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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatatatctatatatatatagatagatataaatgcacaatttaagaccattactgtgtagttgttctttttattcacacaatgtaatctccaacattcagAGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTATTTCATATTGCTTACCCCAGCGCTCCAGAGACATTAAAAACTGAATTAC

Basic information

species Vitis vinifera
transcript Vv17s0000g03870.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 1
tatatatctatatatatatagatagatataaatgcacaatttaagaccattactgtg-tagttgttctttttattcacacaatgtaatctccaacattcagAGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTATTTCATATTGCTTACCCCAGCGCTCCAGAGACATTAAAAACTGAATTAC
| ||  | | |||  | | || ||   | | |||  |   | | || | | | |||| |    ||    || |||  |      || | | |    | |||||  |||||||||| |||||||| || || || ||||| || || || || || ||||||||||||||||| || |||||| |  | || |||||| |  
tttacttgtttatggagaaagttatccacacatgaccttatgatgagcctgattgtggttagagtggcattcatt-gcgtttgttattttgcttgttgcagAGGCTGGCTGCTGGTGAGTGGTTCACGGCACGGGTTTCGTCGTGCGGTTTGTTCCATATTGCTTACCCCAGTGCACCAGAGTCGGTGAAGACTGAACTGA
















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|352763871|gb|FQ465321.1|FQ465321
EST:     CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAG                         AGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
genomic: CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAGgtcagatgat ... caacattcagAGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
EST: gi|110723764|gb|EE101450.1|EE101450
EST:     CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAG                         AGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
genomic: CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAGgtcagatgat ... caacattcagAGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
EST: gi|71858238|gb|DT007293.1|DT007293
EST:     CTCAAATGAGGGAGTCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAG                         AGATTGGCTGCTGGCGAGTGGGTTACTGCTCGAGTTTCCTCATGTGGA
genomic: CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAGgtcagatgat ... caacattcagAGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGA
EST: gi|352781471|gb|FQ468315.1|FQ468315
EST:     CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAG                         AGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
genomic: CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAGgtcagatgat ... caacattcagAGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
EST: gi|352769561|gb|FQ468489.1|FQ468489
EST:     CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAG                         AGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
genomic: CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAGgtcagatgat ... caacattcagAGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
EST: gi|22010752|gb|BQ795786.1|BQ795786
EST:     CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAG                         AGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
genomic: CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAGgtcagatgat ... caacattcagAGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
EST: gi|110698010|gb|EE075532.1|EE075532
EST:     CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAG                         AGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
genomic: CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAGgtcagatgat ... caacattcagAGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
EST: gi|71883706|gb|DT032761.1|DT032761
EST:     CTCACATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAG                         AGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
genomic: CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAGgtcagatgat ... caacattcagAGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
EST: gi|352778272|gb|FQ465582.1|FQ465582
EST:     CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAG                         AGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
genomic: CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAGgtcagatgat ... caacattcagAGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
EST: gi|352763901|gb|FQ465351.1|FQ465351
EST:     CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAG                         AGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
genomic: CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAGgtcagatgat ... caacattcagAGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
EST: gi|37189319|gb|CF608668.1|CF608668
EST:     CTCAAATGAGGGAGCCAGATTTGGTGGAAGCCTTCATTCCATTGGTGAAG                         AGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGA
genomic: CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAGgtcagatgat ... caacattcagAGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGA
EST: gi|352787201|gb|FQ477821.1|FQ477821
EST:     CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAG                         AGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
genomic: CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAGgtcagatgat ... caacattcagAGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
EST: gi|352776769|gb|FQ472656.1|FQ472656
EST:     CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAG                         AGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
genomic: CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAGgtcagatgat ... caacattcagAGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
EST: gi|352773443|gb|FQ472225.1|FQ472225
EST:     CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAG                         AGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
genomic: CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAGgtcagatgat ... caacattcagAGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
EST: gi|352777593|gb|FQ466646.1|FQ466646
EST:     CTCAAATGAGGGAGCTAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAG                         AGATTGGCTGCTGGCCGAGTGGTTTACTGCTCGAGTT
genomic: CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAGgtcagatgat ... caacattcagAGATTGGCTGCTGGC-GAGTGGTTTACTGCTCGAGTT
EST: gi|352768313|gb|FQ469488.1|FQ469488
EST:     CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAG                         AGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
genomic: CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAGgtcagatgat ... caacattcagAGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
EST: gi|156738161|gb|EV242282.1|EV242282
EST:     CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAG                         AGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
genomic: CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAGgtcagatgat ... caacattcagAGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
EST: gi|110696169|gb|EE075018.1|EE075018
EST:     CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAG                         AGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
genomic: CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAGgtcagatgat ... caacattcagAGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
EST: gi|30302057|gb|CB978851.1|CB978851
EST:     CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAG                         AGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
genomic: CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAGgtcagatgat ... caacattcagAGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
EST: gi|352769371|gb|FQ471520.1|FQ471520
EST:     CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAG                         AGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
genomic: CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAGgtcagatgat ... caacattcagAGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
EST: gi|22010753|gb|BQ795787.1|BQ795787
EST:     CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAG                         AGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
genomic: CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAGgtcagatgat ... caacattcagAGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
EST: gi|352772524|gb|FQ471999.1|FQ471999
EST:     CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAG                         AGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA
genomic: CTCAAATGAGGGAGCCAGATTTGGTGGAATCCTTCATTCCTTTGGTGAAGgtcagatgat ... caacattcagAGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accattactgtgtagttgttctttttattcacacaatgtaatctccaacattcagAGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTATTTCATATTGCTTACCCCAGCGCTCCAGAGACATTAAAAACTGAATTAC
                                         tctcc  CT-rich tract
               ttgttctttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatatatctatatatatatagatagatataaatgcacaatttaagaccattactgtgtagttgttctttttattcacacaatgtaatctccaacattcagAGATTGGCTGCTGGCGAGTGGTTTACTGCTCGAGTTTCCTCATGTGGATTATTTCATATTGCTTACCCCAGCGCTCCAGAGACATTAAAAACTGAATTAC

- - - - - - - - - - - - - - - aatgcac
- - - - - - - - - - - - - - - - - - - - - aagacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacaatg