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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatattggcactttgattaatgctatttgcaatattcttttgtttatgcaactttatagtttatctctaactaatatgactatgtagTTACGTGGAATGTACATCAGCTGCACTTCAAGCTTTGACATCATTTAATAAATTTTATCCGGGGCATCGGAGAGAAGAAATAGAACATTGTATTAAAAAA

Basic information

species Vitis vinifera
transcript Vv11s0065g00640.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0065g00640.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA01G00430.2 (Glycine max), 3'ss of exon 14
-------------------------gtaagatattggcactttgattaatgctatttgcaatattcttttgtttatgcaactttatagtttatctctaactaatatgactatgtagTTACGTGGAATGTACATCAGCTGCACTTCAAGCTTTGACATCATTTAATAAATTTTATCCGGGGCATCGGAGAGAAGAAATAGAACATTGTATTAAAAAA
                          |||| | |   ||  ||   |    |    | ||  ||||  || ||| |  |||||| || | | ||  ||     ||||  | | |||||| ||||||||||||||||| ||  ||||||||||| |||||||||  ||||| ||||| ||||||||  ||||||||||| ||||||||||  | |||
gtaagcaatcaaatgcttgtgaaatataagttttatccatcttccattccacctactccaccattcaattttttttttaactttttaatgtttccttat---gtatgg-tgtatagTTATGTGGAATGTACATCAGCAGCGATTCAAGCTTTGGCATCATTTAGGAAATTATATCCTGGGCATCGCCGAGAAGAAATACAACATTGTATCGATAAA

upper sequence: Vv11s0065g00640.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: AT2G07050.1 (Arabidopsis thaliana), 3'ss of exon 13
gtaagatattggcac-tttgattaat---gctatttg--caatattcttttgt-ttatgcaactttatagtttatctctaactaatatgactatgtagTTACGTGGAATGTACATCAGCTGCACTTCAAGCTTTGACATCATTTAATAAATTTTATCCGGGGCATCGGAGAGAAGAAATAGAACATTGTATTAAAAAA
|||||  | | |||  ||  ||| ||      || ||   ||| || |||| | || ||||| ||| |  || || |  ||     |||  | |||||||||||||||||||||||||||||  | |||||||||| |||||||   ||  | ||||| || ||||| |   | ||| ||||  | || ||| | || 
gtaaggcactagcatattccattgattgaatcatctggttaatcttattttatgttttgcaaatttctc-ttgatgtgcaa---gaatggttctgtagTTACGTGGAATGTACATCAGCTGCTATCCAAGCTTTGATATCATTTCGAAAGCTGTATCCTGGTCATCGAAAGAAGGAAGTAGATGAGTGCATTGAGAAG
















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|18458985|gb|BM437263.1|BM437263
EST:     -TAATCAATCCTGCTGAAACTTTTGGCGACATTGTTATTGATTACCC                         TTACGTGGAATGTACATCAGCTGCACTTCAAGCTTTGACATCATTTAATAA
genomic: TTAATCAATCCTGCTGAAACTTTTGGCGACATTGTTATTGATTATCCgtaagatatt ... gactatgtagTTACGTGGAATGTACATCAGCTGCACTTCAAGCTTTGACATCATTTAATAA
EST: gi|71865816|gb|DT014871.1|DT014871
EST:     TTAATCAATCCTGCTGAAACTTTTGGCGACATTGTTATTGATTACCC                         TTACGTGGAATGTACATCAGCTGCACTTCAAGCTTTGACATCATTTAATAA
genomic: TTAATCAATCCTGCTGAAACTTTTGGCGACATTGTTATTGATTATCCgtaagatatt ... gactatgtagTTACGTGGAATGTACATCAGCTGCACTTCAAGCTTTGACATCATTTAATAA
EST: gi|32248816|gb|CD714635.1|CD714635
EST:     TTAATCAATCCTGCTGAAACTTTTGGCGACATTGTTATTGATTACCC                         TTACGTGGAATGTACATCAGCTGCACTTCAAGCTTTGACATCATTTAATAA
genomic: TTAATCAATCCTGCTGAAACTTTTGGCGACATTGTTATTGATTATCCgtaagatatt ... gactatgtagTTACGTGGAATGTACATCAGCTGCACTTCAAGCTTTGACATCATTTAATAA
EST: gi|161713441|gb|FC063719.1|FC063719
EST:     TTAATCAATCCTGCTGAAACTTTTGGCGACATTGTTATTGATTATCC                         TTACGTGGAATGTACATCAGCTGCACTTCAAGCTTTGACATCATTTAATAA
genomic: TTAATCAATCCTGCTGAAACTTTTGGCGACATTGTTATTGATTATCCgtaagatatt ... gactatgtagTTACGTGGAATGTACATCAGCTGCACTTCAAGCTTTGACATCATTTAATAA
EST: gi|30327265|gb|CD010527.1|CD010527
EST:     TTAATCAATCCTGCTGAAACTTTTGGCGACATTGTTATTGATTACCC                         TTACGTGGAATGTACATCAGCTGCACTTCAAGCTTTGACATCATTTAATAA
genomic: TTAATCAATCCTGCTGAAACTTTTGGCGACATTGTTATTGATTATCCgtaagatatt ... gactatgtagTTACGTGGAATGTACATCAGCTGCACTTCAAGCTTTGACATCATTTAATAA
EST: gi|161717232|gb|FC067238.1|FC067238
EST:     TTAATCAATCCTGCTGAAACTTTTGGCGACATTGTTATTGATTATCC                         TTACGTGGAATGTACATCAGCTGCACTTCAAGCTTTGACATCATTTAATAA
genomic: TTAATCAATCCTGCTGAAACTTTTGGCGACATTGTTATTGATTATCCgtaagatatt ... gactatgtagTTACGTGGAATGTACATCAGCTGCACTTCAAGCTTTGACATCATTTAATAA
EST: gi|30299701|gb|CB976495.1|CB976495
EST:     TATTGATTATCC                         TTACGTGGAATGTACATCAGCTGCACTTCAAGCTTTGACATCATTTAATAA
genomic: TATTGATTATCCgtaagatatt ... gactatgtagTTACGTGGAATGTACATCAGCTGCACTTCAAGCTTTGACATCATTTAATAA
EST: gi|32249043|gb|CD714862.1|CD714862
EST:     TTAATCAATCCTGCTGAAACTTTTGGCGACATTGTTATTGATTACCC                         TTACGTGGAATGTACATCAGCTGCACTTCAAGCTTTGACATCATTTAATAA
genomic: TTAATCAATCCTGCTGAAACTTTTGGCGACATTGTTATTGATTATCCgtaagatatt ... gactatgtagTTACGTGGAATGTACATCAGCTGCACTTCAAGCTTTGACATCATTTAATAA
EST: gi|34543141|gb|CF511373.1|CF511373
EST:     CCTGCTGAAACTTTTGGCGACATTGTTATTGATTACCC                         TTACGTGGAATGTACATCAGCTGCACTTCAAGCTTTGACATCATTTAATAA
genomic: CCTGCTGAAACTTTTGGCGACATTGTTATTGATTATCCgtaagatatt ... gactatgtagTTACGTGGAATGTACATCAGCTGCACTTCAAGCTTTGACATCATTTAATAA
EST: gi|32269610|gb|CD718769.1|CD718769
EST:     TTAATCAATCCTGCTGAAACTTTTGGCGACATTGTTATTGATTACCC                         TTACGTGGAATGTACATCAGCTGCACTTCAAGCTTTGACATCATTTAATAA
genomic: TTAATCAATCCTGCTGAAACTTTTGGCGACATTGTTATTGATTATCCgtaagatatt ... gactatgtagTTACGTGGAATGTACATCAGCTGCACTTCAAGCTTTGACATCATTTAATAA
EST: gi|30327518|gb|CD010780.1|CD010780
EST:     TTAATCAATCCTGCTGAAACTTTTGGCGACATTGTTATTGATTACCC                         TTACGTGGAATGTACATCAGCTGCACTTCAAGCTTTGACATCATTTAATAA
genomic: TTAATCAATCCTGCTGAAACTTTTGGCGACATTGTTATTGATTATCCgtaagatatt ... gactatgtagTTACGTGGAATGTACATCAGCTGCACTTCAAGCTTTGACATCATTTAATAA
EST: gi|34543224|gb|CF511456.1|CF511456
EST:     ACATTGTTATTGATTACCC                         TTACGTGGAATGTACATCAGCTGCACTTCAAGCTTTGACATCATTTAATAA
genomic: ACATTGTTATTGATTATCCgtaagatatt ... gactatgtagTTACGTGGAATGTACATCAGCTGCACTTCAAGCTTTGACATCATTTAATAA
EST: gi|161713540|gb|FC063135.1|FC063135
EST:     TTAATCAATCCTGCTGAAACTTTTGGCGACATTGTTATTGATTACCC                         TTACGTGGAATGTACATCAGCTGCACTTCAAGCTTTGACATCATTTAATAA
genomic: TTAATCAATCCTGCTGAAACTTTTGGCGACATTGTTATTGATTATCCgtaagatatt ... gactatgtagTTACGTGGAATGTACATCAGCTGCACTTCAAGCTTTGACATCATTTAATAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattcttttgtttatgcaactttatagtttatctctaactaatatgactatgtagTTACGTGGAATGTACATCAGCTGCACTTCAAGCTTTGACATCATTTAATAAATTTTATCCGGGGCATCGGAGAGAAGAAATAGAACATTGTATTAAAAAA
                                    aactaat  putative branch site (score: 2)
                 aactttatagtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatattggcactttgattaatgctatttgcaatattcttttgtttatgcaactttatagtttatctctaactaatatgactatgtagTTACGTGGAATGTACATCAGCTGCACTTCAAGCTTTGACATCATTTAATAAATTTTATCCGGGGCATCGGAGAGAAGAAATAGAACATTGTATTAAAAAA

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