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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattattttcctcttagtataagttttgcattggctgtgaggtgatgttttccattgatcaattctcatcgaatttttatgtttattcctttttcatttgctctcagGAGCTGACAAGGAAACTGCTCCACTTGATTGGGGTGCCCGGATAAAGGTGGCGCTTGGTGCTGCTCGTGGTCTGGCCTATCTGCATGAAGATTCAAGCCC

Basic information

species Vitis vinifera
transcript Vv11s0016g02150.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g02150.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA15G18470.1 (Glycine max), 3'ss of exon 7
gtattattttcctcttagtataagttttgcattggctgtgaggtgatgttttccattgatcaattctcatcgaatttttatgtttattcctttttcatttgctctcagGAGCTGACAAGGAAACTGCTCCACTTGATTGGGGTGCCCGGATAAAGGTGGCGCTTGGTGCTGCTCGTGGTCTGGCCTATCTGCATGAAGATTCAAGCCC
             | ||   |   | |||  |  |    |||   |   || | |||| | | | ||  |  |  |  |  ||||  |  | |||  | | ||   |||||||||||||||||     |||||||||||| |||| ||| ||||| | || |||||| |||||||||| ||||| |||||||||||||||||||| ||
----------gtacctaacttt--tcttgattcagtctcgagt--accattccaattgtttagtgct--ttaagataatg-gttttcttatatttggtcttctggtagGAGCTGACAAGGAAAACAGCCCACTTGATTGGAGTGCTCGGTTAAAGATAGCTCTTGGTTCTGCTCGTGGACTGGCTTATCTGCATGAAGATTCAAGTCC

upper sequence: Vv11s0016g02150.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA13G16380.1 (Glycine max), 3'ss of exon 8
----gtattattttcctcttagt-ataagttt------tgcattggctgtgaggtgatgttttccattgatcaattctcatcgaatttttatgtttattcctttttcatttgctctcagGAGCTGACAAGGAAACTGCTCCACTTGATTGGGGTGCCCGGATAAAGGTGGCGCTTGGTGCTGCTCGTGGTCTGGCCTATCTGCATGAAGATTCAAGCCC
     ||  |||| | ||||| | ||  | ||      | | |      || |||    |   |  |||   | ||||    ||   |     | | ||  | | |  | |  |   ||| | ||||| || ||     ||||||||||||||||||||||| ||| | || |||||||| |||||||| || || || ||||||||||||||||| ||
gtacttaaaatttgcttcttaattatgtgcttactgcttacttcattcttgtggtagcatgc-cagttgcatagttcttcaagataataatcatattttattctattgtcttatgatagGGGTTGACAGGGGAAACAGCCCACTTGATTGGGGTGCCCGGATGAAGATAGCACTTGGTGCAGCTCGTGGCCTAGCTTACCTGCATGAAGATTCAAGTCC

upper sequence: Vv11s0016g02150.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA17G06250.1 (Glycine max), 3'ss of exon 2
----------------------------------------------gta-ttattttcctcttagtataagttttgcattggctgtgaggtgatgttttccattgatcaattctc--atcgaatttttatgtttattcctttttcatttgctctcagGAGCTGACAAGGAAACTGCTCCACTTGATTGGGGTGCCCGGATAAAGGTGGCGCTTGGTGCTGCTCGTGGTCTGGCCTATCTGCATGAAGATTCAAGCCC
                                              ||| |||   ||  |||  |||  | ||  | |       ||| |    |   |   || | | ||||   |   ||| ||||| | | ||  | | |  | | ||   ||| | ||||| |||||     || |||||||||||||||||||| ||  | || ||||| || |||| |||||| || |||||||||||||||||||| ||
gtatatgaacttgttcccaatggaagtgtggaatcccatttacatggtacttaaaatctgcttcttatttgctt-acttcattctcgagatagcatgc-cggctgtttagttcttcaagataatgtttatttattttgttctgttgtcttctgatagGGGTTGACAGGGAAATCAGCCCCCTTGATTGGGGTGCCCGGATGAAAATAGCTCTTGGAGCAGCTCCTGGTCTTGCTTATCTGCATGAAGATTCAAGTCC

upper sequence: Vv11s0016g02150.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA09G07140.1 (Glycine max), 3'ss of exon 8
gtattattttcctcttagtataagttttgcattggctgtgaggtgatgttttccattgatcaattctcatcgaatttttatgtttattcctttttcatttgctctcagGAGCTGACAAGGAAACTGCTCCACTTGATTGGGGTGCCCGGATAAAGGTGGCGCTTGGTGCTGCTCGTGGTCTGGCCTATCTGCATGAAGATTCAAGCCC
             ||||   |   || |  |||   | ||| ||     | |  |||| | | |||| |  ||  |  |   |||  |  | |||  | | ||   ||||| |||||||||||     |||||||||||| |||| ||| ||||| | || || ||| |||||||||| ||||| ||||| |||||||||||||| ||
----------gtacttaactt---ttcttgattcagtctgaagtaccactctg-attgtttagttcttaaaga--taatggtttttcttatatttggtcttctggtagGAGTTGACAAGGAAAACAGCCCACTTGATTGGAGTGCTCGGTTAAAGATAGCTCTCGGTTCTGCTCGTGGACTGGCTTATCTACATGAAGATTCAAGTCC

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|351057153|gb|FQ450860.1|FQ450860
EST:     CTTAGTGTATGAACTCATTCCAAATGGCAGTGTGGAGTCCCATTTGCATG                         GAGCTGACAAGGAAACTGCTCCACTTGATTGGGGTGCCCGGATAAAGGTGG
genomic: CTTAGTGTATGAACTCATTCCAAATGGCAGTGTGGAGTCCCATTTACATGgtattatttt ... ttgctctcagGAGCTGACAAGGAAACTGCTCCACTTGATTGGGGTGCCCGGATAAAGGTGG
EST: gi|351024294|gb|FQ423717.1|FQ423717
EST:     CTTAGTGTATGAACTCATTCCAAATGGCAGTGTGGAGTCCCATTTACATG                         GAGCTGACAAGGAAACTGCTCCACTTGATTGGGGTGCCCGGATAAAGGTGG
genomic: CTTAGTGTATGAACTCATTCCAAATGGCAGTGTGGAGTCCCATTTACATGgtattatttt ... ttgctctcagGAGCTGACAAGGAAACTGCTCCACTTGATTGGGGTGCCCGGATAAAGGTGG
EST: gi|351047854|gb|FQ459074.1|FQ459074
EST:     CTTAGTGTATGAACTCATTCCAAATGGCAGTGTGGAGTCCCATTTGCATG                         GAGCTGACAAGGAAACTGCTCCACTTGATTGGGGTGCCCGGATAAAGGTGG
genomic: CTTAGTGTATGAACTCATTCCAAATGGCAGTGTGGAGTCCCATTTACATGgtattatttt ... ttgctctcagGAGCTGACAAGGAAACTGCTCCACTTGATTGGGGTGCCCGGATAAAGGTGG
EST: gi|351034058|gb|FQ447975.1|FQ447975
EST:     CTTAGTGTATGAACTCATTCCAAATGGCAGTGTGGAGTCCCATTTACATG                         GAGCTGACAAGGAAACTGCTCCACTTGATTGGGGTGCCCGGATAAAGGTGG
genomic: CTTAGTGTATGAACTCATTCCAAATGGCAGTGTGGAGTCCCATTTACATGgtattatttt ... ttgctctcagGAGCTGACAAGGAAACTGCTCCACTTGATTGGGGTGCCCGGATAAAGGTGG
EST: gi|351034393|gb|FQ463206.1|FQ463206
EST:     CTTAGTGTATGAACTCATTCCAAATGGCAGTGTGGAGTCCCATTTACATG                         GAGCTGACAAGGAAACTGCTCCACTTGATTGGGGTGCCCGGATAAAGGTGG
genomic: CTTAGTGTATGAACTCATTCCAAATGGCAGTGTGGAGTCCCATTTACATGgtattatttt ... ttgctctcagGAGCTGACAAGGAAACTGCTCCACTTGATTGGGGTGCCCGGATAAAGGTGG
EST: gi|351045030|gb|FQ449284.1|FQ449284
EST:     CTTAGTGTATGAACTCATTCCAAATGGCAGTGTGGAGTCCCATTTACATG                         GAGCTGACAAGGAAACTGCTCCACTTGATTGGGGTGCCCGGATAAAGGTGG
genomic: CTTAGTGTATGAACTCATTCCAAATGGCAGTGTGGAGTCCCATTTACATGgtattatttt ... ttgctctcagGAGCTGACAAGGAAACTGCTCCACTTGATTGGGGTGCCCGGATAAAGGTGG
EST: gi|351032339|gb|FQ461592.1|FQ461592
EST:     CTTAGTGTATGAACTCATTCCAAATGGCAGTGTGGAGTCCCATTTGCATG                         GAGCTGACAAGGAAACTGCTCCACTTGATTGGGGTGCCCGGATAAAGGTGG
genomic: CTTAGTGTATGAACTCATTCCAAATGGCAGTGTGGAGTCCCATTTACATGgtattatttt ... ttgctctcagGAGCTGACAAGGAAACTGCTCCACTTGATTGGGGTGCCCGGATAAAGGTGG
EST: gi|110373968|gb|EC938404.1|EC938404
EST:     CTTAGTGTATGAACTCATTCCAAATGGCAGTGTGGAGTCCCATTTACATG                         GAGCTGACAAGGAAACTGCTCCACTTGATTGGGGTGCCCGGATAAAGGTGG
genomic: CTTAGTGTATGAACTCATTCCAAATGGCAGTGTGGAGTCCCATTTACATGgtattatttt ... ttgctctcagGAGCTGACAAGGAAACTGCTCCACTTGATTGGGGTGCCCGGATAAAGGTGG
EST: gi|349819213|gb|FQ412107.1|FQ412107
EST:     CTTAGTGTATGAACTCATTCCAAATGGCAGTGTGGAGTCCCATTTACATG                         GAGCTGACAAGGAAACTGCTCCACTTGATTGGGGTGCCCGGATAAAGGTGG
genomic: CTTAGTGTATGAACTCATTCCAAATGGCAGTGTGGAGTCCCATTTACATGgtattatttt ... ttgctctcagGAGCTGACAAGGAAACTGCTCCACTTGATTGGGGTGCCCGGATAAAGGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgatcaattctcatcgaatttttatgtttattcctttttcatttgctctcagGAGCTGACAAGGAAACTGCTCCACTTGATTGGGGTGCCCGGATAAAGGTGGCGCTTGGTGCTGCTCGTGGTCTGGCCTATCTGCATGAAGATTCAAGCCC
 cattgat  putative branch site (score: 4)
                             tttattcctttttcat  putative PPT
                   aatttttatgtttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattattttcctcttagtataagttttgcattggctgtgaggtgatgttttccattgatcaattctcatcgaatttttatgtttattcctttttcatttgctctcagGAGCTGACAAGGAAACTGCTCCACTTGATTGGGGTGCCCGGATAAAGGTGGCGCTTGGTGCTGCTCGTGGTCTGGCCTATCTGCATGAAGATTCAAGCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA