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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtgaaattcccatatctttctctattttctgattttttttcagaagcgtgaataattgatgatgggaatcttgaaaaattttcagGTTTTGATGTTTGATTCGATGCATGGTAGAACCTGCTTGCACTACGCGGCCTATTACGGCCATTCCGATTGCCTTCAAGCCATACTTTCTGCTGCCCATT

Basic information

species Vitis vinifera
transcript Vv06s0004g04550.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g04550.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G41040.2 (Glycine max), 3'ss of exon 3
gtgtgtgaa-attcccatatc-tttctctattttc-tgattttttttcagaagcgtgaataattgatgatgggaatcttgaaaaattttcagGTTTTGATGTTTGATTCGATGCATGGTAGAACCTGCTTGCACTACGCGGCCTATTACGGCCATTCCGATTGCCTTCAAGCCATACTTTCTGCTGCCCATT
    || ||   | | || || || |||||||  | | ||  | |    |||   || | || |||||           |    ||||||||||||||||||||||| | ||  | || ||||||||||| |||||  | || || |||||||||||   ||||||| | || || ||||| ||||| || |
----gtaaatgcttcaatttcattgctctattgacataataatataaatgaaatttggaaaactgatg----------cgtgtgattttcagGTTTTGATGTTTGATACTATTTACGGGAGAACCTGCTTACACTATTCCGCTTACTACGGCCATTCTTCTTGCCTTAAGGCTATTCTTTCCGCTGCTCAAT
















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|71856591|gb|DT005646.1|DT005646
EST:     TGCACGGAAAGATTTCATGTGTCCAAAAGCTCCTTCAAGCAGGCGCCAAT                         GTTTTGATGTTTGATTCGATGCATGGTAGAACCTGCTTGCACTACGCCGCC
genomic: TGCACGGAAAGATTTCATGTGTCCAAAAGCTCCTTCAAGCAGGCGCCAATgtgtgtgaaa ... aaattttcagGTTTTGATGTTTGATTCGATGCATGGTAGAACCTGCTTGCACTACGCGGCC
EST: gi|110686614|gb|EE064454.1|EE064454
EST:     TGCACGGAAAGATTTCATGTGTCCAAAAGCTCCTTCAAGCAGGCGCCAAT                         GTTTTGATGTTTGATTCGATGCATGGTAGAACCTGCTTGCACTACGCGGCC
genomic: TGCACGGAAAGATTTCATGTGTCCAAAAGCTCCTTCAAGCAGGCGCCAATgtgtgtgaaa ... aaattttcagGTTTTGATGTTTGATTCGATGCATGGTAGAACCTGCTTGCACTACGCGGCC
EST: gi|22013975|gb|BQ799009.1|BQ799009
EST:     TGCACGGAAAGATTTCATGTGTCCAAAAGCTCCTTCAAGCAGGCGCCAAT                         GTTTTGATGTTTGATTCGATGCATGGTAGAACCTGCTTGCACTACGCGGCC
genomic: TGCACGGAAAGATTTCATGTGTCCAAAAGCTCCTTCAAGCAGGCGCCAATgtgtgtgaaa ... aaattttcagGTTTTGATGTTTGATTCGATGCATGGTAGAACCTGCTTGCACTACGCGGCC
EST: gi|110712240|gb|EE089633.1|EE089633
EST:     TGCACGGAAAGATTTCATGTGTCCAAAAGCTCCTTCAAGCAGGCGCCAAT                         GTTTTGATGTTTGATTCGATGCATGGTAGAACCTGCTTGCACTACGCGGCC
genomic: TGCACGGAAAGATTTCATGTGTCCAAAAGCTCCTTCAAGCAGGCGCCAATgtgtgtgaaa ... aaattttcagGTTTTGATGTTTGATTCGATGCATGGTAGAACCTGCTTGCACTACGCGGCC
EST: gi|110699327|gb|EE076228.1|EE076228
EST:     TGCACGGAACGATTTCATGTGTCCAAAAGCTCCTTCAAGCAGGCGCCAAT                         GTTTTGATGTTTGATTCGATGCATGGTAGAACCTGCTTGCACTACGCGGCC
genomic: TGCACGGAAAGATTTCATGTGTCCAAAAGCTCCTTCAAGCAGGCGCCAATgtgtgtgaaa ... aaattttcagGTTTTGATGTTTGATTCGATGCATGGTAGAACCTGCTTGCACTACGCGGCC
EST: gi|71856782|gb|DT005837.1|DT005837
EST:     TGCACGGAAAGATTTCATGTGTCCAAAAGCTCCTTCAAGCAGGCGCCAAT                         GTTTTGATGTTTGATTCGATGCATGGTAGAACCTGCTTGCACTACGCCGCC
genomic: TGCACGGAAAGATTTCATGTGTCCAAAAGCTCCTTCAAGCAGGCGCCAATgtgtgtgaaa ... aaattttcagGTTTTGATGTTTGATTCGATGCATGGTAGAACCTGCTTGCACTACGCGGCC
EST: gi|71857386|gb|DT006441.1|DT006441
EST:     TGCACGGAAAGATTTCATGTGCCCAAAAGCTCCTTCAAGCAGGCGCCAAT                         GTTTTGATGTTTGATTCGATGCATGGTAGAACCTGCTTGCACTACGCGGCC
genomic: TGCACGGAAAGATTTCATGTGTCCAAAAGCTCCTTCAAGCAGGCGCCAATgtgtgtgaaa ... aaattttcagGTTTTGATGTTTGATTCGATGCATGGTAGAACCTGCTTGCACTACGCGGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattttttttcagaagcgtgaataattgatgatgggaatcttgaaaaattttcagGTTTTGATGTTTGATTCGATGCATGGTAGAACCTGCTTGCACTACGCGGCCTATTACGGCCATTCCGATTGCCTTCAAGCCATACTTTCTGCTGCCCATT
                                                ttttc  CT-rich tract
                                    aatcttgaaaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtgaaattcccatatctttctctattttctgattttttttcagaagcgtgaataattgatgatgggaatcttgaaaaattttcagGTTTTGATGTTTGATTCGATGCATGGTAGAACCTGCTTGCACTACGCGGCCTATTACGGCCATTCCGATTGCCTTCAAGCCATACTTTCTGCTGCCCATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC