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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATAATTGCTCTAGCATTTGTAAAGCATGTGATTTTCTGTTGTCCAAGCAGCTTGCTTCTGGTGGTTGGGGCGAGAGTTACCTTTCGTGTCAGAACAAGgttaagtctgtttttatttttttttcttattttatttttttataatatgaaacttacctttctttcttctcaagaaaatgcatgacatataaactcaatc...

Basic information

species Vitis vinifera
transcript Vv11s0065g00640.t01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0065g00640.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: LOC_Os11g08569.1 (Oryza sativa), 5'ss of exon 15
CAATAATTGCTCTAGCATTTGTAAAGCATGTGATTTTCTGTTGTCCAAGCAGCTTGCTTCTGGTGGTTGGGGCGAGAGTTACCTTTCGTGTCAGAACAAGgttaagtctgtttttatttttttttcttattttatttt-tttataatatgaaacttacctttctttcttctcaagaaaatgcatgacatataaactcaatc-
    ||| || |||   || | || |||||||| ||||| ||||| || |||||| |||| ||||| ||||||||||| ||  | || |||||  || |||| |  |  |  |     || |    ||     ||||  ||||||     |   | |  |||  |  |  |        | | |    ||     |   |  
TGGGAATAGCGCTACAGTTAGAAAGGCATGTGACTTTCTCTTGTCAAAACAGCTTCCTTCGGGTGGCTGGGGCGAGAGCTATTTGTCATGTCATGACGAGgtaactttcgcatcagccttatcagtttggacaatttcgtttatacccctattttgatgtttaatattgattttatccttactt--tttagggttttcgttt

upper sequence: Vv11s0065g00640.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GRMZM2G469298_T01 (Zea mays), 5'ss of exon 10
CAATAATTGCTCTAGCATTTGTAAAGCATGTGATTTTCTGTTGTCCAAGCAGCTTGCTTCTGGTGGTTGGGGCGAGAGTTACCTTTCGTGTCAGAACAAGgttaagtctgtttttatttttttttcttattttatttttttataatatgaaacttacctttctttcttctcaagaaaatgcatgacatataaactcaatc
||| ||| |  ||   ||    || |||||||||||||| ||||| ||| ||||| | || ||||| ||||| ||||||||  | || |||||||||||||| || |    || || | |||    |  ||||  ||| |     | |                                                    
CAACAATAGTCCTGTAATAAAAAAGGCATGTGATTTTCTTTTGTCGAAGGAGCTTCCATCCGGTGGATGGGGAGAGAGTTATTTGTCATGTCAGAACAAGgt-aacttgtcttatactctttccgttcttttttatttgtcgcgttttag--------------------------------------------------

upper sequence: Vv11s0065g00640.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GRMZM2G341010_T01 (Zea mays), 5'ss of exon 15
CAATAATTGCTCTAGCATTTGTAAAGCATGTGATTTTCTGTTGTCCAAGCAGCTTGCTTCTGGTGGTTGGGGCGAGAGTTACCTTTCGTGTCAGAACAAGgttaagtctgtttttatttttttttcttattttatttttttataatatgaaacttacctttctttcttctcaagaaaatgcatgacatataaactcaatc--
| |  |  |  ||   |||   || |||||||| ||||||||||| ||  ||||| |||||||||| ||||| ||||| ||| | || |||||| ||||||| |  ||  |        | |||  | ||||| |      ||||||  |||  ||    | |      | |   |  || ||   |  |  | |||| |  
CGAGGACAGTCCTGCAATTAAAAAGGCATGTGAGTTTCTGTTGTCAAAAGAGCTTCCTTCTGGTGGCTGGGGAGAGAGCTACTTGTCATGTCAGGACAAGgtaacttcgatc---gacctgtttgttcattttttaaaaaaataataataaa--tagtagtatggacgttgatacatgtg-attctaactggattcaaacag

upper sequence: Vv11s0065g00640.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA01G00430.2 (Glycine max), 5'ss of exon 16
CAATAATTGCTCTAGCATTTGTAAAGCATGTGATTTTCTGTTGTCCAAGCAGCTTGCTTCTGGTGGTTGGGGCGAGAGTTACCTTTCGTGTCAGAACAAGgttaagt---ctgtttttatttttttttcttattttattttttt----ataatatgaaacttacctttctttcttctcaagaaaatgcatgacatataaactcaatc
|| ||||||||| |||||  ||||||| ||||| |||||| |||||||||||||| |||||||||| ||||| |||||||| || || ||||| |||||||| || |   ||||||||||| |   |    ||||| ||||  |    | ||  |  |||  ||      |  ||  |  || | ||  || || |    ||     
CAGTAATTGCTCAAGCATCCGTAAAGCTTGTGAATTTCTGCTGTCCAAGCAGCTTCCTTCTGGTGGCTGGGGAGAGAGTTATCTGTCCTGTCAAAACAAGgtcaaatttgctgtttttattgtcggtatcaattttcttttactctgcacaacctataacaaacaccagctagtttccctgaga-tgtgtg-caaaagtgct-----

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|32265187|gb|CD716776.1|CD716776
EST:     AGCTTGCTTCTGGTGGTTGGGGCGAGAGTTACCTTTCGTGTCAGAACAAG                         GTGTATTCAAATCTTGATGGCAACAGATCTCATGTAGTAAATACCGCATGG
genomic: AGCTTGCTTCTGGTGGTTGGGGCGAGAGTTACCTTTCGTGTCAGAACAAGgttaagtctg ... tgttttacagGTGTATTCAAATCTTGATGGCAACAGATCTCATGTAGTAAATACCGCATGG
EST: gi|18458985|gb|BM437263.1|BM437263
EST:     AGCTTGCTTCTGGTGGTTGGGGCGAGAGTTACCTTTCGTGTCAGAACAAG                         GTGTATTCAAATCTTGATGGCAACAGATCTCATGTAGTAAATACCGCATGG
genomic: AGCTTGCTTCTGGTGGTTGGGGCGAGAGTTACCTTTCGTGTCAGAACAAGgttaagtctg ... tgttttacagGTGTATTCAAATCTTGATGGCAACAGATCTCATGTAGTAAATACCGCATGG
EST: gi|32248816|gb|CD714635.1|CD714635
EST:     AGCTTGCTTCTGGTGGTTGGGGCGAGAGTTACCTTTCGTGTCAGAACAAG                         GTGTATTCAAATCTTGATGGCAACAGATCTCATGTAGTAAATACCGCATGG
genomic: AGCTTGCTTCTGGTGGTTGGGGCGAGAGTTACCTTTCGTGTCAGAACAAGgttaagtctg ... tgttttacagGTGTATTCAAATCTTGATGGCAACAGATCTCATGTAGTAAATACCGCATGG
EST: gi|161717232|gb|FC067238.1|FC067238
EST:     AGCTTGCTTCTGGTGGTTGGGGCGAGAGTTACCTTTCGTGTCAGAACAAG                         GTGTATTCAAATCTTGATGGCAACAGATCTCATGTAGTAAATACCGCATGG
genomic: AGCTTGCTTCTGGTGGTTGGGGCGAGAGTTACCTTTCGTGTCAGAACAAGgttaagtctg ... tgttttacagGTGTATTCAAATCTTGATGGCAACAGATCTCATGTAGTAAATACCGCATGG
EST: gi|30299701|gb|CB976495.1|CB976495
EST:     AGCTTGCTTCTGGTGGTTGGGGCGAGAGTTACCTTTCGTGTCAGAACAAG                         GTGTATTCAAATCTTGATGGCAACAGATCTCATGTAGTAAATACCGCATGG
genomic: AGCTTGCTTCTGGTGGTTGGGGCGAGAGTTACCTTTCGTGTCAGAACAAGgttaagtctg ... tgttttacagGTGTATTCAAATCTTGATGGCAACAGATCTCATGTAGTAAATACCGCATGG
EST: gi|110391126|gb|EC956083.1|EC956083
EST:     AGCTTGCTTCTGGTGGTTGGGGCGAGAGTTACCTTTCGTGTCAGAACAAG                         GTGTATTCAAATCTTGATGGCAACAGATCTCATGTAGTAAATACCGCATGG
genomic: AGCTTGCTTCTGGTGGTTGGGGCGAGAGTTACCTTTCGTGTCAGAACAAGgttaagtctg ... tgttttacagGTGTATTCAAATCTTGATGGCAACAGATCTCATGTAGTAAATACCGCATGG
EST: gi|32270024|gb|CD719183.1|CD719183
EST:     AGCTTGCTTCTGGTGGTTGGGGCGAGAGTTACCTTTCGTGTCAGAACAAG                         GTGTATTCAAATCTTGATGGCAACAGATCTCATGTAGTAAATACCGCATGG
genomic: AGCTTGCTTCTGGTGGTTGGGGCGAGAGTTACCTTTCGTGTCAGAACAAGgttaagtctg ... tgttttacagGTGTATTCAAATCTTGATGGCAACAGATCTCATGTAGTAAATACCGCATGG
EST: gi|32249043|gb|CD714862.1|CD714862
EST:     AGCTTGCTTCTGGTGGTTGGGGCGAGAGTTACCTTTCGTGTCAGAACAAG                         GTGTATTCAAATCTTGATGGCAACAGATCTCATGTAGTANATACCGCATGG
genomic: AGCTTGCTTCTGGTGGTTGGGGCGAGAGTTACCTTTCGTGTCAGAACAAGgttaagtctg ... tgttttacagGTGTATTCAAATCTTGATGGCAACAGATCTCATGTAGTAAATACCGCATGG
EST: gi|34543141|gb|CF511373.1|CF511373
EST:     AGCTTGCTTCTGGTGGTTGGGGCGAGAGTTACCTTTCGTGTCAGAACAAG                         GTGTATTCAAATCTTGATGGCAACAGATCTCATGTAGTAAATACCGCATGG
genomic: AGCTTGCTTCTGGTGGTTGGGGCGAGAGTTACCTTTCGTGTCAGAACAAGgttaagtctg ... tgttttacagGTGTATTCAAATCTTGATGGCAACAGATCTCATGTAGTAAATACCGCATGG
EST: gi|32269610|gb|CD718769.1|CD718769
EST:     AGCTTGCTTCTGGTGGTTGGNGCGAGAGTTACCTTTCGTGTCAGAACAAG                         GTGTATTCAAATCTTGATGGCAACAGATCTCATGTAGTAAATACCGCATGG
genomic: AGCTTGCTTCTGGTGGTTGGGGCGAGAGTTACCTTTCGTGTCAGAACAAGgttaagtctg ... tgttttacagGTGTATTCAAATCTTGATGGCAACAGATCTCATGTAGTAAATACCGCATGG
EST: gi|30320591|gb|CD003853.1|CD003853
EST:     AGCTTGCTTCTGGTGGTTGGGGCGAGAGTTACCTTTCGTGTCAGAACAAG                         GTGTATTCAAATCTTGATGGCAACAGATCTCATGTAGTAAATACCGCATGG
genomic: AGCTTGCTTCTGGTGGTTGGGGCGAGAGTTACCTTTCGTGTCAGAACAAGgttaagtctg ... tgttttacagGTGTATTCAAATCTTGATGGCAACAGATCTCATGTAGTAAATACCGCATGG
EST: gi|30327518|gb|CD010780.1|CD010780
EST:     AGCTTGCTTCTGGTGGTTGNGGCGAGAGTTACCTTTCGTGTCAGAACAAG                         GTGTATTCAAATCTTGATGGCA-CAGATCTCATGTA
genomic: AGCTTGCTTCTGGTGGTTGGGGCGAGAGTTACCTTTCGTGTCAGAACAAGgttaagtctg ... tgttttacagGTGTATTCAAATCTTGATGGCAACAGATCTCATGTA
EST: gi|352785395|gb|FQ477609.1|FQ477609
EST:     AGCTTGCTTCTGGTGGTTGGGGCGAGAGTTACCTTTCGTGTCAGAACAAG                         GTGTATTCAAATCTTGATGGCAACAGATCTCATGTAGTAAATACCGCATGG
genomic: AGCTTGCTTCTGGTGGTTGGGGCGAGAGTTACCTTTCGTGTCAGAACAAGgttaagtctg ... tgttttacagGTGTATTCAAATCTTGATGGCAACAGATCTCATGTAGTAAATACCGCATGG
EST: gi|30328066|gb|CD011328.1|CD011328
EST:     AGCTTGCTTCTGGTGGTTGGGGCCAGAGTTACCTTTCGTGTCAGAACAAG                         GTGTATTCAAATC
genomic: AGCTTGCTTCTGGTGGTTGGGGCGAGAGTTACCTTTCGTGTCAGAACAAGgttaagtctg ... tgttttacagGTGTATTCAAATC
EST: gi|34543224|gb|CF511456.1|CF511456
EST:     AGCTTGCTTCTGGTGGTTGGGGCGAGAGTTACCTTTCGTGTCAGAACAAG                         GTGTATTCAAATCTTGATGGCAACAGATCTCATGTAGTAAATACCGCATGG
genomic: AGCTTGCTTCTGGTGGTTGGGGCGAGAGTTACCTTTCGTGTCAGAACAAGgttaagtctg ... tgttttacagGTGTATTCAAATCTTGATGGCAACAGATCTCATGTAGTAAATACCGCATGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAATAATTGCTCTAGCATTTGTAAAGCATGTGATTTTCTGTTGTCCAAGCAGCTTGCTTCTGGTGGTTGGGGCGAGAGTTACCTTTCGTGTCAGAACAAGgttaagtctgtttttatttttttttcttattttatttttttataatatgaaacttacctttctttcttctcaagaaaatgcatgacatataaactcaatc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaaaa