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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGTGTGCGTGACTGGTGCAGGAGGGTATATAGCTTCGTGGGTCGTCAAGTTTCTCCTCTCAAAGGGTTATATTGTTCATGGAACGGTCAGAGACCCAAgtaatatcctctgttctccctttcatttctgtacttttttttttttttttttttggaaaataagtctttaccatcatttttattacttcggagctcttcctattttgattacatattctattggccaaaaactgtgtagtttttctgaaaattttccttctattcctattaaaactctcttttcag

Basic information

species Vitis vinifera
transcript Vv18s0122g00630.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0122g00630.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: AT1G76470.1 (Arabidopsis thaliana), 5'ss of exon 1
AGAGTGTGCGTGACTGGTGCAGGAGGGTATATAGCTTCGTGGGTCGTCAAGTTTCTCCTCTCAAAGGGTTATATTGTTCATGGAACGGTCAGAGACCCAAgtaatatcctctgttctccctttcatttctgtacttttttttttttttttttttggaaaataagtctttaccatcatttttattacttcggagctcttcctattttgattacatattctattggccaaaaactgtgtagtttttctgaaaattttccttctattcctattaaaactctcttttcag
|  || || || |||||||||||||||| ||| ||||| ||| ||||||||||||| |||||    || || | ||| |||||||| ||  |||| ||  ||||        |   |    |  |   |    | | | |||||| |    ||| ||| ||   ||| |       ||| |     ||   |    | | |   |||||  ||| |  | |  |                                                              
AAGGTCTGTGTTACTGGTGCAGGAGGGTTTATTGCTTCATGGCTCGTCAAGTTTCTTCTCTCTCGTGGCTACACTGTCCATGGAACCGTTCGAGATCCTTgtaa--------gggataagatagaaaacaaatcctctcttttttgtgaacttttgaatat---tctctg------tttcttgagtttgaaaaagttgcatgcattgatcccat-tgttctcag--------------------------------------------------------------
















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|110728908|gb|EE104890.1|EE104890
EST:     TCATGGAACGGTCAGAGACCCAA                         GTGATGAAAAGAACAGCCATCTAAAGAAATTGGAGAAGGCTTTGGAGAATC
genomic: TCATGGAACGGTCAGAGACCCAAgtaatatcct ... ctcttttcagGTGATGAAAAGAACAGCCATCTAAAGAAATTGGAGAAGGCTTTGGAAAATC
EST: gi|351055237|gb|FQ440576.1|FQ440576
EST:     GTTTCTCCTCTCAAAGGGTTATATTGTTCATGGAACGGTCAGAGACCCAA                         GTGATGAAAAGAACAGCCATCTAAAGAAATTGGAGAAGGCTTTGGAGAATC
genomic: GTTTCTCCTCTCAAAGGGTTATATTGTTCATGGAACGGTCAGAGACCCAAgtaatatcct ... ctcttttcagGTGATGAAAAGAACAGCCATCTAAAGAAATTGGAGAAGGCTTTGGAAAATC
EST: gi|351035526|gb|FQ463371.1|FQ463371
EST:     GTTTCTCCTCTCAAAGGGTTATATTGTTCATGGAACGGTCAGAGACCCAA                         GTGATGAAAAGAACAGCCATCTAAAGAAATTGGAGAAGGCTTTGGAGAATC
genomic: GTTTCTCCTCTCAAAGGGTTATATTGTTCATGGAACGGTCAGAGACCCAAgtaatatcct ... ctcttttcagGTGATGAAAAGAACAGCCATCTAAAGAAATTGGAGAAGGCTTTGGAAAATC
EST: gi|351029342|gb|FQ436736.1|FQ436736
EST:     GTTTCTCCTCTCAAAGGGTTATATTGTTCATGGAACGGTCAGAGACCCAA                         GTGATGAAAAGAACAGCCATCTAAAGAAATTGGAGAAGGCTTTGGAGAATC
genomic: GTTTCTCCTCTCAAAGGGTTATATTGTTCATGGAACGGTCAGAGACCCAAgtaatatcct ... ctcttttcagGTGATGAAAAGAACAGCCATCTAAAGAAATTGGAGAAGGCTTTGGAAAATC
EST: gi|352791001|gb|FQ479994.1|FQ479994
EST:     GTTTCTCCTCTCAAAGGGTTATATTGTTCATGGAACGGTCAGAGACCCAA                         GTGATGAAAAGAACAGCCATCTAAAGAAATTGGAGAAGGCTTTGGAGAATC
genomic: GTTTCTCCTCTCAAAGGGTTATATTGTTCATGGAACGGTCAGAGACCCAAgtaatatcct ... ctcttttcagGTGATGAAAAGAACAGCCATCTAAAGAAATTGGAGAAGGCTTTGGAAAATC
EST: gi|71856193|gb|DT005248.1|DT005248
EST:     GTTTCTCCTCTCAAAGGGTTATATTGTTCATGGAACGGTCAGAGACCCAA                         GTGATGAAAAGAACAGCCATCTAAAGAAATTGGAGAAGGCTTTGGAGAATC
genomic: GTTTCTCCTCTCAAAGGGTTATATTGTTCATGGAACGGTCAGAGACCCAAgtaatatcct ... ctcttttcagGTGATGAAAAGAACAGCCATCTAAAGAAATTGGAGAAGGCTTTGGAAAATC
EST: gi|351033973|gb|FQ463028.1|FQ463028
EST:     GTTTCTCCTCTCAAAGGGTTATATTGTTCATGGAACGGTCAGAGACCCAA                         GTGATGAAAAGAACAGCCATCTAAAGAAATTGGAGAAGGCTTTGGAGAATC
genomic: GTTTCTCCTCTCAAAGGGTTATATTGTTCATGGAACGGTCAGAGACCCAAgtaatatcct ... ctcttttcagGTGATGAAAAGAACAGCCATCTAAAGAAATTGGAGAAGGCTTTGGAAAATC
EST: gi|349820738|gb|FQ408567.1|FQ408567
EST:     GTTTCTCCTCTCAAAGGGTTATATTGTTCATGGAACGGTCAGAGACCCAA                         GTGATGAAAAGAACAGCCATCTAAAGAAATTGGAGAAGGCTTTGGAGAATC
genomic: GTTTCTCCTCTCAAAGGGTTATATTGTTCATGGAACGGTCAGAGACCCAAgtaatatcct ... ctcttttcagGTGATGAAAAGAACAGCCATCTAAAGAAATTGGAGAAGGCTTTGGAAAATC
EST: gi|351015778|gb|FQ431733.1|FQ431733
EST:     GTTTCTCCTCTCAAAGGGTTATATTGTTCATGGAACGGTCAGAGACCCAA                         GTGATGAAAAGAACAGCCATCTAAAGAAATTGGAGAAGGCTTTGGAGAATC
genomic: GTTTCTCCTCTCAAAGGGTTATATTGTTCATGGAACGGTCAGAGACCCAAgtaatatcct ... ctcttttcagGTGATGAAAAGAACAGCCATCTAAAGAAATTGGAGAAGGCTTTGGAAAATC
EST: gi|351046584|gb|FQ453200.1|FQ453200
EST:     GTTTCTCCTCTCAAAGGGTTATATTGTTCATGGAACGGTCAGAGACCCAA                         GTGATGAAAAGAACAGCCATCTAAAGAAATTGGAGAAGGCTTTGGAGAATC
genomic: GTTTCTCCTCTCAAAGGGTTATATTGTTCATGGAACGGTCAGAGACCCAAgtaatatcct ... ctcttttcagGTGATGAAAAGAACAGCCATCTAAAGAAATTGGAGAAGGCTTTGGAAAATC
EST: gi|351019824|gb|FQ439641.1|FQ439641
EST:     GTTTCTCCTCTCAAAGGGTTATATTGTTCATGGAACGGTCAGAGACCCAA                         GTGATGAAAAGAACAGCCATCTAAAGAAATTGGAGAAGGCTTTGGAGAATC
genomic: GTTTCTCCTCTCAAAGGGTTATATTGTTCATGGAACGGTCAGAGACCCAAgtaatatcct ... ctcttttcagGTGATGAAAAGAACAGCCATCTAAAGAAATTGGAGAAGGCTTTGGAAAATC
EST: gi|349822332|gb|FQ412596.1|FQ412596
EST:     GTTTCCCCTCTCAAAGGGTTATATTGTTCATGGAACGGTCAGAGACCCAA                         GTGATGAAAAGAACAGCCATCTAAAGAAATTGGAGAAGGCTTTGGAGAATC
genomic: GTTTCTCCTCTCAAAGGGTTATATTGTTCATGGAACGGTCAGAGACCCAAgtaatatcct ... ctcttttcagGTGATGAAAAGAACAGCCATCTAAAGAAATTGGAGAAGGCTTTGGAAAATC
EST: gi|351019644|gb|FQ439461.1|FQ439461
EST:     GTTTCTCCTCTCAAAGGGTTATATTGTTCATGGAACGGTCAGAGACCCAA                         GTGATGAAAAGAACAGCCATCTAAAGAAATTGGAGAAGGCTTTGGAGAATC
genomic: GTTTCTCCTCTCAAAGGGTTATATTGTTCATGGAACGGTCAGAGACCCAAgtaatatcct ... ctcttttcagGTGATGAAAAGAACAGCCATCTAAAGAAATTGGAGAAGGCTTTGGAAAATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGTGTGCGTGACTGGTGCAGGAGGGTATATAGCTTCGTGGGTCGTCAAGTTTCTCCTCTCAAAGGGTTATATTGTTCATGGAACGGTCAGAGACCCAAgtaatatcctctgttctccctttcatttctgtacttttttttttttttttttttggaaaataagtctttaccatcatttttattacttcggagctcttcctattttgattacatattctattggccaaaaactgtgtagtttttctgaaaattttccttctattcctattaaaactctcttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA