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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaatttttatttatctttagttaggtgtataaaccttcaattggcatttaacacctatgtaagtgagtgagttcatcaaaatcaactcttttcttataattgtttgtttccattatgaaagatgtttcttctcttcttgcagGAAATAGCTTCAGAAGTACAGAGTGAAACCAAATGGAAGCAGTTGGGAGAATTAGCTATGTCCAATGGAAAG

Basic information

species Vitis vinifera
transcript Vv11s0016g04180.t01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 17
gtaagaatttttatttatctttagttaggtgtataaaccttcaattggcatttaacacctatgtaagtgagtgagttcatcaaaatcaactcttttcttataattgtttgtttccattatgaaagatgt--ttcttctcttct-tgcagGAAATAGCTTCAGAAGTACAGAGTGAAACCAAATGGAAGCAGTTGGGAGAATTAGCTATGTCCAATGGAAAG
                                        |   | |   ||||   |  |  | ||  || | |  |  ||||         | |   | ||  | |    |  ||||| | |  | |  ||| | | | || | ||||  || |    ||||| |||||||||| | ||||||||||||||||| ||| | || |||||||  || |||
--------------------------------------tatttgtcgcggtttagttcaaaaatgagctagcggg--cgacaaa---------tattcgagaacggatgtagtatattataagacctctcattcctatttactgttcagGCTATCGTCATAGAAGCACAGAGTGAATCTAAATGGAAGCAGTTGGGTGAACTCGCCATGTCCACAGGCAAG

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 7
gtaagaatttttatttatctttagttaggtgtataaaccttcaattggcatttaacacctatgtaagtgagtgagttcatcaaaatcaactcttttcttataattgtttgtttccattatgaaagatgtttcttctcttcttgcagGAAATAGCTTCAGAAGTACAGAGTGAAACCAAATGGAAGCAGTTGGGAGAATTAGCTATGTCCAATGGAAAG
|||||    || || | |   |     | | ||| |     |   ||  |||| | | || ||  | | | |   |||  ||     || |         |   | |  ||||  ||| |||   ||| |  |  |||| |||||||  || ||||| ||||| ||||||||  ||||||||||||| |||||||||||||| ||||| | |||||||
gtaag----ttcatatgttcctgcaaggatatattatttgactcgtgaaatttcataactctgctatttaatt--ttctgcatttctaatttgcactagtttgatttgagtttatattgtgagtaatgctcatcttctt-ttgcagGGTATTGCTTCTGAAGTGCAGAGTGAGTCCAAATGGAAGCAATTGGGAGAATTAGCCATGTCTACTGGAAAG

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 18
gtaagaatttttatttatctttagttaggtgtataaacc-ttcaattggcatttaacacctatgtaagtgagtgagttcatcaaaatcaactcttttcttataattgtttgtttccattatgaaagatgtttcttctcttct--tgcagGAAATAGCTTCAGAAGTACAGAGTGAAACCAAATGGAAGCAGTTGGGAGAATTAGCTATGTCCAATGGAAAG
    | ||  | || ||  | |   ||   | | | |   || |||| |            |  |  ||   | | ||  |  |  ||   || |   ||  | ||||   |||  || |  ||  || |  || || |||   |||||   || ||   |||| | ||||| ||  | ||||||||||| |||||||||||||||||||| | |||||||
----gtatgctcatgtaa-tatgtctacaaggagatattgtttaatttgtgaaagctgttaacttgggtatctaattttcttcatttctcttcatcagtttgatttgtcattttatatcacaaataatatacctccttttcccatgcagAGTATTGCAATAGAATTGCAGAGCGAGCCTAAATGGAAGCAATTGGGAGAATTAGCTATGTCTACTGGAAAG

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 18
gtaagaatttttatttatctttagttaggtgtataaacc-ttcaattggcatttaacacctatgtaagtgagtgagttcatcaaaatcaactcttttcttataattgtttgtttccattatgaaagatgtttcttctcttc--ttgcagGAAATAGCTTCAGAAGTACAGAGTGAAACCAAATGGAAGCAGTTGGGAGAATTAGCTATGTCCAATGGAAAG
    | || || ||  |  | ||  ||   | | | |   || |||| |     |      |  |  ||     |  |  |  |  ||   || |   ||  | ||||   |||  || |  ||  || |  || || ||   ||||||   || ||   |||| ||||||| ||  | |||||||||||||||||||||||| ||||||| | |||||||
----gtatgttcatgcaa-tatatctacaaggagatattgtttaatttgtgaaaattgttaacttgggtatccaatattcttcatttcttttcatcagtttgatttgtcattttatatcacaaataatatacctcctttttctttgcagAGTATTGCAATAGAATTACAGAGCGAGCCTAAATGGAAGCAGTTGGGAGAATTAACTATGTCTACTGGAAAG

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 18
gtaagaatttttatttatctttagttaggtgtataaaccttcaattggcatttaacacctatgtaagtgagtgagttcatcaaaatcaactcttttcttataattgtttgtttccattatgaaagatgtttcttctcttcttgcagGAAATAGCTTCAGAAGTACAGAGTGAAACCAAATGGAAGCAGTTGGGAGAATTAGCTATGTCCAATGGAAAG
|||||    || || | |   |     | | ||| |   | |   ||  |||||| | |  ||  | | | |   |||  ||     || |         |   | |  ||||  ||| |||   |||||  || |  | |||||||  || ||  | ||||| || |||||  ||||||||||||| |||||||||||||| ||||| | |||||||
gtaag----ttcatatgttcctgcaaggatatattattttacttgtgaaatttaataacactgctatttaatt--ttctgcatttctaatttgcacgagtttgatttgagtttatattgtgagcaatgttcattgttcttttgcagGGTATTGCCACTGAAGTGCATAGTGAGTCCAAATGGAAGCAATTGGGAGAATTAGCCATGTCTACTGGAAAG

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 18
gtaagaatttttatttatctttagttaggtgtataaaccttcaattggcatttaacacctatgtaagtgagtgagttcatcaaaatcaactcttttcttataattgtttgtttccattatgaaagatgtttcttctcttcttgcagGAAATAGCTTCAGAAGTACAGAGTGAAACCAAATGGAAGCAGTTGGGAGAATTAGCTATGTCCAATGGAAAG
                                        | |  |   || | |  | ||  |   |        | |    | || ||||||||   |       || |||   ||||      | | | |||  | |||| ||||||| |||  |||||||||||| ||  | |||||||||||||| ||||| ||||| ||||||   || |||
---------------------------------------gtaatatcatatgtgatgcttaattgcttagaca---ttactttactctactctttttggaagtagaattttttttcttatc-----tttgttttccatgcttgtagGAAATTGCTGAAGAAGTACAGAGCGAGTCTAAATGGAAGCAGTTAGGAGAGTTAGCCATGTCCTCGGGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttcttataattgtttgtttccattatgaaagatgtttcttctcttcttgcagGAAATAGCTTCAGAAGTACAGAGTGAAACCAAATGGAAGCAGTTGGGAGAATTAGCTATGTCCAATGGAAAG
                                   tgtttcttctcttctt  CT-rich tract
      ttataattgtttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaatttttatttatctttagttaggtgtataaaccttcaattggcatttaacacctatgtaagtgagtgagttcatcaaaatcaactcttttcttataattgtttgtttccattatgaaagatgtttcttctcttcttgcagGAAATAGCTTCAGAAGTACAGAGTGAAACCAAATGGAAGCAGTTGGGAGAATTAGCTATGTCCAATGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA