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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggcttgagactgctcttatgtttctgttgaataagtccagattgagtccttgagaagtcaagagaatgaattgttaaaattttcacctttcttttgcagGTCCAGAGTGACTTGGAACAAGGTATTGTTGGTGCTGTGCCCATCCCACCAGATGATGCAGGGAAAGAGGAGGTGATTGCGGCTTTGGTTGCTAACGTGG

Basic information

species Vitis vinifera
transcript Vv19s0014g02480.t01
intron # 7
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 7
lower sequence: GLYMA12G35390.1 (Glycine max), 3'ss of exon 7
aggcttgagactgctcttatgtttctgttgaataagtccagattgagtccttgagaagtcaagagaa--tgaattgttaaa-attttcacctttcttttg-cagGTCCAGAGTGACTTGGAACAAGGTATTGTTGGTGCTGTGCCCATCCCACCAGATGATGCAGGGAAAGAGGAGGTGATTGCGGCTTTGGTTGCTAACGTGG
      || | | | ||| | | |   ||||  |     |||||   |   |      |  ||||||  || |   || |  | |  | | ||| || |  ||||| ||||||||| | |||||||| ||||  ||||||||||| ||||| || |||||||| ||||||||||| ||  |||| ||  | ||||| || ||| 
--caaggataatacactt-tatcttaattgag-atccagagatttcatgtatattgtattcagagaatttggaccattgactactggctcattttttataacagGTTCAGAGTGACCTTGAACAAGGGATTGCAGGTGCTGTGCCTATCCCTCCTGATGATGCTGGGAAAGAGGAAGTCGTTGCTGCACTCGTTGCCAATGTGA

upper sequence: Vv19s0014g02480.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA13G35120.2 (Glycine max), 3'ss of exon 7
aggcttgagactgctcttatgtttctgttgaataag-tccaga--ttgagtccttgagaagtcaagagaa--tgaattgttaaaattt--tcacctttcttttgcagGTCCAGAGTGACTTGGAACAAGGTATTGTTGGTGCTGTGCCCATCCCACCAGATGATGCAGGGAAAGAGGAGGTGATTGCGGCTTTGGTTGCTAACGTGG
      |||  |  |   |  ||| | || | | || || |||  ||   |   |      |  ||||||  ||||   || |  | |       ||||| |  ||||| || |||||| | |||||||| ||||  ||||||||||| ||||| ||||||||||| |||||| |||| || ||||| ||  | ||||| || ||||
-----cgaggataata--agctttatcttaattgagatctagagttttcatgtatattgtattcagagaatttgaaccattgacttctagctcattttctataacagGTTCAAAGTGACCTTGAACAAGGGATTGCAGGTGCTGTGCCTATCCCTCCAGATGATGCTGGGAAACAGGAAGTCATTGCTGCACTTGTTGCCAATGTGG
















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:     CGTATGAGACTGATGAAACTCAGGATGATATCAAGTTGTTGCGCACTCAG                         GTCCAGAGTGACTTGGAACAAGGTATTGTTGGTGCTGTGCCCATCCCACCA
genomic: CGTATGAGACTGATGAAACTCAGGATGATATCAAGTTGTTGCGCACTCAGgtaagatttt ... tcttttgcagGTCCAGAGTGACTTGGAACAAGGTATTGTTGGTGCTGTGCCCATCCCACCA
EST: gi|30126149|gb|CB911488.1|CB911488
EST:     TGTATGAGACTGATGAAACTCAGGATGATATCAAGTTGTTGCGCACTCAG                         GTCCAGAGTGACTTGGAACAAGGTATTGTTGGTGCTGTTCCCATCCCACCA
genomic: CGTATGAGACTGATGAAACTCAGGATGATATCAAGTTGTTGCGCACTCAGgtaagatttt ... tcttttgcagGTCCAGAGTGACTTGGAACAAGGTATTGTTGGTGCTGTGCCCATCCCACCA
EST: gi|29785157|gb|CB341909.2|CB341909
EST:     CGTATGAGACTGATGAAACTCAGGATGATATCAAGTTGTTGCGCACTCAG                         GTCCAGAGTGACTTGGAACAAGGTATTGTTGGTGCTGTGCCCATCCCACCA
genomic: CGTATGAGACTGATGAAACTCAGGATGATATCAAGTTGTTGCGCACTCAGgtaagatttt ... tcttttgcagGTCCAGAGTGACTTGGAACAAGGTATTGTTGGTGCTGTGCCCATCCCACCA
EST: gi|110378704|gb|EC943848.1|EC943848
EST:     CGTATGAGACTGATGAAACTCAGGATGATATCAAGTTGTTGCGCACTCAG                         GTCCAGAGTGACTTGGAACAAGGTATTGTTGGTGCTGTGCCCATCCCACCA
genomic: CGTATGAGACTGATGAAACTCAGGATGATATCAAGTTGTTGCGCACTCAGgtaagatttt ... tcttttgcagGTCCAGAGTGACTTGGAACAAGGTATTGTTGGTGCTGTGCCCATCCCACCA
EST: gi|18458739|gb|BM437017.1|BM437017
EST:     CGTATGAGACTGATGAAACTCAGGATGATATCAAGTTGTTGCGCACTCAG                         GTCCAGAGTGACTTGGAACAAGGTATTGTTGGTGCTGTGCCCATCCCACCA
genomic: CGTATGAGACTGATGAAACTCAGGATGATATCAAGTTGTTGCGCACTCAGgtaagatttt ... tcttttgcagGTCCAGAGTGACTTGGAACAAGGTATTGTTGGTGCTGTGCCCATCCCACCA
EST: gi|110412327|gb|EC978073.1|EC978073
EST:     CGTATGAGACTGATGAAACTCAGGATGATATCAAGTTGTTGCGCACTCAG                         GTCCAGAGTGACTTGGAACAAGGTATTGTTGGTGCTGTGCCCATCCCACCA
genomic: CGTATGAGACTGATGAAACTCAGGATGATATCAAGTTGTTGCGCACTCAGgtaagatttt ... tcttttgcagGTCCAGAGTGACTTGGAACAAGGTATTGTTGGTGCTGTGCCCATCCCACCA
EST: gi|110731568|gb|EE106093.1|EE106093
EST:     GTATGAGACTGATGAAACTCCAG-ATGATATCAAGTTGTTGCGCACTCAG                         GTCCAGAATGACTTGGAACAA
genomic: GTATGAGACTGATGAAACTC-AGGATGATATCAAGTTGTTGCGCACTCAGgtaagatttt ... tcttttgcagGTCCAGAGTGACTTGGAACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtccttgagaagtcaagagaatgaattgttaaaattttcacctttcttttgcagGTCCAGAGTGACTTGGAACAAGGTATTGTTGGTGCTGTGCCCATCCCACCAGATGATGCAGGGAAAGAGGAGGTGATTGCGGCTTTGGTTGCTAACGTGG
                                   ttttcacctttctttt  CT-rich tract
                  agaatgaattgttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggcttgagactgctcttatgtttctgttgaataagtccagattgagtccttgagaagtcaagagaatgaattgttaaaattttcacctttcttttgcagGTCCAGAGTGACTTGGAACAAGGTATTGTTGGTGCTGTGCCCATCCCACCAGATGATGCAGGGAAAGAGGAGGTGATTGCGGCTTTGGTTGCTAACGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - -agactgc
- - - - - - - - - - - - - - -gaataag
- - - - - - - - - - - - - - - - - - - - - - - - ccttgag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagagaa