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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAATGGGAATTTGGAGCAATGGCTTCATGGAGCTATGCGCCAGCATGGATTTCTTACTTGGGATGCCCGCATGAAGATTCTTCTCGGGACAGCTAAGGCgtaagtcaattactttatgtccttgccagcatttctttcctcatttaatgtgatatactggttgcag

Basic information

species Vitis vinifera
transcript Vv14s0060g00460.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g00460.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA10G28490.1 (Glycine max), 5'ss of exon 3
GCAATGGGAATTTGGAGCAATGGCTTCATGGAGCTATGCGCCAGCATGGATTTCTTACTTGGGATGCCCGCATGAAGATTCTTCTCGGGACAGCTAAGGCgtaagtcaattactttatgtccttgccagcatttctt-tcctcatttaatgtgatatactggttgcag------------------------
  ||||| || || |||||||||||||||||||||||||| || ||||||| |||||| ||||| || || || |||||||| || || |||||||||| || |||   ||  | | ||  | | |  || ||| |  ||||||||    | | |||  | ||   |                         
ATAATGGAAACTTAGAGCAATGGCTTCATGGAGCTATGCGACATCATGGATATCTTACCTGGGAAGCACGTATCAAGATTCTCCTTGGCACAGCTAAGGGgtgagttgctttgtctgtgctccttcgggcttttgtagtcctcattcttagggttatcttagtgctaatttaaagcaatatacttgtttcag

upper sequence: Vv14s0060g00460.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA20G22550.1 (Glycine max), 5'ss of exon 3
GCAATGGGAATTTGGAGCAATGGCTTCATGGAGCTATGCGCCAGCATGGATTTCTTACTTGGGATGCCCGCATGAAGATTCTTCTCGGGACAGCTAAGGCgtaagtcaattactttatgtccttgccagcatttctt-tcctcatttaatgtgatatactggttgcag------------------------
  ||||| || || |||||||||||||||||||| ||||| || ||||||| |||||| ||||| || || || || ||||| || || |||||||||| || |||   ||  | ||||  | | |  || ||| |  ||||||||    | | |||  | ||   |                         
ATAATGGAAACTTAGAGCAATGGCTTCATGGAGCAATGCGACATCATGGATATCTTACCTGGGAAGCACGTATTAAAATTCTCCTTGGCACAGCTAAGGGgtgagttgctttgtctatgctccttcatgcttttgtagtcctcattcttagggttatcttagtgctaatttgaagcaatatacttattttag

upper sequence: Vv14s0060g00460.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA03G38800.1 (Glycine max), 5'ss of exon 3
GCAATGGGAATTTGGAGCAATGGCTTCATGGAGCTATGCGCCAGCATGGATTTCTTACTTGGGATGCCCGCATGAAGATTCTTCTCGGGACAGCTAAGGCgtaagtcaattactttatgtccttgccagcatttctttcctcatt-taatgtgatatactggttgcag
  ||||| || || |||||||||||||||||||||||||| || |||||||  ||||| ||||| || || || |||||||| || || ||||| || |||| |||   |   | | |||   | | |   ||||  |  || |  |||    || |||  ||| |||
ATAATGGAAACTTAGAGCAATGGCTTCATGGAGCTATGCGTCACCATGGATACCTTACGTGGGAAGCACGTATCAAGATTCTCCTTGGCACAGCCAAAGCgtgagtgtctccatctgtgttgcttctattttttccctagtcctcataaaccaatttacatgtttcag

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|110725970|gb|EE102993.1|EE102993
EST:     TTTCTTACTTGGGATGCCCGCATGAAGATTCTTCTCGGGACAGCTAAGGC                         TCTTGCCTACTTGCATGAGGCCATTGAGCCAAAAGTGGTGCACCGGGACAT
genomic: TTTCTTACTTGGGATGCCCGCATGAAGATTCTTCTCGGGACAGCTAAGGCgtaagtcaat ... ctggttgcagTCTTGCCTACTTGCATGAGGCCATTGAGCCAAAAGTGGTGCACCGGGACAT
EST: gi|110415976|gb|EC981921.1|EC981921
EST:     TTTCTTACTTGGGATGCCCGCATGAAGATTCTTCTCGGGACAGCTAAGGC                         TCTTGCCTACTTGCATGAGGCCATTGAGCCAAAAGTGGTGCACCGGGACAT
genomic: TTTCTTACTTGGGATGCCCGCATGAAGATTCTTCTCGGGACAGCTAAGGCgtaagtcaat ... ctggttgcagTCTTGCCTACTTGCATGAGGCCATTGAGCCAAAAGTGGTGCACCGGGACAT
EST: gi|34543460|gb|CF511692.1|CF511692
EST:     TTTCTTACTTGGGATGCCCGCATGAAGATTCTTCTCGGGACAGCTAAGGC                         TCTTGCCTACTTGCATGAGGCCATTGAGCCAAAAGTGGTGCACCGGGACAT
genomic: TTTCTTACTTGGGATGCCCGCATGAAGATTCTTCTCGGGACAGCTAAGGCgtaagtcaat ... ctggttgcagTCTTGCCTACTTGCATGAGGCCATTGAGCCAAAAGTGGTGCACCGGGACAT
EST: gi|161719711|gb|FC065745.1|FC065745
EST:     TTTCTTACTTGGGATGCCCGCATGAAGATTCTTCTCGGGACAGCTAAGGC                         TCTTGCCTACTTGCATGAGGCCATTGAGCCAAAAGTGGTGCACCGGGACAT
genomic: TTTCTTACTTGGGATGCCCGCATGAAGATTCTTCTCGGGACAGCTAAGGCgtaagtcaat ... ctggttgcagTCTTGCCTACTTGCATGAGGCCATTGAGCCAAAAGTGGTGCACCGGGACAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAATGGGAATTTGGAGCAATGGCTTCATGGAGCTATGCGCCAGCATGGATTTCTTACTTGGGATGCCCGCATGAAGATTCTTCTCGGGACAGCTAAGGCgtaagtcaattactttatgtccttgccagcatttctttcctcatttaatgtgatatactggttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA