaactatt-ttggtggaatgacaacattgatattataaatttgcag
|  ||||| ||||||||||| || ||||||||| |||||||| | || ||||||||||| || || |||||||||||||||||||| ||||| || ||||||||   ||   |     | ||   ||   |    | |  ||   ||||| ||   ||||     |    |  |||  ||||| | |||| |  |  ||   || ||  |     ||||  ||  | ||||  ||| ||  || ||  |         
CCTCCACTTGATGAAATGTCAATTGCTTGCATTCTACGTGATTTGCTTCATGCAATTGATTACCTACATAATGAAGGAAAAATTCATAGAGACATTAAAGgtatcaacagtga-cattctctccattgtttttcctgtgctt---tgaaacag---ctttccccctctcataattagaaattt-tataatcatggacttcaattttttattagctctatcattcatagaatttcaatatcaattttgcag--------

upper sequence: Vv19s0014g02310.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA13G34970.1 (Glycine max), 5'ss of exon 6
CAACCACTGGATGAAATGTCTATAGCTTGCATTTTACGTGATCTACTCCATGCAATTGAGTATCTCCATAATGAAGGAAAAATTCACAGAGATATCAAAGgtattgtcatcaaatggaccctttgttaactcaagtatctttgcttgaaatagtgtcttttgatttgctgtttttaataatttctctaatta--gagcttttctttcttcttgtaaactattttggtggaatgacaacattgatattataaatttgcag
|  || || ||||||||||| || ||||||||| |||||||  | || |||||  |||| ||||| |||| ||||||||||||||| ||||| || ||||||||    | |||     ||| |||  |    |  | || |   ||||||      ||| |  | |  ||| | ||   | || | || | |  ||  |||  ||| |  || || | ||  || ||  | ||||| |||| | ||  ||| | | |||
CCTCCCCTTGATGAAATGTCAATTGCTTGCATTCTACGTGACTTGCTGCATGCTGTTGATTATCTACATAGTGAAGGAAAAATTCATAGAGACATTAAAGgtatcagaagcaac----cccattgccattgaatttttcgtactttgaaa------cttcttttctcttgtctatatgtagttttgtagtcatggaattttcttttttgtttttacattagctttgta-attgacagcatttacatgttaattatacag

upper sequence: Vv19s0014g02310.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA12G35510.1 (Glycine max), 5'ss of exon 5
CAACCACTGGATGAAATGTCTATAGCTTGCATTTTACGTGATCTACTCCATGCAATTGAGTATCTCCATAATGAAGGAAAAATTCACAGAGATATCAAAGgtattgtcatcaaatggaccctttgttaactcaagtatctttgcttgaaatagtgtcttttgatttgctgtttttaataatttctctaattagagcttttctttcttcttgtaaactattttggtggaatgacaacattgatattataaatttgcag
|  || || ||||||||||| || ||||||||| |||||||  | || |||||  |||| ||||| || | ||||||||||||||| ||||| || ||||||||    | |||     |||  |    | | || | | | | | |  |||    ||||||   ||| | ||| |  | |  | | |||||       ||  |   ||   || ||                                         
CCTCCCCTTGATGAAATGTCAATTGCTTGCATTCTACGTGACTTGCTGCATGCTGTTGATTATCTACACAGTGAAGGAAAAATTCATAGAGACATTAAAGgtatcagaagcaa-----ccccatcgccattgaattttttgtacattgaat----tctttt---ttgttttttct--ttagctttataattgacagcattaatatgtcaattatacag---------------------------------------

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|352772708|gb|FQ473746.1|FQ473746
EST:     TGCAATTGAGTATCTCCATAATGAAGGAAAAATTCACAGAGATATCAAAG                         CGGCAAACATTTTGTTGACTGAGAATGGCGATGTTAAG
genomic: TGCAATTGAGTATCTCCATAATGAAGGAAAAATTCACAGAGATATCAAAGgtattgtcat ... aaatttgcagCGGCAAACATTTTGTTGACTGAGAATGGCGATGTTAAG
EST: gi|71861562|gb|DT010617.1|DT010617
EST:     CATAATGAAGGAAAAATTCACAGAGATATCAAAG                         CGGCAAACATTTTGTTGACTGAGAATGGTGATGTTAAG
genomic: CATAATGAAGGAAAAATTCACAGAGATATCAAAGgtattgtcat ... aaatttgcagCGGCAAACATTTTGTTGACTGAGAATGGCGATGTTAAG
EST: gi|352768969|gb|FQ468160.1|FQ468160
EST:     TGCAATTGAGTATCTCCATAATGAAGGAAAAATTCACAGAGATATCAAAG                         CGGCAAACATTTTGTTGACTGAGAATGGCGATGTTAAG
genomic: TGCAATTGAGTATCTCCATAATGAAGGAAAAATTCACAGAGATATCAAAGgtattgtcat ... aaatttgcagCGGCAAACATTTTGTTGACTGAGAATGGCGATGTTAAG
EST: gi|352781734|gb|FQ469032.1|FQ469032
EST:     TGCAATTGAGTATCTCCATAATGAAGGAAAAATTCACAGAGATATCAAAG                         CGGCAAACATTTTGTTGACTGAGAATGGCGATGTTAAG
genomic: TGCAATTGAGTATCTCCATAATGAAGGAAAAATTCACAGAGATATCAAAGgtattgtcat ... aaatttgcagCGGCAAACATTTTGTTGACTGAGAATGGCGATGTTAAG
EST: gi|352781360|gb|FQ468204.1|FQ468204
EST:     TGCAATTGAGTATCTCCATAATGAAGGAAAAATTCACAGAGATATCAAAG                         CGGCAAACATTTTGTTGACTGAGAATGGCGATGTTAAG
genomic: TGCAATTGAGTATCTCCATAATGAAGGAAAAATTCACAGAGATATCAAAGgtattgtcat ... aaatttgcagCGGCAAACATTTTGTTGACTGAGAATGGCGATGTTAAG
EST: gi|352769491|gb|FQ468419.1|FQ468419
EST:     TGCAATTGAGTATCTCCATAATGAAGGAAAAATTCACAGAGATATCAAAG                         CGGCAAACATTTTGTTGACTGAGAATGGCGATGTTAAGGTTGCA
genomic: TGCAATTGAGTATCTCCATAATGAAGGAAAAATTCACAGAGATATCAAAGgtattgtcat ... aaatttgcagCGGCAAACATTTTGTTGACTGAGAATGGCGATGTTAAGGTTGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAACCACTGGATGAAATGTCTATAGCTTGCATTTTACGTGATCTACTCCATGCAATTGAGTATCTCCATAATGAAGGAAAAATTCACAGAGATATCAAAGgtattgtcatcaaatggaccctttgttaactcaagtatctttgcttgaaatagtgtcttttgatttgctgtttttaataatttctctaattagagcttttctttcttcttgtaaactattttggtggaatgacaacattgatattataaatttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA