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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attctctaaccctagtgtaatattgatatgcctagtcctttaaacctattttgtgatagaccacaggactgaagttccatcgctccactgtggttgacagGTATGGCTACAAGGATGTTCGCAAAGAGAATCATCAGACATTTGAGCAGCTGCTAATAGAGAGCCTTGAGAAGTTCATTCGACGTGAGGCCCAGGAACGG

Basic information

species Vitis vinifera
transcript Vv12s0142g00170.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0142g00170.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G19120.1 (Glycine max), 3'ss of exon 10
attctct-aaccctagtgtaatattgatatgcctagtcctttaaacctattttgtgatagaccacaggactgaagttccatcgctccactgtggttgacagGTATGGCTACAAGGATGTTCGCAAAGAGAATCATCAGACATTTGAGCAGCTGCTAATAGAGAGCCTTGAGAAGTTCATTCGACGTGAGGCCCAGGAACGG
 |  | | || |  ||  |   ||| |         |  |  | |  |||||| |  |     | |  | ||   ||   ||       |    |  |||||||||| ||||| |||||||| ||||| ||||| ||||| |||||||||||||| || |||||||| |||||||| || || |||||||| |||||  ||
ttcatgtgaaactgagcatctcattaagggataatttagtgaatatgtattttatcctct-taataaaaatgtctttttgtctgaatttttatatcaacagGTATGGTTACAAAGATGTTCGGAAAGAAAATCACCAGACTTTTGAGCAGCTGCTGATTGAGAGCCTAGAGAAGTTTATACGTCGTGAGGCTCAGGAGAGG

upper sequence: Vv12s0142g00170.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA15G05880.1 (Glycine max), 3'ss of exon 9
attctctaaccctagtgtaatattgatatgcc-tagtcctttaaacc-tat-tttgtgatagacc--acaggactgaagttccatc-gctccactgtggttgacagGTATGGCTACAAGGATGTTCGCAAAGAGAATCATCAGACATTTGAGCAGCTGCTAATAGAGAGCCTTGAGAAGTTCATTCGACGTGAGGCCCAGGAACGG
       |||    | | | | |   || ||  || |  | | ||   | | ||| | ||   |   |    | ||   ||   || |      | ||    |||||||||| ||||| |||||||| ||||| ||||||||||| |||||||||||||| || ||||| || ||||| || || || |||||||| |||||  ||
-----tgaacaactgagca-tctcagtaagcgataattttgtgaataatgtatttattatcctcttaatgaaaatgtctttttgtctgaatttttatgtcaaacagGTATGGTTACAAAGATGTTCGGAAAGAAAATCATCAGACTTTTGAGCAGCTGCTGATTGAGAGTCTAGAGAAATTTATACGTCGTGAGGCTCAGGAGAGG

upper sequence: Vv12s0142g00170.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G07720.1 (Glycine max), 3'ss of exon 7
attctctaaccctag-tgtaatat-tgatatgcctagtcctttaaac----ctattttgtgatagaccacaggactgaagttccatcgctccactgtggttgacagGTATGGCTACAAGGATGTTCGCAAAGAGAATCATCAGACATTTGAGCAGCTGCTAATAGAGAGCCTTGAGAAGTTCATTCGACGTGAGGCCCAGGAACGG
    | |||   |   | || ||| || | | ||| ||  || ||       | |||| |  |  | |  |  ||     |  ||    |    | |  |  |||||||||| ||||| |||||||||||||| ||||| || || |||||||| ||||| || |||||||| |||||||| || || |||||||| || ||  ||
---ttgtaattttccctatagtatatgctgtccct-gtaattaaagtgtttttttttttttgtcaatcctaaaaccctgat--cagaaattttatatcttcaacagGTATGGTTACAAAGATGTTCGCAAAGAAAATCACCAAACTTTTGAGCAACTGCTGATGGAGAGCCTAGAGAAGTTTATACGTCGTGAGGCTCAAGAGAGG

upper sequence: Vv12s0142g00170.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA05G24530.1 (Glycine max), 3'ss of exon 9
attctctaaccctagtg-taatat-tgatatgcctagtcctttaaa---cctattttgtgatagaccacaggactgaagttccatcgctccactgtggttgacagGTATGGCTACAAGGATGTTCGCAAAGAGAATCATCAGACATTTGAGCAGCTGCTAATAGAGAGCCTTGAGAAGTTCATTCGACGTGAGGCCCAGGAACGG
  | | |||   |     || ||| || | | ||| ||  || ||      | |||| |  |  | |  |  ||     ||  |    |    | |  |  |||||||||| ||||| |||||||||||||| ||||| || || |||||||| ||||| || |||||| | |||||||| || || |||||||| |||||| ||
--tttgtaattttctcaatagtatatgctgtccct-gtaattaaagtgttttttttttttgtcaatcctataaccctgattaga--aattttatatcttcaacagGTATGGTTACAAAGATGTTCGCAAAGAAAATCACCAAACTTTTGAGCAACTGCTGATGGAGAGCTTAGAGAAGTTTATACGTCGTGAGGCTCAGGAAAGG

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|37187922|gb|CF607273.1|CF607273
EST:     TTCCGCAGAGTCTGCCCAAAAAGCTACCACATATTTCGCTGCATTGCCAG                         GTATGGCTACAAGGATGTTCGCAAAGAGAATCATCAGACATTTGAGCAGCT
genomic: TTCCGCAGAGTCTGCCCAAAAAGCTACCACATATTTCGCTGCATTGCCAGgtagcagtct ... tggttgacagGTATGGCTACAAGGATGTTCGCAAAGAGAATCATCAGACATTTGAGCAGCT
EST: gi|32269031|gb|CD718190.1|CD718190
EST:     TTCCGCAGAGTCTGCCCAAAAAGCTACCACATATTTCGCTGCATTGCCAG                         GTATGGCTACAAGGATGTTCGCAAAGAGAATCATCAGACATTTGAGCAGCT
genomic: TTCCGCAGAGTCTGCCCAAAAAGCTACCACATATTTCGCTGCATTGCCAGgtagcagtct ... tggttgacagGTATGGCTACAAGGATGTTCGCAAAGAGAATCATCAGACATTTGAGCAGCT
EST: gi|30324910|gb|CD008172.1|CD008172
EST:     TTCCGCAGAGTCTGCCCAAAAAGCTACCACATATTTCGCTGCATTGCCAG                         GTATGGCTACAAGGATGTTCGCAAAGAGAATCATCAGACATTTGAGCAGCT
genomic: TTCCGCAGAGTCTGCCCAAAAAGCTACCACATATTTCGCTGCATTGCCAGgtagcagtct ... tggttgacagGTATGGCTACAAGGATGTTCGCAAAGAGAATCATCAGACATTTGAGCAGCT
EST: gi|37188453|gb|CF607802.1|CF607802
EST:     TTCCGCAGAGTCTGCCCAAAAAGCTACCACATATTTCGCTGCATTGCCAG                         GTATGGCTACAAGGATGTTCGCAAAGAGAATCATCAGACATTTGAGCAGCT
genomic: TTCCGCAGAGTCTGCCCAAAAAGCTACCACATATTTCGCTGCATTGCCAGgtagcagtct ... tggttgacagGTATGGCTACAAGGATGTTCGCAAAGAGAATCATCAGACATTTGAGCAGCT
EST: gi|32270233|gb|CD719392.1|CD719392
EST:     TTCCGCAGAGTCTGCCCAAAAAGCTACCACATATTTCGCTGCATTGCCAG                         GTATGGCTACAAGGATGTTCGCAAAGAGAATCATCAGACATTTGAGCAGCT
genomic: TTCCGCAGAGTCTGCCCAAAAAGCTACCACATATTTCGCTGCATTGCCAGgtagcagtct ... tggttgacagGTATGGCTACAAGGATGTTCGCAAAGAGAATCATCAGACATTTGAGCAGCT
EST: gi|30327536|gb|CD010798.1|CD010798
EST:     TTCCGCAGAGTCTGCCCAAAAAGCTACCACATATTTCGCTGCATTGCCAG                         GTATGGCTACAAGGATGTTCGCAAAGAGAATCATCAGACATTTGAGCAGCT
genomic: TTCCGCAGAGTCTGCCCAAAAAGCTACCACATATTTCGCTGCATTGCCAGgtagcagtct ... tggttgacagGTATGGCTACAAGGATGTTCGCAAAGAGAATCATCAGACATTTGAGCAGCT
EST: gi|32248831|gb|CD714650.1|CD714650
EST:     TTCCGCAGAGTCTGCCCAAAAAGCTACCACATATTTCGCTGCATTGCCAG                         GTATGGCTACAAGGATGTTCGCAAAGAGAATCATCAGACATTTGAGCAGCT
genomic: TTCCGCAGAGTCTGCCCAAAAAGCTACCACATATTTCGCTGCATTGCCAGgtagcagtct ... tggttgacagGTATGGCTACAAGGATGTTCGCAAAGAGAATCATCAGACATTTGAGCAGCT
EST: gi|30325279|gb|CD008541.1|CD008541
EST:     TTCCGCAGAGTCTGCCCAAAAAGCTACCACATATTTCGCTGCATTGCCAG                         GTATGGCTACAAGGATGTTCGCAAAGAGAATCATCAGACATTTGAGCAGCT
genomic: TTCCGCAGAGTCTGCCCAAAAAGCTACCACATATTTCGCTGCATTGCCAGgtagcagtct ... tggttgacagGTATGGCTACAAGGATGTTCGCAAAGAGAATCATCAGACATTTGAGCAGCT
EST: gi|110700216|gb|EE078004.1|EE078004
EST:     TTCCGCAGAGTCTGCCCAAAAAGCTACCACATATTTCGCTGCATTGCCAG                         GTATGGCTACNANGATGTTCGCAAAGAAGA-TCATCAGACATTTGAGCAGC
genomic: TTCCGCAGAGTCTGCCCAAAAAGCTACCACATATTTCGCTGCATTGCCAGgtagcagtct ... tggttgacagGTATGGCTACAAGGATGTTCGCAAAGA-GAATCATCAGACATTTGAGCAGC
EST: gi|30327238|gb|CD010500.1|CD010500
EST:     TTCCGCAGAGTCTGCCCAAAAAGCTACCACATATTTCGCTGCATTGCCAG                         GTATGGCTACAAGGATGTTCGCAAAGAGAATCATCAGACATTTGAGCAGCT
genomic: TTCCGCAGAGTCTGCCCAAAAAGCTACCACATATTTCGCTGCATTGCCAGgtagcagtct ... tggttgacagGTATGGCTACAAGGATGTTCGCAAAGAGAATCATCAGACATTTGAGCAGCT
EST: gi|110699249|gb|EE076080.1|EE076080
EST:     TTCCGCAGAGTCTGCCCAAAAAGCTACCACATATTTCGCTGCATTGCCAG                         GTATGGCTACAAGGATGTTCGCAAAGAGAATCATCAGACATTTGAGCAGCT
genomic: TTCCGCAGAGTCTGCCCAAAAAGCTACCACATATTTCGCTGCATTGCCAGgtagcagtct ... tggttgacagGTATGGCTACAAGGATGTTCGCAAAGAGAATCATCAGACATTTGAGCAGCT
EST: gi|110388090|gb|EC952806.1|EC952806
EST:     CAAAAAGCTACCACATATTTCGCTGCATTGCCTG                         GTATGGCTACAAGGATGTTCGCAAAGAGAATCATCAGACATTTGAGCAGCT
genomic: CAAAAAGCTACCACATATTTCGCTGCATTGCCAGgtagcagtct ... tggttgacagGTATGGCTACAAGGATGTTCGCAAAGAGAATCATCAGACATTTGAGCAGCT
EST: gi|30132699|gb|CB918038.1|CB918038
EST:     TTCCGCAGAGTCTGCCCAAAAAGCTACCACATATTTCGCTGCATTGCCAG                         GTATGGCTACAAGGATGTTCGCAAAGAGAATCATCAGACATTTGAGCAGCT
genomic: TTCCGCAGAGTCTGCCCAAAAAGCTACCACATATTTCGCTGCATTGCCAGgtagcagtct ... tggttgacagGTATGGCTACAAGGATGTTCGCAAAGAGAATCATCAGACATTTGAGCAGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attctctaaccctagtgtaatattgatatgcctagtcctttaaacctattttgtgatagaccacaggactgaagttccatcgctccactgtggttgacagGTATGGCTACAAGGATGTTCGCAAAGAGAATCATCAGACATTTGAGCAGCTGCTAATAGAGAGCCTTGAGAAGTTCATTCGACGTGAGGCCCAGGAACGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - -ctaaccc
- - - - - - - - - - - - - tatgcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccacagg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctccac