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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctaaacgttagatgctgttctgtttgattatttgatggtaaaggccatctttttgcattctgttggcaatgtaaactcactgattgttccctcaaacagGTGTACATATATTCTAGTGGTAGCAGGTTGGCTCAAAGGCTTCTATTTGGATACACAAACTATGGGGACCTAAGAAAATATTTATGTGGATTTTTCGACA

Basic information

species Vitis vinifera
transcript Vv19s0014g02480.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0014g02480.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA13G35120.3 (Glycine max), 3'ss of exon 7
--------gctaaacgttagatgctgttctgtttgattatttgatggtaa-aggccatctttttgcattctgttggcaatgtaaactcactgattgttccctcaaacagGTGTACATATATTCTAGTGGTAGCAGGTTGGCTCAAAGGCTTCTATTTGGATACACAAACTATGGGGACCTAAGAAAATATTTATGTGGATTTTTCGACA
           |    | | ||  |||  |  ||  | || ||||| |   ||  ||| ||||    ||   || | | ||  |  ||      || ||  |  ||||||| ||||||||||||||||||||||| ||||||||||||||  |||||||| | || ||| |||||||||||||||||||||||| ||| ||||| ||||
atgaaataaagagcaatcacattttgtgttcattcttcatctgatgtttgcagagcattttttc---ttacatttgaattgctatttc------tgatctatgcaacagGTATACATATATTCTAGTGGTAGCAGATTGGCTCAAAGGCTAATATTTGGAAAAACCAACCATGGGGACCTAAGAAAATATTTATCTGGGTTTTTTGACA

upper sequence: Vv19s0014g02480.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA12G35390.1 (Glycine max), 3'ss of exon 9
----gctaaacg----ttagatgctgttctgtttgattatttgatggt-aaaggccatctttttgcattctgttggcaatgtaaactcactgattgttccctcaaacagGTGTACATATATTCTAGTGGTAGCAGGTTGGCTCAAAGGCTTCTATTTGGATACACAAACTATGGGGACCTAAGAAAATATTTATGTGGATTTTTCGACA
     |||||      | | ||  |||     ||  | || ||||| |   ||  ||| ||||    || |||| |      ||   | ||   || ||  |  ||||||| ||||||||||||||||||||||| ||||||||||||||  |||||||| | || ||| |||||||||||||||||||||||| ||| ||||| ||||
atgaactaaagagcaatcacattttgtgtgcattcttcatctgatgtttggagagcatattttc---ttgtgtttg------aattcctctttctgatctatgcaacagGTATACATATATTCTAGTGGTAGCAGATTGGCTCAAAGGCTAATATTTGGAAAAACCAACCATGGGGACCTAAGAAAATATTTATCTGGGTTTTTTGACA

upper sequence: Vv19s0014g02480.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA06G36620.1 (Glycine max), 3'ss of exon 9
--------gctaaacgttagatgctgttctgtttgattatttgatg---gtaaaggccatctttttgcattctgttggcaatgtaaactcactgattgttccctcaaacagGTGTACATATATTCTAGTGGTAGCAGGTTGGCTCAAAGGCTTCTATTTGGATACACAAACTATGGGGACCTAAGAAAATATTTATGTGGATTTTTCGACA
          || | || | |   | |     ||  |||| ||||    | ||   |  | ||||||||||||  | || || |  | |      ||||        |||||| ||||||||||||||||| || || ||||||||||||||  |||||||| | |||||| |||||||||||||||||||||||| ||| ||||| ||||
atggagtaaatagatgtaacacattttggatgtttgttatctgatatctggaagacctttttttttgcattctaattgctattttgaat------ttgtgt-----gacagGTATACATATATTCTAGTGGCAGTAGATTGGCTCAAAGGCTAATATTTGGACATACAAACCATGGGGACCTAAGAAAATATTTATCTGGCTTTTTTGACA

upper sequence: Vv19s0014g02480.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT5G53850.3 (Arabidopsis thaliana), 3'ss of exon 10
gctaaacgttagatgctgttctgtttgattatttgatggtaaaggccatctttttgcattctgttggcaatgtaaactcactgattgttccctcaaacagGTGTACATATATTCTAGTGGTAGCAGGTTGGCTCAAAGGCTTCTATTTGGATACACAAACTATGGGGACCTAAGAAAATATTTATGTGGATTTTTCGACA----------
                      || || | || |     | || |  ||       |||| | ||  ||          | || || |||   | || |||| |||||||||||||| |||||  | || || |||| |||||| |||||  ||||| ||||||| || || ||||| ||| ||| ||| ||||||||||          
----------------------gtatgttcatgtagcttttaaagaaatg-----acatttttttcacag-----gtctaatggtt-ttcatgcgaataggtttacatatattctagCGGTAGTCGATTAGCGCAAAAGCTTCTCTTTGGGAACACAGACTATGGAGATCTGAGAAAGTATATATCTGGCTTTTTCGACACTACAATCGG

upper sequence: Vv19s0014g02480.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT5G53850.2 (Arabidopsis thaliana), 3'ss of exon 9
gctaaacgttagatgctgttctgtttgattatttgatggtaaaggccatctttttgcattctgttggcaatgtaaactcactgattgttccctcaaacagGTGTACATATATTCTAGTGGTAGCAGGTTGGCTCAAAGGCTTCTATTTGGATACACAAACTATGGGGACCTAAGAAAATATTTATGTGGATTTTTCGACA
                      || || | || |     | || |  ||       |||| | ||  ||          | || || |||   | || |||| |||||||||||||| |||||  | || || |||| |||||| |||||  ||||| ||||||| || || ||||| ||| ||| ||| ||||||||||
----------------------gtatgttcatgtagcttttaaagaaatg-----acatttttttcacag-----gtctaatggtt-ttcatgcgaatagGTTTACATATATTCTAGCGGTAGTCGATTAGCGCAAAAGCTTCTCTTTGGGAACACAGACTATGGAGATCTGAGAAAGTATATATCTGGCTTTTTCGACA

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|352768679|gb|FQ467891.1|FQ467891
EST:     TTGAGGATGTGCCAGAAGCTCTTCAGAAGTGGCATGCTTCAGGAATAAAG                         GTGTACATATATTCTAGTGGTAGCAGGTTGGCTCAAAGGCTTCTATTTGGA
genomic: TTGAGGATGTGCCAGAAGCTCTTCAGAAGTGGCATGCTTCAGGAATAAAGgttactcttg ... cctcaaacagGTGTACATATATTCTAGTGGTAGCAGGTTGGCTCAAAGGCTTCTATTTGGA
EST: gi|30126149|gb|CB911488.1|CB911488
EST:     TTGAGGATGTGCCAGAAGCTCTTCAGAAGTGGCATGCTTCAGGAATAAAG                         GTGTACATATATTCTAGTGGTAGCAGGTTGGCTCANAGGCTTCTATTTGGA
genomic: TTGAGGATGTGCCAGAAGCTCTTCAGAAGTGGCATGCTTCAGGAATAAAGgttactcttg ... cctcaaacagGTGTACATATATTCTAGTGGTAGCAGGTTGGCTCAAAGGCTTCTATTTGGA
EST: gi|29785157|gb|CB341909.2|CB341909
EST:     TTGAGGATGTGCCAGAAGCTCTCCAGAAGTGGCATGCTTCAGGAATAAAG                         GTGTACATATATTCTAGTGGTAGCAGGTTGGCTCAAAGGCTTCTATTTGGA
genomic: TTGAGGATGTGCCAGAAGCTCTTCAGAAGTGGCATGCTTCAGGAATAAAGgttactcttg ... cctcaaacagGTGTACATATATTCTAGTGGTAGCAGGTTGGCTCAAAGGCTTCTATTTGGA
EST: gi|110378704|gb|EC943848.1|EC943848
EST:     TTGAGGATGTGCCAGAAGCTCTTCAGAAGTGGCATGCTTCAGGAATAAAG                         GTGTACATATATTCTAGTGGTAGCAGGTTGGCTCAAAGGCTTCTATTTGGA
genomic: TTGAGGATGTGCCAGAAGCTCTTCAGAAGTGGCATGCTTCAGGAATAAAGgttactcttg ... cctcaaacagGTGTACATATATTCTAGTGGTAGCAGGTTGGCTCAAAGGCTTCTATTTGGA
EST: gi|32245843|gb|CD711662.1|CD711662
EST:     TTGAGGATGTGCCAGAAGCTCTTCAGAAGTGGCATGCTTCAGGAATAAAG                         GTGTACATATATTCTAGTGGTAGCAGGTTGGCTCAAAGGCTTCTATTTGGA
genomic: TTGAGGATGTGCCAGAAGCTCTTCAGAAGTGGCATGCTTCAGGAATAAAGgttactcttg ... cctcaaacagGTGTACATATATTCTAGTGGTAGCAGGTTGGCTCAAAGGCTTCTATTTGGA
EST: gi|18458739|gb|BM437017.1|BM437017
EST:     TTGAGGATGTGCCAGAAGCTCTTCAGAAGTGGCATGCTTCAAGA-TAAAG                         GTGTACATATATTCTAGTG
genomic: TTGAGGATGTGCCAGAAGCTCTTCAGAAGTGGCATGCTTCAGGAATAAAGgttactcttg ... cctcaaacagGTGTACATATATTCTAGTG
EST: gi|110412327|gb|EC978073.1|EC978073
EST:     TTGAGGATGTGCCAGAAGCTCTTCAGAAGTGGCATGCTTCAGGAATAAAG                         GTGTACATATATTCTAGTGGTAGCAGGTTGGCTCAAAGGCTTCTATTTGGA
genomic: TTGAGGATGTGCCAGAAGCTCTTCAGAAGTGGCATGCTTCAGGAATAAAGgttactcttg ... cctcaaacagGTGTACATATATTCTAGTGGTAGCAGGTTGGCTCAAAGGCTTCTATTTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatctttttgcattctgttggcaatgtaaactcactgattgttccctcaaacagGTGTACATATATTCTAGTGGTAGCAGGTTGGCTCAAAGGCTTCTATTTGGATACACAAACTATGGGGACCTAAGAAAATATTTATGTGGATTTTTCGACA
                                       ttgttccctc  CT-rich tract
                       aatgtaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctaaacgttagatgctgttctgtttgattatttgatggtaaaggccatctttttgcattctgttggcaatgtaaactcactgattgttccctcaaacagGTGTACATATATTCTAGTGGTAGCAGGTTGGCTCAAAGGCTTCTATTTGGATACACAAACTATGGGGACCTAAGAAAATATTTATGTGGATTTTTCGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - -gatgctg
- - - - - - - - - - ctgtttg
- - - - - - - - - - - - - - - - -tgatggt
- - - - - - - - - - - - - - - - - - - - aaaggcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcactg