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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTCAAAGGGCCAGCTAGGGGTCAAGTTCAAGCCATTTTCAAAGgtattactcatgtttttttgattttgataatagtagtatcttcttgtgatgttttgtgtaattgaaactgttgattaattttcatgcaaaaggatccatg...

Basic information

species Vitis vinifera
transcript Vv11s0103g00120.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0103g00120.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G078756_T01 (Zea mays), 5'ss of exon 7
TTCTCAAAGGGCCAGCTAGGGGTCAAGTTCAAGCCATTTTCAAAGgtattactcatgtttttttgattttgataatagtagtatcttcttgtgatgttttgtgtaattgaaactgttgattaattttcatgcaaaaggatccatg----------
|||||| | ||| |||| || |||||||||||||||||||||||||||| |    ||| ||| || || |  |   |     |   | || |||     |      || |   || || | |||| |  ||    |   |  ||           
TTCTCAGAAGGCAAGCTTGGTGTCAAGTTCAAGCCATTTTCAAAGgtataatctctgtgtttctgtttcttgtttaatctacactattttttgagaaaataatc--ttcatcttggtg-tcaattatgctgactgacagtttattgtttgtttag

upper sequence: Vv11s0103g00120.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: AC211349.4_FGT001 (Zea mays), 5'ss of exon 7
TTCTCAAAGGGCCAGCTAGGGGTCAAGTTCAAGCCATTTTCAAAGgtattactcatgtttttttgattttga--taata---gtagtatcttcttgtgatgttttgtgtaattgaaactgttgattaattttcatgcaaaaggatccatg------------
|||||| | ||| |||| || |||||||||||||||||||||||||||| |    | | ||| ||  | | |  ||||         || || ||| ||   |     | ||      ||| |||||   |   ||  |    |||  |             
TTCTCAGAAGGCAAGCTTGGTGTCAAGTTCAAGCCATTTTCAAAGgtataatctctatgtttctgtctcttatttaatgtacacttcatttttttgagaaaatagtcttcatcttgg-tgtcgattatgctcactgacagtttatcactattgtttgtttag
















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|351045887|gb|FQ441270.1|FQ441270
EST:     TTCTCAAAGGGCCAGCTAGGGGTCAAGTTCAAGCCATTTTCAAAG                         TATCCTCCT-GTTATAAAGACATGAGTTTTTGGATTA
genomic: TTCTCAAAGGGCCAGCTAGGGGTCAAGTTCAAGCCATTTTCAAAGgtattactca ... ctttttgcagTATCCTCCTTGTTATAAGGACATGAGTTTTTGGATTA
EST: gi|351045846|gb|FQ441031.1|FQ441031
EST:     TTCTCAAAGGGCCAGCTAGGGGTCAAGTTTCA-GCCATTTTCAAAG                         TATCCTCCTTGT-ATAAGG
genomic: TTCTCAAAGGGCCAGCTAGGGGTCAAGTT-CAAGCCATTTTCAAAGgtattactca ... ctttttgcagTATCCTCCTTGTTATAAGG
EST: gi|46919639|gb|CN548968.1|CN548968
EST:     TCAATTCTCAAAGGGCCAGCTAGGGGTCAAGTTCAAGCCATTTTCAAAG                         TATCCTCCTTGTTATAAGGACATGAGTTTTTGGATTAATGAGTCATTCACA
genomic: TCAATTCTCAAAGGGCCAGCTAGGGGTCAAGTTCAAGCCATTTTCAAAGgtattactca ... ctttttgcagTATCCTCCTTGTTATAAGGACATGAGTTTTTGGATTAATGAGTCATTCACA
EST: gi|351052538|gb|FQ456386.1|FQ456386
EST:     TTCTCAAAAGGCCAGCTAGGGGTCAAGTTCAAGCCATTTTCAAAG                         TATCCTCCTTGTTATAAGGACATGA
genomic: TTCTCAAAGGGCCAGCTAGGGGTCAAGTTCAAGCCATTTTCAAAGgtattactca ... ctttttgcagTATCCTCCTTGTTATAAGGACATGA
EST: gi|349807616|gb|FQ402007.1|FQ402007
EST:     TTCTCAAAGGGCCAGCTAGGGGGTCAAGTTCAAGCAATTTTCAAAG                         TATCCCTCCTTGTTATAAAGACAT
genomic: TTCTCAAAGGGCCAGCTAGGGG-TCAAGTTCAAGCCATTTTCAAAGgtattactca ... ctttttgcagTATCC-TCCTTGTTATAAGGACAT
EST: gi|352764071|gb|FQ467641.1|FQ467641
EST:     TTCTCAAAGGGCCAGCTGGGGGTCAAGTTCAAGCCATTTTCAAAG                         TATCCTCCTTGTTATAAGGACATGAGTTTTTGGATTATTGAGTCATTCACA
genomic: TTCTCAAAGGGCCAGCTAGGGGTCAAGTTCAAGCCATTTTCAAAGgtattactca ... ctttttgcagTATCCTCCTTGTTATAAGGACATGAGTTTTTGGATTAATGAGTCATTCACA
EST: gi|33406146|gb|CF211773.1|CF211773
EST:     TTCTCAAAGGGCCAGCTAGGGGTCAAGTTCAAGCCATTTTCAAAG                         TATCCTCCTTGTTATAAGGACATGAGTTTTTGGATTAATGAGTCATTCACA
genomic: TTCTCAAAGGGCCAGCTAGGGGTCAAGTTCAAGCCATTTTCAAAGgtattactca ... ctttttgcagTATCCTCCTTGTTATAAGGACATGAGTTTTTGGATTAATGAGTCATTCACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCTCAAAGGGCCAGCTAGGGGTCAAGTTCAAGCCATTTTCAAAGgtattactcatgtttttttgattttgataatagtagtatcttcttgtgatgttttgtgtaattgaaactgttgattaattttcatgcaaaaggatccatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaaaag