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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaagttgttgagttctcaagcttggttttggaagatgtctctttccctcccccaccttttttttttcttcttttcaaagcttggactgctggcctgaaagttaaatttcacagGGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCT

Basic information

species Vitis vinifera
transcript Vv17s0000g03870.t01
intron # 12
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 12
lower sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 10
gtgaagttgttgagttctcaagcttggttttggaagatgtctctttccctcccccaccttttttttttcttcttttcaaagcttggactgctggcctgaaagttaaatttcacagGGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCT
                               | || ||    | |||| | | ||   |||| | | ||||| |||   |||  |  ||  | || ||         | |  |||||||||||| || || |||||||| ||||| ||||||||||| || |  || || || || ||||||
-------------------------------gtaaaattgtgcattccttactcc---ttttgtgtgtcttcattt--gagccagtgctcatagcatg---------tcttgcagGGTACCCAATATCAAATTCAATGTAGCTAAAGTGTTGCAGTCTCTCATCCCAATTGTTGATCAGTCT

upper sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA09G31760.1 (Glycine max), 3'ss of exon 11
gtgaagttgttgagttctcaagcttggttttggaagatgtctctttccctcccccaccttttttttttcttcttttcaaagcttggactgctggcctgaaagttaaatttcacagGGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCT
                               | || ||      |||| | | ||   |||| | | ||||| |||||  ||  |  ||  | || ||         | |  |||||||||||| || || |||||||| ||||| ||||||||||| || |  || || || || ||||||
-------------------------------gtaaaattgtgtattccttactcc---ttttgtgtgtcttcatttca--gccagtgctcatagcatg---------tcttgcagGGTACCCAATATCAAATTCAATGTAGCTAAAGTGTTGCAGTCTCTCATCCCAATTGTTGATCAGTCT
















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|71877536|gb|DT026591.1|DT026591
EST:     ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAG                         GGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
genomic: ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAGgtgaagttgt ... aatttcacagGGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
EST: gi|349825185|gb|FQ415732.1|FQ415732
EST:     ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAG                         GGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
genomic: ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAGgtgaagttgt ... aatttcacagGGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
EST: gi|352769560|gb|FQ468488.1|FQ468488
EST:     ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAG                         GGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
genomic: ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAGgtgaagttgt ... aatttcacagGGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
EST: gi|352776768|gb|FQ472655.1|FQ472655
EST:     ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAG                         GGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
genomic: ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAGgtgaagttgt ... aatttcacagGGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
EST: gi|27584295|gb|CB006990.1|CB006990
EST:     ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAG                         GGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
genomic: ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAGgtgaagttgt ... aatttcacagGGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
EST: gi|352763870|gb|FQ465320.1|FQ465320
EST:     ATTACATGCTCGAAACTTCTGCCGGTGGTCATTAATGCAGCAAAAGACGG                         GGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
genomic: ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAGgtgaagttgt ... aatttcacagGGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
EST: gi|110414406|gb|EC980237.1|EC980237
EST:     ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAG                         GGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
genomic: ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAGgtgaagttgt ... aatttcacagGGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
EST: gi|71880317|gb|DT029372.1|DT029372
EST:     ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAG                         GGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
genomic: ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAGgtgaagttgt ... aatttcacagGGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
EST: gi|30134721|gb|CB920059.1|CB920059
EST:     ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAG                         GGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
genomic: ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAGgtgaagttgt ... aatttcacagGGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
EST: gi|352787200|gb|FQ477820.1|FQ477820
EST:     ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAG                         GGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
genomic: ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAGgtgaagttgt ... aatttcacagGGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
EST: gi|22012824|gb|BQ797858.1|BQ797858
EST:     ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAG                         GGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
genomic: ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAGgtgaagttgt ... aatttcacagGGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
EST: gi|33404973|gb|CF210600.1|CF210600
EST:     ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAG                         GGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
genomic: ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAGgtgaagttgt ... aatttcacagGGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
EST: gi|32246186|gb|CD712005.1|CD712005
EST:     GTGGTCATTAATGCAGCAAAAGACAG                         GGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
genomic: GTGGTCATTAATGCAGCAAAAGACAGgtgaagttgt ... aatttcacagGGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
EST: gi|110691608|gb|EE069902.1|EE069902
EST:     ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAG                         GGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
genomic: ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAGgtgaagttgt ... aatttcacagGGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
EST: gi|110399866|gb|EC966397.1|EC966397
EST:     ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAG                         GGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
genomic: ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAGgtgaagttgt ... aatttcacagGGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
EST: gi|33405058|gb|CF210685.1|CF210685
EST:     ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAG                         GGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
genomic: ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAGgtgaagttgt ... aatttcacagGGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
EST: gi|110429193|gb|EC995682.1|EC995682
EST:     ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAG                         GGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
genomic: ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAGgtgaagttgt ... aatttcacagGGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
EST: gi|22012767|gb|BQ797801.1|BQ797801
EST:     ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAG                         GGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
genomic: ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAGgtgaagttgt ... aatttcacagGGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
EST: gi|110697249|gb|EE074074.1|EE074074
EST:     ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAG                         GGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
genomic: ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAGgtgaagttgt ... aatttcacagGGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
EST: gi|351031302|gb|FQ445327.1|FQ445327
EST:     ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAG                         GGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
genomic: ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAGgtgaagttgt ... aatttcacagGGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
EST: gi|110428387|gb|EC994857.1|EC994857
EST:     ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAG                         GGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
genomic: ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAGgtgaagttgt ... aatttcacagGGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
EST: gi|30300336|gb|CB977130.1|CB977130
EST:     ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAG                         GGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
genomic: ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAGgtgaagttgt ... aatttcacagGGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
EST: gi|110388878|gb|EC953676.1|EC953676
EST:     ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAG                         GGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
genomic: ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAGgtgaagttgt ... aatttcacagGGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
EST: gi|110411876|gb|EC977604.1|EC977604
EST:     ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAG                         GGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
genomic: ATTACATGCTCGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAGgtgaagttgt ... aatttcacagGGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
EST: gi|110420001|gb|EC986261.1|EC986261
EST:     CGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAG                         GGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC
genomic: CGAAACTTCTGCCAGTGGTCATTAATGCAGCAAAAGACAGgtgaagttgt ... aatttcacagGGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttttcttcttttcaaagcttggactgctggcctgaaagttaaatttcacagGGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCT
                                    tgaaagttaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaagttgttgagttctcaagcttggttttggaagatgtctctttccctcccccaccttttttttttcttcttttcaaagcttggactgctggcctgaaagttaaatttcacagGGTACCCAACATAAAGTTCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA