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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGATATGGAGAGGAAGGAAGCTTCTCTTTTCCAAATGTTCCACCCAAGGCAGATTTAGTTTATGAAGTTGAGCTCATTGGCTTTGATGAAACCAAAGAAgtaagttgccattaaattatggatggctgtggacttggttagatgcttacggcacctgatttcacag

Basic information

species Glycine max
transcript GLYMA09G36250.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G36250.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G133624_T01 (Zea mays), 5'ss of exon 4
AGGATATGGAGAGGAAGGAAGCTTCTCTTTTCCAAATGTTCCACCCAAGGCAGATTTAGTTTATGAAGTTGAGCTCATTGGCTTTGATGAAACCAAAGAAgtaagttgccattaaattatggatggctgtggacttggttagatgcttacggcacctgatttcacag-----------------------------------------------------------------------------------
||| |||||  | |||||||| || || || |||||||| || || | ||||||  | |||||||||||||| |||||||| ||||||||    ||||| |||||   | |      ||  |    |     || |  | |    ||||    |     ||  | ||                                                                                   
AGGCTATGGCAAAGAAGGAAGTTTTTCATTCCCAAATGTCCCTCCAATGGCAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAGgtaagaaacaaa-ggtctactgcctccaccccacattatgattcacttatattattcttttgaagagtaggctgagattattcatattggttagcattacttacttttctcaatgtgggaagttccaaataatgataaactgtgaatcag

upper sequence: GLYMA09G36250.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv13s0064g00580.t01 (Vitis vinifera), 5'ss of exon 5
AGGATATGGAGAGGAAGGAAGCTTCTCTTTTCCAAATGTTCCACCCAAGGCAGATTTAGTTTATGAAGTTGAGCTCATTGGCTTTGATGAAACCAAAGAAgtaagttgccattaaattatggatggctgtggacttggt-tagatgcttacggcacctgatttcacag--------------------------------------------------------
 || |||||  | |||||||| || ||||| || |||||||| || | ||||||| |  | |||||||||||||| ||||||||||||||||| ||||| ||||||| |   |   | |||  |  |    |  |   | | | || || | || |   | ||||  |                                                        
GGGCTATGGGAAAGAAGGAAGTTTTTCTTTCCCGAATGTTCCGCCTATGGCAGATATTTTGTATGAAGTTGAGCTTATTGGCTTTGATGAAACTAAAGAGgtaagtttctcct---tcatgattttccaaagtttctttattgctgtttcctgc-ctaaacttcattgtatgcgagctcattatagaattcaatatatgaacctacaagcaacgcatgttacag
















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|192332872|gb|FK024969.1|FK024969
EST:     GAAACCAAAGAA                         GGCAAAGCTCGCAGTGATATGACTGTGGAAGAAAGGATTGGTGCAGCAGAC
genomic: GAAACCAAAGAAgtaagttgcc ... gatttcacagGGCAAAGCTCGCAGTGATATGACTGTGGAAGAAAGGATTGGTGCAGCAGAC
EST: gi|254317052|gb|GR825997.1|GR825997
EST:     CAGATTTAGTTTATGAAGTTGAGCTCATTGGCTTTGATGAAACCAAAGAA                         GGCAAAGCTCGCAGTGATATGACTGTGGAAGAAAGGATTGGTGCAGCAGAC
genomic: CAGATTTAGTTTATGAAGTTGAGCTCATTGGCTTTGATGAAACCAAAGAAgtaagttgcc ... gatttcacagGGCAAAGCTCGCAGTGATATGACTGTGGAAGAAAGGATTGGTGCAGCAGAC
EST: gi|192298374|gb|FG988420.1|FG988420
EST:     TTTGATGAAACCCAAAGAA                         GGCAAAGCTCGCAGTGATATGACTGTGGAAGAAAGGATTGGTGCAGCAGA
genomic: TTTGATGAAA-CCAAAGAAgtaagttgcc ... gatttcacagGGCAAAGCTCGCAGTGATATGACTGTGGAAGAAAGGATTGGTGCAGCAGA
EST: gi|151402485|gb|EV272298.1|EV272298
EST:     CAGATTTAGTTTATGAAGTTGAGCTCATTGGCTTTGATGAAACCAAAGAG                         GGCAAAGCTCGCAGTGATATGACTGTGGAAGAAAGGATTGGTGCAGCAGAC
genomic: CAGATTTAGTTTATGAAGTTGAGCTCATTGGCTTTGATGAAACCAAAGAAgtaagttgcc ... gatttcacagGGCAAAGCTCGCAGTGATATGACTGTGGAAGAAAGGATTGGTGCAGCAGAC
EST: gi|23054744|gb|BU577634.1|BU577634
EST:     CAGATTTAGTTTATGAAGTTGAGCTCATTGGCTTTGATGAAACCAAAGAA                         GGCAAAGCTCGCAGTGATATGACTGTGGAAGAAAGGATTGGTGCAGCAGAC
genomic: CAGATTTAGTTTATGAAGTTGAGCTCATTGGCTTTGATGAAACCAAAGAAgtaagttgcc ... gatttcacagGGCAAAGCTCGCAGTGATATGACTGTGGAAGAAAGGATTGGTGCAGCAGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGATATGGAGAGGAAGGAAGCTTCTCTTTTCCAAATGTTCCACCCAAGGCAGATTTAGTTTATGAAGTTGAGCTCATTGGCTTTGATGAAACCAAAGAAgtaagttgccattaaattatggatggctgtggacttggttagatgcttacggcacctgatttcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA