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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtgcaccttattttgtactggtgatggttttattgcatttgtggtagtccaccatattgtactggtgatatttttattactttctgatggtacattctaagttcaatctcttttaattgattattaagCTTTCAAATGCTGGGGGACGGCTTATTATTGCTTCTGATGGAATCTGGGATGCTTTATCATCTGACATGGCTGCTAAGTCTTGTCGGGGTTTGCCTGCAG

Basic information

species Vitis vinifera
transcript Vv14s0060g01580.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g01580.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA19G41810.2 (Glycine max), 3'ss of exon 5
gtgtgtgcaccttattttgtactggtgatggttttattgcatttgtggtagtccaccatattgtactggtgatatttttattactttctgatggtacattctaagttcaatctcttttaattgattattaagCTTTCAAATGCTGGGGGACGGCTTATTATTGCTTCTGATGGAATCTGGGATGCTTTATCATCTGACATGGCTGCTAAGTCTTGTCGGGGTTTGCCTGCAG
                        | | |||||| |||    |  |  | ||         |||    |||| |  |||  || ||     |   ||        || ||  | | |  |||||||  | |||||||||||||||| ||| |||||||||| ||||||||||| || |||||||||||||||||||| |||||||||||||||||||||||| | |||||||
----------------------gtgagctggtttcattattatgttttttgtttggtggcctgtttatgtgaaagcttt--tagttctaagtttcactgctc---ttaaacatttgtctattgatttctcagCTTTCAAATGCTGGTGGAAGGCTTATTATAGCTTCTGATGGTATTTGGGATGCTTTATCATCTGATATGGCTGCTAAGTCTTGTCGGGGTCTACCTGCAG

upper sequence: Vv14s0060g01580.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA03G39260.1 (Glycine max), 3'ss of exon 5
gtgtgtgcaccttattttgtactggtgatggttttattgcatttgtggtagtccaccatattgtactggtgatatttttattactttctgatggtacattctaagttcaatctcttttaattgattattaagCTTTCAAATGCTGGGGGACGGCTTATTATTGCTTCTGATGGAATCTGGGATGCTTTATCATCTGACATGGCTGCTAAGTCTTGTCGGGGTTTGCCTGCAG
                        | | ||||||||||   ||| | ||  |  |  |  |  |  ||  ||   ||||| | |||  |     | | || |||     |  | | |  |||||||  | ||||||| |||| ||| ||| |||||||||| ||||||||||| || ||||||||||||||||| || |||||||||||||||||||| ||| | |||||||
----------------------gtgagctggttttattatgttttttgt--ttgatgacctgtttatgtggaagcttttagttcttagtttctctgc-ttgtaa-----acatttgtctattgatttctcagCTTTCCAATGTTGGTGGAAGGCTTATTATAGCTTCTGATGGTATTTGGGATGCTTTATCATCCGATATGGCTGCTAAGTCTTGTCGAGGTCTACCTGCAG

upper sequence: Vv14s0060g01580.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G38270.1 (Glycine max), 3'ss of exon 5
gtgtgtgcaccttattttgtactggtgatggttttattgcatttgtggtagtccaccatattgtactggtgatatttttattactttctgatggtacattctaagttcaatctcttttaattgattattaagCTTTCAAATGCTGGGGGACGGCTTATTATTGCTTCTGATGGAATCTGGGATGCTTTATCATCTGACATGGCTGCTAAGTCTTGTCGGGGTTTGCCTGCAG
||  |      | |||||| |   ||  | ||||   |  |||  ||||          ||| |  ||  || || |||| ||||   |    | ||    | |     | ||  | | |||| ||    |||||||||||||||| ||| | |||||||| ||||||||||| || |||||||||||||| ||||| |||||||| ||||| || || ||| | |||||||
gtaagctagtttcattttgaa---gtcttagttta--tatattgatggt---------catttttatgtggagatgtttagtactaaatttcagcac----tga---tgaccttctcttattggttccccagCTTTCAAATGCTGGTGGAAGACTTATTATAGCTTCTGATGGTATTTGGGATGCTTTATCTTCTGATATGGCTGCCAAGTCATGCCGAGGTGTACCTGCAG

upper sequence: Vv14s0060g01580.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G29060.1 (Glycine max), 3'ss of exon 5
gtgtgtgcaccttattttgtactggtgatggttttattgcatttgtggtagtccaccatattgtactggtgatatttttattactttctgatggtacattctaagttcaatctcttttaattgattattaagCTTTCAAATGCTGGGGGACGGCTTATTATTGCTTCTGATGGAATCTGGGATGCTTTATCATCTGACATGGCTGCTAAGTCTTGTCGGGGTTTGCCTGCAG
||  |      | ||||||||         || ||| |  |||  | |  | |||  || | | | ||        |||| ||||   |    | || | || |       ||  | | |||| ||    |||| ||||||||||| ||| | |||||||| ||||||||||| || |||||||||||||| ||||| |||||||| ||||| || |||||| | |||||||
gtaagctagtttcattttgta---------gtcttagtttattgatcgatggccattatgtggaagtg--------tttagtactaaatttcagcac-tcctga------ccttctcttattggttccccagCTATCAAATGCTGGTGGAAGACTTATTATAGCTTCTGATGGTATTTGGGATGCTTTATCTTCTGATATGGCTGCCAAGTCATGCCGGGGTGTACCTGCAG

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|37189043|gb|CF608392.1|CF608392
EST:     CAGATGTGGGAGAATTCATTGTCCCAATACCACATGTTAAGCAAGTGAAG                         CTTTCAAATGCTGGGGGACGGCTTATTATTGCTTCTGATGGAATCTGGGAT
genomic: CAGATGTGGGAGAATTCATTGTCCCAATACCACATGTTAAGCAAGTGAAGgtgtgtgcac ... gattattaagCTTTCAAATGCTGGGGGACGGCTTATTATTGCTTCTGATGGAATCTGGGAT
EST: gi|110687916|gb|EE065868.1|EE065868
EST:     CAGATGTGGGAGAATTCATTGTCCCAATACCACATGTTAAGCAAGTGAAG                         CTTTCAAATGCTGGGGGACGGCTTATTATTGCTTCTGATGGAATCTGGGAT
genomic: CAGATGTGGGAGAATTCATTGTCCCAATACCACATGTTAAGCAAGTGAAGgtgtgtgcac ... gattattaagCTTTCAAATGCTGGGGGACGGCTTATTATTGCTTCTGATGGAATCTGGGAT
EST: gi|71890427|gb|DT039482.1|DT039482
EST:     CAGATGTGGGAGAATTCATTGTCCCAATACCACATGTTAAGCAAGTGAAG                         CTTTCAAATGCTGGGGGACGGCTTATTATTGCTTCTGATGGAATCTGGGAT
genomic: CAGATGTGGGAGAATTCATTGTCCCAATACCACATGTTAAGCAAGTGAAGgtgtgtgcac ... gattattaagCTTTCAAATGCTGGGGGACGGCTTATTATTGCTTCTGATGGAATCTGGGAT
EST: gi|254914412|gb|GR906513.1|GR906513
EST:     CAGATGTGGGAGAATTCATTGTCCCAATACCACATGTTAAGCAAGTGGAG                         CTTTCAAATGCTGGGGGACGGCTTATTATTGCTTCTGATGGAATCTGGGAT
genomic: CAGATGTGGGAGAATTCATTGTCCCAATACCACATGTTAAGCAAGTGAAGgtgtgtgcac ... gattattaagCTTTCAAATGCTGGGGGACGGCTTATTATTGCTTCTGATGGAATCTGGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattactttctgatggtacattctaagttcaatctcttttaattgattattaagCTTTCAAATGCTGGGGGACGGCTTATTATTGCTTCTGATGGAATCTGGGATGCTTTATCATCTGACATGGCTGCTAAGTCTTGTCGGGGTTTGCCTGCAG
                               aatctcttttaattga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtgcaccttattttgtactggtgatggttttattgcatttgtggtagtccaccatattgtactggtgatatttttattactttctgatggtacattctaagttcaatctcttttaattgattattaagCTTTCAAATGCTGGGGGACGGCTTATTATTGCTTCTGATGGAATCTGGGATGCTTTATCATCTGACATGGCTGCTAAGTCTTGTCGGGGTTTGCCTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG