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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatagcactagaactaaattcatctttggattatgcccaaaagttctgaaaaataaaatgtaattcacatgtgatgccgataattctactcctattgcagGTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTTGTTGGATTAGGATTGTCCAAGCTTTTCCATGCCTCCAAGTTGGAAGATT

Basic information

species Vitis vinifera
transcript Vv03s0038g00450.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g00450.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA12G04220.3 (Glycine max), 3'ss of exon 5
aatagcactagaactaaattcatctttggattatgcccaaaagttctgaaaaataaaatgtaattcacatgtgatgccgataattctactcctattgcagGTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTTGTTGGATTAGGATTGTCCAAGCTTTTCCATGCCTCCAAGTTGGAAGATT
| || || |  | ||    | |  | |   |||      |   | |||  ||   |  | |   |    |    |   || ||   |  |  | |||||||| ||||| ||||||||||||||||||||||| |||||||| || |||||||||||  | || || || |||||||||||||| ||    |  |||||| 
attatcagtgcatctctcctaaattcttatttacagagcactatgctgcgaagggatttctgcattgtcttgatttatgacaagagttttttttttgcagGTAGAAACAATTGATGACTATGATGAATATTGTCACTATGTGGCGGGACTTGTTGGGCTGGGTTTATCAAAGCTTTTCCATGCGTCTGGTTCAGAAGATC

upper sequence: Vv03s0038g00450.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G11960.3 (Glycine max), 3'ss of exon 5
aatagcactagaactaaattcatctttggattatgcccaaaagttctgaaaaata---aaatgtaattcacatgtgatgccgataattctactcctattgcagGTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTTGTTGGATTAGGATTGTCCAAGCTTTTCCATGCCTCCAAGTTGGAAGATT
 |  |||      ||||||||   | || |    || | |   | |  |  |||      ||    || |  | |||         || |  |  | || ||||| ||||| ||||||||||||||||||||||| |||||||| || |||||||||||  | || || || |||||||||||||| ||    |  |||||| 
-agtgcatctatcctaaattc--ttatgtacagagcactatgctgcaaaggaattcctgcatcatcttgatttatgacaagagatttttttatttttttccagGTAGAAACAATTGATGACTATGATGAATATTGTCACTATGTGGCGGGACTTGTTGGGCTGGGTTTATCAAAGCTTTTCCATGCGTCTGGTTCAGAAGATC

upper sequence: Vv03s0038g00450.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT4G34650.1 (Arabidopsis thaliana), 3'ss of exon 5
---aatagcac-tagaactaaattcatctttggattatgcccaaaagttctgaaaaataaaatgtaattcacatgtgatgccgataattctactcctattg--cagGTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTTGTTGGATTAGGATTGTCCAAGCTTTTCCATGCCTCCAAGTTGGAAGATT
     |   ||  ||||      | || |     ||||       |||| ||||    |  ||  ||    | ||    || || | || |     |||||  ||||| ||||| |||||||||||||||||||| ||||| ||||  |||||||||||||| ||||| ||||| ||  | |||  ||| ||  | || |||    
gtttgtgatacacagaatctttgtgatgtagattttatttttttcagttttgaagttaagcatcaaaacttc-tgaagagctga-acttatttgtgtattggacagGTAGAAACAATTGATGACTATGATGAATACTGCCATTATGCTGCAGGACTTGTTGGTTTAGGTTTGTCAAAAATCTTCATTGCTTCGGAATTAGAAATAC

upper sequence: Vv03s0038g00450.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT4G34640.1 (Arabidopsis thaliana), 3'ss of exon 5
aatagcactagaa----ctaaattcatctttggattatgcccaaaagttctgaaaaataaaatgtaattcacatgtgatgccgataattctactcctat-tgcagGTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTTGTTGGATTAGGATTGTCCAAGCTTTTCCATGCCTCCAAGTTGGAAGATT
||| | | |  ||    | ||| | || | |   || ||   | || |      |||| |  |||    |      | ||       ||  |||  |||   ||||| |||||  |||||||||| |||||||| ||||||||||| || || |||||||| ||||| ||||| || || ||||  ||  |    |  || | ||
aattgtattgaaagtaccaaaacttatttataagttttgtaaagaaat-----gaaatcatttgtttaccgatccagttgatccagttttcactattatacacagGTAGAAACTGTTGATGACTACGATGAATACTGCCACTATGTTGCTGGGCTTGTTGGTTTAGGTTTGTCGAAACTCTTCCTCGCTGCAGGATCAGAGGTTT

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|33405611|gb|CF211238.1|CF211238
EST:     ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAG                         GTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
genomic: ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAGgtttgtaatg ... cctattgcagGTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
EST: gi|110723345|gb|EE100551.1|EE100551
EST:     ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAG                         GTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
genomic: ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAGgtttgtaatg ... cctattgcagGTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
EST: gi|110687328|gb|EE064642.1|EE064642
EST:     ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAG                         GTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
genomic: ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAGgtttgtaatg ... cctattgcagGTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
EST: gi|33402993|gb|CF208620.1|CF208620
EST:     ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAG                         GTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
genomic: ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAGgtttgtaatg ... cctattgcagGTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
EST: gi|161707107|gb|FC057297.1|FC057297
EST:     ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAG                         GTGGAAACCATTGATGACTATGATGAA
genomic: ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAGgtttgtaatg ... cctattgcagGTGGAAACCATTGATGACTATGATGAA
EST: gi|110687067|gb|EE064151.1|EE064151
EST:     ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAG                         GTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
genomic: ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAGgtttgtaatg ... cctattgcagGTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
EST: gi|110699270|gb|EE076122.1|EE076122
EST:     ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAG                         GTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
genomic: ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAGgtttgtaatg ... cctattgcagGTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
EST: gi|110710584|gb|EE087069.1|EE087069
EST:     ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAG                         GTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
genomic: ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAGgtttgtaatg ... cctattgcagGTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
EST: gi|161717774|gb|FC068163.1|FC068163
EST:     ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAG                         GTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
genomic: ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAGgtttgtaatg ... cctattgcagGTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
EST: gi|161713197|gb|FC063653.1|FC063653
EST:     ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAG                         GTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
genomic: ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAGgtttgtaatg ... cctattgcagGTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
EST: gi|110700987|gb|EE078120.1|EE078120
EST:     ACATCACCAAACGAATGGGGGCANGAATGGCAAAATTTATTTGCAAAGAG                         GTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
genomic: ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAGgtttgtaatg ... cctattgcagGTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
EST: gi|110693784|gb|EE070316.1|EE070316
EST:     ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAG                         GTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
genomic: ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAGgtttgtaatg ... cctattgcagGTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
EST: gi|110688718|gb|EE067590.1|EE067590
EST:     ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAG                         GTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
genomic: ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAGgtttgtaatg ... cctattgcagGTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
EST: gi|34546786|gb|CF515018.1|CF515018
EST:     ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAG                         GTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
genomic: ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAGgtttgtaatg ... cctattgcagGTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
EST: gi|22007996|gb|BQ793030.1|BQ793030
EST:     ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAG                         GTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
genomic: ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAGgtttgtaatg ... cctattgcagGTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
EST: gi|33405294|gb|CF210921.1|CF210921
EST:     ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAG                         GTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
genomic: ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAGgtttgtaatg ... cctattgcagGTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
EST: gi|71856514|gb|DT005569.1|DT005569
EST:     ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAG                         GTGGAAACCATTGATGACTAT
genomic: ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAGgtttgtaatg ... cctattgcagGTGGAAACCATTGATGACTAT
EST: gi|32269974|gb|CD719133.1|CD719133
EST:     ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAG                         GTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
genomic: ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAGgtttgtaatg ... cctattgcagGTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
EST: gi|110725866|gb|EE102817.1|EE102817
EST:     ACATCACCAAACGAATGGNGGCAGGAATGGCAAAATTTATTTGCAAAGAG                         GTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGAACT
genomic: ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAGgtttgtaatg ... cctattgcagGTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGA-CT
EST: gi|110369584|gb|EC933748.1|EC933748
EST:     ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAG                         GTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
genomic: ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAGgtttgtaatg ... cctattgcagGTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTT
EST: gi|110708357|gb|EE085806.1|EE085806
EST:     ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAG                         GTGGGAAAC-ATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACT
genomic: ACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAGgtttgtaatg ... cctattgcagGTGG-AAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgaaaaataaaatgtaattcacatgtgatgccgataattctactcctattgcagGTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTTGTTGGATTAGGATTGTCCAAGCTTTTCCATGCCTCCAAGTTGGAAGATT
                                      ttctactcct  CT-rich tract
     aaataaaatgtaattc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatagcactagaactaaattcatctttggattatgcccaaaagttctgaaaaataaaatgtaattcacatgtgatgccgataattctactcctattgcagGTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTTGTTGGATTAGGATTGTCCAAGCTTTTCCATGCCTCCAAGTTGGAAGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - -aactaaa
- - - - - - - - - - - - - - - - - -cccaaaa
- - - - - - - - - - - - - - - - - - - - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgccg