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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATATTCTGGGTGAGGCTCTTAGCTCTCTGAACTTTAAGGAACTCAAGAATCTGGAGACCAGGTTGGAGAAAGGTATCAGCAGAATCAGATCCAAAAAGgtacctactatatgtttcctttgtgactatgttttctactgtcaagtcttttcatcagttcaatgcccttttcctgtgttctaacttgctcttattctgccag

Basic information

species Vitis vinifera
transcript Vv12s0142g00360.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0142g00360.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA14G03100.2 (Glycine max), 5'ss of exon 4
GCATATTCTGGGTGAGGCTCTTAGCTCTCTGAACTTTAAGGAACTCAAGAATCTGGAGACCAGGTTGGAGAAAGGTATCAGCAGAATCAGATCCAAAAAGgtacctactatatgtttcctttgtgactatgttttctactgtcaagtcttttcatcagttcaatgcccttttcctgtgttctaacttgctcttattctgccag-----
||| || || ||||| ||||||||||||||||   | |||||| | ||||| |||||||  ||  ||||||||||| | |||||| | ||||||| |||||||       |||  |  |    |||     | ||   ||   || | | |    || |   |     | |   | ||   ||| ||  |   |  ||  ||      
GCACATCCTTGGTGAAGCTCTTAGCTCTCTGAGTCTGAAGGAATTAAAGAACCTGGAGAGTAGACTGGAGAAAGGTTTAAGCAGAGTTAGATCCAGAAAGgtat------tatactatcagcatgaa-gcatcttaagcttctaaatatatagg-cattgtgaatttatgtagatatgcaataagttagtaaaaaactagcaactaat
















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|110728991|gb|EE105103.1|EE105103
EST:     ATCTGGAGACCAGGTTGGAGAAAGGTATCANCAGAATCAGATCCAAAAAG                         AATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGG
genomic: ATCTGGAGACCAGGTTGGAGAAAGGTATCAGCAGAATCAGATCCAAAAAGgtacctacta ... attctgccagAATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGG
EST: gi|110726323|gb|EE102002.1|EE102002
EST:     ATCTGGAGACCAGGTTGGAGAAAGGTATCAGCAGAATCAGATCCAAAAAG                         AATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGG
genomic: ATCTGGAGACCAGGTTGGAGAAAGGTATCAGCAGAATCAGATCCAAAAAGgtacctacta ... attctgccagAATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGG
EST: gi|110715529|gb|EE093682.1|EE093682
EST:     ATCTGGAGACCAGGTTGGAGAAAGGTATCAGCAGAATCAGATCCAAAAAG                         AATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGG
genomic: ATCTGGAGACCAGGTTGGAGAAAGGTATCAGCAGAATCAGATCCAAAAAGgtacctacta ... attctgccagAATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGG
EST: gi|110730325|gb|EE107273.1|EE107273
EST:     ATCTGGAGACCAGGTTGGAGAAAGGTATCAGCAGAATCAGATCCAAAAAG                         AATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGG
genomic: ATCTGGAGACCAGGTTGGAGAAAGGTATCAGCAGAATCAGATCCAAAAAGgtacctacta ... attctgccagAATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGG
EST: gi|30298144|gb|CB974938.1|CB974938
EST:     ATCTGGAGACCTGGTTGGAGAAAGGTATCAGCAGAATCAGATCCAAAAAG                         AATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAGGAGG
genomic: ATCTGGAGACCAGGTTGGAGAAAGGTATCAGCAGAATCAGATCCAAAAAGgtacctacta ... attctgccagAATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGG
EST: gi|30135782|gb|CB921120.1|CB921120
EST:     ATCTGGAGACCAGGTTGGAGAAAGGTATCAGCAGAATCAGATCCAAAAAG                         AATGAATTGCTGTTTGCTGAAATCGAGTACATGCAAAAGAGG
genomic: ATCTGGAGACCAGGTTGGAGAAAGGTATCAGCAGAATCAGATCCAAAAAGgtacctacta ... attctgccagAATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGG
EST: gi|110710338|gb|EE086596.1|EE086596
EST:     ATCTGGAGACCAGGTTGGAGAAAGGTATCAGCAGAATCAGATCCAAAAAG                         AATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGG
genomic: ATCTGGAGACCAGGTTGGAGAAAGGTATCAGCAGAATCAGATCCAAAAAGgtacctacta ... attctgccagAATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGG
EST: gi|30133145|gb|CB918484.1|CB918484
EST:     ATCTGGAGACCAGGTTGGAGAAAGGTATCAGCAGAATCAGATCCAAAAAG                         AATGAATTGCTGTTTGCTGAAATCGAGTACATGCAAAAGAGG
genomic: ATCTGGAGACCAGGTTGGAGAAAGGTATCAGCAGAATCAGATCCAAAAAGgtacctacta ... attctgccagAATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGG
EST: gi|30298778|gb|CB975572.1|CB975572
EST:     ATCTGGAGACCAGGTTGGAGAAAGGTATCAGCAGAATCAGATCCAAAAAG                         AATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGG
genomic: ATCTGGAGACCAGGTTGGAGAAAGGTATCAGCAGAATCAGATCCAAAAAGgtacctacta ... attctgccagAATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGG
EST: gi|110726263|gb|EE101892.1|EE101892
EST:     ATCTGGAGACCAGGTTGGAGAAAGGTATCAGCAGAATCAGATCCAAAAAG                         AATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGG
genomic: ATCTGGAGACCAGGTTGGAGAAAGGTATCAGCAGAATCAGATCCAAAAAGgtacctacta ... attctgccagAATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATATTCTGGGTGAGGCTCTTAGCTCTCTGAACTTTAAGGAACTCAAGAATCTGGAGACCAGGTTGGAGAAAGGTATCAGCAGAATCAGATCCAAAAAGgtacctactatatgtttcctttgtgactatgttttctactgtcaagtcttttcatcagttcaatgcccttttcctgtgttctaacttgctcttattctgccag

- - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA