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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttggacaattttgcacttttctagcattgaattctttcagaattgcatacatactaggaatttggattttttatgtgttgctttatttggctttttcagATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACGGTTCTAGTGGGAGGCCAGCGAAGGGCATTGGGCGTGGCCTAGATGATGG

Basic information

species Vitis vinifera
transcript Vv07s0005g00230.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g00230.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA03G37170.2 (Glycine max), 3'ss of exon 5
cttggacaattttgcacttttctagcattgaattct-ttcagaattgcataca--tact-aggaatttggattttttatgtgttgctttatttggctttttcagATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACGGTTCTAGTGGGAGGCCAGCGAAGGGCATTGGGCGTGGCCTAGATGATGG
     |   |  |  |    | ||  ||  | | || ||||   || | | ||  | || |  ||  | ||  || | ||  |    | |     ||||||||||| | || |||||||| || ||||||||||| || |||||||||||||| ||| || ||||| | ||| | || || ||||||||||| || ||||||||
tgaaaatgctaatttagccgtatattatgaactgctattcatgcttccttccagttgctgaaaaaactagacattctctgattaatatcac----ctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAGGTCCTGGTGGGCGCCCAACAAAAGGAATTGGGCGTGGTCTTGATGATGG

upper sequence: Vv07s0005g00230.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA19G39780.1 (Glycine max), 3'ss of exon 5
cttggacaattttgcacttttctagcattgaattctttcagaattgcatacatactaggaatttggattttttatgtgttgctttatttggc-tttttcagATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACGGTTCTAGTGGGAGGCCAGCGAAGGGCATTGGGCGTGGCCTAGATGATGG
  |  |   |  |  |    | ||  ||  | |  | |      ||| | |  | | |        | |    ||    || || ||||  | |||||||||| | || |||||||| || || |||||||| || |||||||||||||| ||| || ||||| | ||||| || || ||||||||||| || ||||||||
tgtaaatgctaatttagccatgtattataaactgatattcatgctgccttc-cagttgctggcaaaactagacattctctgattaatttcacctttttcagATCGCAAACCACCTGGAGTGGGACGTGGAAGGGGAAGAGGCAGAGAGGATGGTCCTGGTGGGCGCCCAGCAAAAGGAATTGGGCGTGGTCTTGATGATGG

upper sequence: Vv07s0005g00230.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA03G37170.3 (Glycine max), 3'ss of exon 5
cttggacaattttgcacttttctagcattgaattct-ttcagaattgcataca--tact-aggaatttggattttttatgtgttgctttatttggctttttcagATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACGGTTCTAGTGGGAGGCCAGCGAAGGGCATTGGGCGTGGCCTAGATGATGG
     |   |  |  |    | ||  ||  | | || ||||   || | | ||  | || |  ||  | ||  || | ||  |    | |     ||||||||||| | || |||||||| || ||||||||||| || |||||||||||||| |                                                 
tgaaaatgctaatttagccgtatattatgaactgctattcatgcttccttccagttgctgaaaaaactagacattctctgattaatatcac----ctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG-------------------------------------------------

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|349828814|gb|FQ419147.1|FQ419147
EST:     GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG                         ATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
genomic: GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAGgtatgaatag ... gctttttcagATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
EST: gi|349819985|gb|FQ404707.1|FQ404707
EST:     GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG                         ATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
genomic: GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAGgtatgaatag ... gctttttcagATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
EST: gi|349819983|gb|FQ404705.1|FQ404705
EST:     GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG                         ATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
genomic: GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAGgtatgaatag ... gctttttcagATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
EST: gi|110372194|gb|EC936345.1|EC936345
EST:     GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG                         ATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
genomic: GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAGgtatgaatag ... gctttttcagATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
EST: gi|110383606|gb|EC947989.1|EC947989
EST:     GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG                         ATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
genomic: GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAGgtatgaatag ... gctttttcagATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
EST: gi|349827595|gb|FQ422463.1|FQ422463
EST:     GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG                         ATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
genomic: GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAGgtatgaatag ... gctttttcagATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
EST: gi|351029470|gb|FQ436864.1|FQ436864
EST:     GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG                         ATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
genomic: GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAGgtatgaatag ... gctttttcagATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
EST: gi|110692708|gb|EE068197.1|EE068197
EST:     GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG                         ATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
genomic: GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAGgtatgaatag ... gctttttcagATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
EST: gi|351012236|gb|FQ426958.1|FQ426958
EST:     GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG                         ATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
genomic: GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAGgtatgaatag ... gctttttcagATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
EST: gi|351044635|gb|FQ443166.1|FQ443166
EST:     GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG                         ATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
genomic: GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAGgtatgaatag ... gctttttcagATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
EST: gi|351025082|gb|FQ433499.1|FQ433499
EST:     GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG                         ATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
genomic: GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAGgtatgaatag ... gctttttcagATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
EST: gi|349828184|gb|FQ415512.1|FQ415512
EST:     GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG                         ATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
genomic: GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAGgtatgaatag ... gctttttcagATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
EST: gi|351056955|gb|FQ443582.1|FQ443582
EST:     GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG                         ATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
genomic: GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAGgtatgaatag ... gctttttcagATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
EST: gi|110374587|gb|EC939452.1|EC939452
EST:     GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG                         ATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
genomic: GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAGgtatgaatag ... gctttttcagATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
EST: gi|351038850|gb|FQ448493.1|FQ448493
EST:     GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG                         ATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
genomic: GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAGgtatgaatag ... gctttttcagATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
EST: gi|110372487|gb|EC936658.1|EC936658
EST:     GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG                         ATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
genomic: GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAGgtatgaatag ... gctttttcagATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
EST: gi|352790730|gb|FQ478278.1|FQ478278
EST:     GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG                         ATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
genomic: GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAGgtatgaatag ... gctttttcagATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
EST: gi|349828185|gb|FQ415513.1|FQ415513
EST:     GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG                         ATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG
genomic: GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAGgtatgaatag ... gctttttcagATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatacatactaggaatttggattttttatgtgttgctttatttggctttttcagATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACGGTTCTAGTGGGAGGCCAGCGAAGGGCATTGGGCGTGGCCTAGATGATGG
                                              ctttttc  CT-rich tract
              aatttggattttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttggacaattttgcacttttctagcattgaattctttcagaattgcatacatactaggaatttggattttttatgtgttgctttatttggctttttcagATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACGGTTCTAGTGGGAGGCCAGCGAAGGGCATTGGGCGTGGCCTAGATGATGG

- - - - -ttttgca
- - - - - - - - - - - - - - - - - - - - - - -gcataca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgct