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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttaatccttgttcctcgacttattaatctgtgaatagcttcatggtgttacttatgtttttggggtggtggatatttttgataaatgaatagtgaataccatgggtccttcacccttgtctatttctgttgaacattgtgcagCCTGGTATGAAAGAAGGCAAATGAAAAAGATCTACTCTCCACTTCTGGAAGGACTCCTAGCCCTTTATCTTGGGTTTGAATGGATCCAG

Basic information

species Vitis vinifera
transcript Vv02s0012g01220.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0012g01220.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA01G40650.2 (Glycine max), 3'ss of exon 6
gtttaatccttgttcctcgacttattaatctgtgaatagcttcatggtgtt-acttatgtttttggggtggtggatatttttgataaatgaatagtgaataccatgggtccttcacccttgtctatttctgttgaacattgtgcagCCTGGTATGAAAGAAGGCAAATGAAAAAGATCTACTCTCCACTTCTGGAAGGACTCCTAGCCCTTTATCTTGGGTTTGAATGGATCCAG
                                            ||||||| |   |   |  |   |    |   |   |   |   || ||  |  | |  |||    ||| | |     |  | | | ||      | ||||||||||||||||| | ||||||||||||| ||||| || ||||||||||||||||| || || || || || || || || |||||||| 
------------------------------------------gttggtgtttaggaaaaatgattcagaaaagagaagcctaactttgtgcattttctacat-atgatgtcttaatctcaaccattctatttttgg---tttgcagCCTGGTATGAAAAACGGCAAATGAAAAAAATCTATTCCCCACTTCTGGAAGGACTGCTGGCACTATACCTAGGTTTCGAGTGGATCCAA

upper sequence: Vv02s0012g01220.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA01G40650.1 (Glycine max), 3'ss of exon 7
gtttaatccttgttcctcgacttattaatctgtgaatagcttcatggtgtt-acttatgtttttggggtggtggatatttttgataaatgaatagtgaataccatgggtccttcacccttgtctatttctgttgaacattgtgcagCCTGGTATGAAAGAAGGCAAATGAAAAAGATCTACTCTCCACTTCTGGAAGGACTCCTAGCCCTTTATCTTGGGTTTGAATGGATCCAG-----------
                                            ||||||| |   |   |  |   |    |   |   |   |   || ||  |  | |  |||    ||| | |     |  | | | ||      | ||||||||||||||||| | ||||||||||||| ||||| || ||||||||||||||||| || || || || || || || || ||||||||            
------------------------------------------gttggtgtttaggaaaaatgattcagaaaagagaagcctaactttgtgcattttctacat-atgatgtcttaatctcaaccattctatttttgg---tttgcagCCTGGTATGAAAAACGGCAAATGAAAAAAATCTATTCCCCACTTCTGGAAGGACTGCTGGCACTATACCTAGGTTTCGAGTGGATCCAAGTAATCCTCAA

upper sequence: Vv02s0012g01220.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA11G04660.2 (Glycine max), 3'ss of exon 7
gtttaatccttgttcctcgacttattaatctgtgaatagcttcatggtgttacttatgtttttggggtggtggatatttttgataaatgaatagtgaataccatgggtccttcacccttgtctatttctgttgaacattgtgcagCCTGGTATGAAAGAAGGCAAATGAAAAAGATCTACTCTCCACTTCTGGAAGGACTCCTAGCCCTTTATCTTGGGTTTGAATGGATCCAG
                                ||  | | |   | | |  | | ||    |  |      ||  |  ||||   | |   |  |  |||  |||  |   || |  |  |||||||||| |        ||||||||||||||| | | ||||||||||||| ||||| || ||||||||||||||||| || || || || || || |  || |||||||| 
-------------------------------ttgtgttggtgtttagggaaaatgat----tcagaaaaaagggcaactttgtgcatt---ttctacatatgatgtcttaatctcaatattctatttctggtt-------tgcagCCTGGTATGAGAAACGGCAAATGAAAAAAATCTATTCCCCACTTCTGGAAGGACTGCTGGCACTATACCTAGGTTGCGAGTGGATCCAA

upper sequence: Vv02s0012g01220.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT2G35260.1 (Arabidopsis thaliana), 3'ss of exon 7
gtttaatccttgttcctcgacttatta-atctgtgaatagcttcatggtgttacttatgtttttggggtggtggatatttttgataaatgaatagtgaataccatgggtccttcacccttgtctatttctgttgaacattgtgcagCCTGGTATGAAAGAAGGCAAATGAAAAAGATCTACTCTCCACTTCTGGAAGGACTCCTAGCCCTTTATCTTGGGTTTGAATGGATCCAG
||        | ||| | | || || | || |||    ||    |   ||  |  ||   |  | |  | |   | |        ||||  | |  |  |    |  ||   |||       || ||| |  |   | ||||||||| |||||||| |  || || ||||| ||||| ||||||||||| || ||||||||| ||||||| ||||| ||  |||||||| | |||
gtacttgttctcttcttggtctgatcatatttgttttgagaaagaatatgaaagataaactaatagaatagcttagagaacaaggaaatataaaccggtttgt-tctgttactcatgaaatcctctttgtcatttgctttgtgcagCTTGGTATGAGAAGAGACAGATGAAGAAGATTTACTCTCCACTCCTTGAAGGACTCTTAGCCCTCTATCTCGGTATTGAATGGGTTCAG

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|352769120|gb|FQ471068.1|FQ471068
EST:     AGTTTTGCAATCTCGCTCCGGTCGTGCGGATCTAAAAAAGCTCTTTGCAG                         CCTGGTATGAAAGAAGGCAAATGAAAAAGATCTACTCTCCACTTCTGGAAG
genomic: AGTTTTGCAATCTCGCTCCGGTCGTGCGGATCTAAAAAAGCTCTTTGCAGgtttaatcct ... cattgtgcagCCTGGTATGAAAGAAGGCAAATGAAAAAGATCTACTCTCCACTTCTGGAAG
EST: gi|352776642|gb|FQ465440.1|FQ465440
EST:     GTTTTGCAATCTCGCTCCGGTCGTGCGGATCTNNNNNNNGCTCTTTGCAG                         CCTGGTATGAAAGAAGGCAAATGAAAAAGATCTACTCTCCACTTCTGGAAG
genomic: GTTTTGCAATCTCGCTCCGGTCGTGCGGATCT-AAAAAAGCTCTTTGCAGgtttaatcct ... cattgtgcagCCTGGTATGAAAGAAGGCAAATGAAAAAGATCTACTCTCCACTTCTGGAAG
EST: gi|352781173|gb|FQ466486.1|FQ466486
EST:     GTTTTGCAATCTCGCTCCGGTCGTGCGGATCTNNNNNNNGCTCTTTGCAG                         CCTGGTATGAAAGAAGGCAAATGAAAAAGATTTACTCTCCACTTCTGGAAG
genomic: GTTTTGCAATCTCGCTCCGGTCGTGCGGATCT-AAAAAAGCTCTTTGCAGgtttaatcct ... cattgtgcagCCTGGTATGAAAGAAGGCAAATGAAAAAGATCTACTCTCCACTTCTGGAAG
EST: gi|156737157|gb|EV241278.1|EV241278
EST:     AGTTTTGCAATCTCGCTCCGGTCGTGCGGATCTAAAAAAGCTCTTTGCAG                         CCTGGTATGAAAGAAGGCAAATGAAAAAGATCTACTCTCCACTTCTGGAAG
genomic: AGTTTTGCAATCTCGCTCCGGTCGTGCGGATCTAAAAAAGCTCTTTGCAGgtttaatcct ... cattgtgcagCCTGGTATGAAAGAAGGCAAATGAAAAAGATCTACTCTCCACTTCTGGAAG
EST: gi|110363320|gb|EC926898.1|EC926898
EST:     AGTTTTGCAATCTCGCTCCGGTCGTGCGGATCTAAAAAAGCTCTTTGCAG                         CCTGGTATGAAAGAAGGCAAATGAAAAAGATCTACTCTCCACTTCTTGAAG
genomic: AGTTTTGCAATCTCGCTCCGGTCGTGCGGATCTAAAAAAGCTCTTTGCAGgtttaatcct ... cattgtgcagCCTGGTATGAAAGAAGGCAAATGAAAAAGATCTACTCTCCACTTCTGGAAG
EST: gi|349828983|gb|FQ419515.1|FQ419515
EST:     AGTTTTGCAATCTCGCTCCGGTCGTGCGGATCTAAAAAAGCTCTTTGCAG                         CCTGGTATGAAAGAAGGCAAATGAAAAAGATCTACTCTCCACTTCTTGAAG
genomic: AGTTTTGCAATCTCGCTCCGGTCGTGCGGATCTAAAAAAGCTCTTTGCAGgtttaatcct ... cattgtgcagCCTGGTATGAAAGAAGGCAAATGAAAAAGATCTACTCTCCACTTCTGGAAG
EST: gi|110380859|gb|EC946157.1|EC946157
EST:     AGTTTTGCAATCTCGCTCCGGTCGTGCGGATCTAAAAAAGCTCTTTGCAG                         CCTGGTATGAAAGAAGGCAAATGAAAAAGATCTACTCTCCACTTCTTGAAG
genomic: AGTTTTGCAATCTCGCTCCGGTCGTGCGGATCTAAAAAAGCTCTTTGCAGgtttaatcct ... cattgtgcagCCTGGTATGAAAGAAGGCAAATGAAAAAGATCTACTCTCCACTTCTGGAAG
EST: gi|352769544|gb|FQ468472.1|FQ468472
EST:     AGTTTTGCAATCTCGCTCCGGTCGTGCGGATCTAAAAAAGCTCTTTGCAG                         CCTGGTATGAAAGAAGGCAAATGAAAAAGATCTACTCTCCACTTCTGGAAG
genomic: AGTTTTGCAATCTCGCTCCGGTCGTGCGGATCTAAAAAAGCTCTTTGCAGgtttaatcct ... cattgtgcagCCTGGTATGAAAGAAGGCAAATGAAAAAGATCTACTCTCCACTTCTGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagtgaataccatgggtccttcacccttgtctatttctgttgaacattgtgcagCCTGGTATGAAAGAAGGCAAATGAAAAAGATCTACTCTCCACTTCTGGAAGGACTCCTAGCCCTTTATCTTGGGTTTGAATGGATCCAG
                              tctattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttaatccttgttcctcgacttattaatctgtgaatagcttcatggtgttacttatgtttttggggtggtggatatttttgataaatgaatagtgaataccatgggtccttcacccttgtctatttctgttgaacattgtgcagCCTGGTATGAAAGAAGGCAAATGAAAAAGATCTACTCTCCACTTCTGGAAGGACTCCTAGCCCTTTATCTTGGGTTTGAATGGATCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG