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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttttcttctatcacatggatgattagttttctcccatttcctctacactgttctttctgcaactttgtttagggattttatgctggtgcagCACTATGACAGACGGGGCCAATATGACATTGCTCTCACTAAAATTGATGAGGCTATAGAGCACACTCCGACTGTTATTGATTTATACTCAGTCAAG

Basic information

species Vitis vinifera
transcript Vv09s0002g05110.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g05110.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA15G01580.1 (Glycine max), 3'ss of exon 13
gtttttcttctatcacatggatgattagttttctcccatttcctc-tacactgttctttctgcaactttgtttagggattttatgctggtgcagCACTATGACAGACGGGGCCAATATGACATTGCTCTCACTAAAATTGATGAGGCTATAGAGCACACTCCGACTGTTATTGATTTATACTCAGTCAAG
    ||  |  ||    | ||||||  |||||    |||||  |  |    |  ||  | |     | |  | || || ||| || | |||||||| ||||||||||||||||||||||| ||||||||  |||||||  |||||||||| || ||||| || || || |||||| | || |||||||||
---gtttgtgcattttttagatgat--gttttgatacatttttttgtgggttcctccatatttttttctactcagtgaatttttgtttgtgcagCATTATGACAGACGGGGCCAATATGAAATTGCTCTTTCTAAAATCAATGAGGCTATTGATCACACACCTACCGTCATTGATCTGTATTCAGTCAAG

upper sequence: Vv09s0002g05110.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA13G43760.1 (Glycine max), 3'ss of exon 13
gtttttcttctatcacatggatgattagttttctcccatt-tcctctacactgttctttctgcaactttgtttagggattttatgctggtgcagCACTATGACAGACGGGGCCAATATGACATTGCTCTCACTAAAATTGATGAGGCTATAGAGCACACTCCGACTGTTATTGATTTATACTCAGTCAAG
  |||     |||    | ||||||  |||||    |||| |  | |    |  ||  | |     | |  | |  || ||| |  |||||||||| ||||||||||||||||||||||| ||||||||   ||||||  |||||||||| || ||||| || || || |||||| | || |||||||||
-gtttgtgcatattttttagatgat--gttttgatacattattttgtgggttcctccatatttt-ttctactcattgaatttttattggtgcagCATTATGACAGACGGGGCCAATATGAAATTGCTCTTTTTAAAATCAATGAGGCTATTGATCACACACCTACCGTCATTGATCTGTATTCAGTCAAG

upper sequence: Vv09s0002g05110.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA07G03850.1 (Glycine max), 3'ss of exon 13
gtttttcttctatcacatggatgattagttttctcccatttcctctacactgttctttctgcaactttgtttagggattttatgctggtgcagCACTATGACAGACGGGGCCAATATGACATTGCTCTCACTAAAATTGATGAGGCTATAGAGCACACTCCGACTGTTATTGATTTATACTCAGTCAAG
                        || ||   ||   ||||  | |  |   ||| || | |   |||  | ||  | ||| | ||||||||||| |||||||| || ||||||||||| ||||||||  ||||||| ||||| |||||||| || || || || || |||||| |||| || ||||||
-----------------------gttggtag-ctattatttgatttttag-attcattatccccgtttactaagataatttgtactggtgcagCATTATGACAGGCGAGGCCAATATGAAATTGCTCTTTCTAAAATCGATGAAGCTATAGAACATACGCCTACAGTCATTGATCTATATTCTGTCAAG

upper sequence: Vv09s0002g05110.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA08G22180.1 (Glycine max), 3'ss of exon 13
gtttttcttctatcacatggatgattagttttctcccatttcctctacactgttctttctgcaactttgtttagggattttatgctggtgcagCACTATGACAGACGGGGCCAATATGACATTGCTCTCACTAAAATTGATGAGGCTATAGAGCACACTCCGACTGTTATTGATTTATACTCAGTCAAG
                        || ||   ||   ||||  | |  |   ||| || | |   ||   | ||  | ||| | ||||||||||| |||||||| || |||||||||||  |||||||  ||||||||||||| |||||||| || || || || || |||||| |||| || || |||
-----------------------gttggtag-ctattatttgatttttag-attcattatccccattcactaagataatttgtactggtgcagCATTATGACAGGCGAGGCCAATATGAAGTTGCTCTTTCTAAAATTGATGAAGCTATAGAACATACACCTACAGTCATTGATCTATATTCTGTTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcctctacactgttctttctgcaactttgtttagggattttatgctggtgcagCACTATGACAGACGGGGCCAATATGACATTGCTCTCACTAAAATTGATGAGGCTATAGAGCACACTCCGACTGTTATTGATTTATACTCAGTCAAG
                                      attttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttttcttctatcacatggatgattagttttctcccatttcctctacactgttctttctgcaactttgtttagggattttatgctggtgcagCACTATGACAGACGGGGCCAATATGACATTGCTCTCACTAAAATTGATGAGGCTATAGAGCACACTCCGACTGTTATTGATTTATACTCAGTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA