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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATGATAGCTTGGTCTTGAGTTTAAGGTCTCTTCAGTTTGACCTTGCATGGGAACGTTGTAGACAGCTTCAAGCTGAAGATGTCACAGTCAAGGGTAAGgtgggtttcctttcctcgtactatgagactgtgttgttggattcagttactcctattaccactctgcaataaggttaatttgatcttaagattattggtttatttattgtgttaacag

Basic information

species Glycine max
transcript GLYMA17G04190.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G04190.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv05s0077g00450.t01 (Vitis vinifera), 5'ss of exon 2
AGATGATAGCTTGGTCTTGAGTTTAAGGTCTCTTCAGTTTGACCTTGCATGGGAACGTTGTAGACAGCTTCAAGCTGAAGATGTCACAGTCAAGGGTAAGgtgggtttcctttcctcgtactatgagactgtgttgttggattcagttactcctattaccactctgcaataaggttaatttgatcttaagattattggtttatttattgtgttaacag
 |||||||||||| ||||||| ||||||||  | |||| ||| |||||||||||||| |||||||||||||| ||||| |||||    || |||||||||||||||| | |   | |  |||||  || | | ||  |        ||  | | |||     | | || |||||||    |  ||   ||||  ||   |||| || || |||     
TGATGATAGCTTGATCTTGAGCTTAAGGTCAATCCAGTATGATCTTGCATGGGAACGATGTAGACAGCTTCAGGCTGAGGATGTTGTTGTGAAGGGTAAGgtgggtt-cttgcacacaaactatttgatttt-ttact--------ttgtttccatttttgttatacagtaaggtt---ctactcaatagatgtttttgttatataatgagtt-----
















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|15287053|gb|BI470944.1|BI470944
EST:     GGGAACGTTGTAGACAGCTTCAAGCTGAAGATGTCACAGTCAAGGGTAAG                         ATTGTGGGGGTGAACAAAGGTGGAGTGGTGGCTGAGTTGGAAAGGCTTANA
genomic: GGGAACGTTGTAGACAGCTTCAAGCTGAAGATGTCACAGTCAAGGGTAAGgtgggtttcc ... gtgttaacagATTGTGGGGGTGAACAAAGGTGGAGTGGTGGCTGAGTTGGAAGGGCTTAGA
EST: gi|209699735|gb|BW655774.1|BW655774
EST:     GGGAACGTTGTAGACAGCTTCAAGCTGAAGATGTCACAGTCAAGGGTAAG                         ATTGTGGGGGTGAACAAAGGTGGAGTGGTGGCTGAGTTGGAAGGGCTTAGA
genomic: GGGAACGTTGTAGACAGCTTCAAGCTGAAGATGTCACAGTCAAGGGTAAGgtgggtttcc ... gtgttaacagATTGTGGGGGTGAACAAAGGTGGAGTGGTGGCTGAGTTGGAAGGGCTTAGA
EST: gi|18735320|gb|BM528697.1|BM528697
EST:     GGGAACGTTGTAGACAGCTTCAAGCTGAAGATGTCACAGTCAAGGGTAAG                         ATTGTGGGGGGTGAACAAAG
genomic: GGGAACGTTGTAGACAGCTTCAAGCTGAAGATGTCACAGTCAAGGGTAAGgtgggtttcc ... gtgttaacagATTGTGGGGG-TGAACAAAG
EST: gi|209699736|gb|BW655775.1|BW655775
EST:     GACAGCTTCAAGCTGAAGATGTCACAGTCAAGGGTAAG                         ATTGTGGGGGTGAACAAAGGTGGAGTGGTGGCTGAGTT-GAAGGGGCTTAG
genomic: GACAGCTTCAAGCTGAAGATGTCACAGTCAAGGGTAAGgtgggtttcc ... gtgttaacagATTGTGGGGGTGAACAAAGGTGGAGTGGTGGCTGAGTTGGAA-GGGCTTAG
EST: gi|31561839|gb|CD487677.1|CD487677
EST:     GGGAACGTTGTAGACAGCTTCAAGCTGAAGATGTCACAGTCAAGGGTAAG                         ATTGTGGGGGTGAACAAAGGTGGAGTGGTGGCTGAGTTGGAAGGGCTTAGA
genomic: GGGAACGTTGTAGACAGCTTCAAGCTGAAGATGTCACAGTCAAGGGTAAGgtgggtttcc ... gtgttaacagATTGTGGGGGTGAACAAAGGTGGAGTGGTGGCTGAGTTGGAAGGGCTTAGA
EST: gi|23052926|gb|BU577417.1|BU577417
EST:     GGGAACGTTGTAGACAGCTTCAAGCTGAAGATGTCACAGTCAAGGGTAAG                         ATTGTGGGGGTGAACAAAGGTGGAGTGGTGGCT
genomic: GGGAACGTTGTAGACAGCTTCAAGCTGAAGATGTCACAGTCAAGGGTAAGgtgggtttcc ... gtgttaacagATTGTGGGGGTGAACAAAGGTGGAGTGGTGGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATGATAGCTTGGTCTTGAGTTTAAGGTCTCTTCAGTTTGACCTTGCATGGGAACGTTGTAGACAGCTTCAAGCTGAAGATGTCACAGTCAAGGGTAAGgtgggtttcctttcctcgtactatgagactgtgttgttggattcagttactcctattaccactctgcaataaggttaatttgatcttaagattattggtttatttattgtgttaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG