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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGTTACCATGTCGGACGATGAGAGAGAGGAGAAGGAGTTGGATCTCACTTCTCCGGAAGTTGTCACCAAGTACAAGAGCGCCGCGGAGATTGTTAACAgtgtgttacactctcattttttgttaaattcttaatgggtttttggtttttggtacattgggttcattactttgatgggttattgttaatgggttatttgcgtttttatttttcttatgttgatgagttatgttttgttttgttttaattaaacag

Basic information

species Glycine max
transcript GLYMA03G07420.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G07420.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv08s0217g00020.t01 (Vitis vinifera), 5'ss of exon 1
GAGGTTACCATGTCGGACGATGAGAGAGAGGAGAAGGAGTTGGATCTCACTTCTCCGGAAGTTGTCACCAAGTACAAGAGCGCCGCGGAGATTGTTAACAgtgtgttacactctcattttttgttaaattcttaatgggtttttggtttttggtacattgggttcattactttgatgggttattgttaatgggttatttgcgtttttatttttcttatgttgatgagttatgttttgttttgttttaattaaacag
   |  || |||||||| || || |||||||||||||||||||||||||||||||| ||||| |||||||| ||||||||||| || ||||||| |||||||       ||| || || || ||  |  | |  ||  ||||||  |  |  | | ||     |    | |||      || || ||  |||| | |    | |||   ||                                             
CTCGAAACGATGTCGGATGACGAAAGAGAGGAGAAGGAGTTGGATCTCACTTCTCCTGAAGTCGTCACCAAATACAAGAGCGCTGCTGAGATTGCTAACAgt------tactttctttcttcgtatatatatatatttgttttttctgatatgcatatatatgttgcgattttt-----ttttttttggtggggtttcgttggtttgggtt---------------------------------------------

upper sequence: GLYMA03G07420.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S119_137V6.1 (Physcomitrella patens), 5'ss of exon 1
GAGGTTACCATGTCGGACGATGAGA---GAGAGGAGAAGGAGTTGGATCTCACTTCTCCGGAAGTTGTCACCAAGTACAAGAGCGCCGCGGAGATTGTTAACAgtgtgt---tacact-ctcattttttgttaaattcttaatgggtttttggtttttggtacattgggttcattactt-tgatgggttattgttaatgggttatttgcgtttttatttttcttatgttgatgagttatgttttgttttgttttaattaaacag
   ||  ||||||||||||| ||||     |||||||||||| | ||||| |||||||| || || ||||||||||||||  ||||||| ||| |||  ||||||  ||     | || || |||||     | | | |  ||   |||  |||||  || |  | | |||    | || || ||  |  |  | | |||  |                                                             
---GTCGCCATGTCGGACGACGAGATGAAGGAGGAGAAGGAGCTCGATCTGACTTCTCCCGATGTGGTCACCAAGTACAAATGCGCCGCTGAGGTTGCCAACAgtaagtacccgcgctgctgattttgctgcagagtttggattactttagggtttaagggaattggagttttggagttgtggtgattcgtgttcactggcat-------------------------------------------------------------
















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|213616512|gb|DB965710.1|DB965710
EST:     TTCTCCGGAAGTTGTCACCAAGTACAAGAGCGCCGCGGAGATTGTTAACA                         GGGCTTTGCAGTTAGTTATTTCAGAATGTAAACCGAAGGCAAAGATTGTTG
genomic: TTCTCCGGAAGTTGTCACCAAGTACAAGAGCGCCGCGGAGATTGTTAACAgtgtgttaca ... aattaaacagGGGCTTTGCAGTTAGTTATTTCAGAATGTAAACCGAAGGCAAAGATTGTTG
EST: gi|192330310|gb|FK020580.1|FK020580
EST:     TTCTCCGGAAGTTGTCACCAAGTACAAGAGCGCCGCGGAGATTGTTAACA                         GGGCTTTGCAGTTAGTTATTTCAGAATGTAAACCGAAGGCAAAGATTGTTG
genomic: TTCTCCGGAAGTTGTCACCAAGTACAAGAGCGCCGCGGAGATTGTTAACAgtgtgttaca ... aattaaacagGGGCTTTGCAGTTAGTTATTTCAGAATGTAAACCGAAGGCAAAGATTGTTG
EST: gi|193520125|gb|FK474196.1|FK474196
EST:     CGCCGCGGAGATTGTTAACA                         GGGCTTTGCAGTTAGTTATTTCAGAATGTAAACCGAAGGCAAAGATTGTTG
genomic: CGCCGCGGAGATTGTTAACAgtgtgttaca ... aattaaacagGGGCTTTGCAGTTAGTTATTTCAGAATGTAAACCGAAGGCAAAGATTGTTG
EST: gi|7685524|gb|AW756172.1|AW756172
EST:     TTCTCCGGAAGTTGTCACCAAGTACAAGAGCGCCGCGGAGATTGTTAACA                         GGGCTTTGCAGTTAGTTATTTCAGAATGTAAACCGAAGGCAAAGATTGTTG
genomic: TTCTCCGGAAGTTGTCACCAAGTACAAGAGCGCCGCGGAGATTGTTAACAgtgtgttaca ... aattaaacagGGGCTTTGCAGTTAGTTATTTCAGAATGTAAACCGAAGGCAAAGATTGTTG
EST: gi|151408709|gb|EV278517.1|EV278517
EST:     TTCTCCGGAAGTTGTCACCAAGTACAAGAGCGCCGCGGAGATTGTTAACA                         GGGCTTTGCAGTTAGTTATTTCAGAATGTAAACCGAAGGCAAAGATTGTTG
genomic: TTCTCCGGAAGTTGTCACCAAGTACAAGAGCGCCGCGGAGATTGTTAACAgtgtgttaca ... aattaaacagGGGCTTTGCAGTTAGTTATTTCAGAATGTAAACCGAAGGCAAAGATTGTTG
EST: gi|213591699|gb|DB969799.1|DB969799
EST:     TTCTCCGGAAGTTGTCACCAAGTACAAGAGCGCCGCGGAGATTGTTAACA                         GGGCTTTGCAGTTAGTTATTTCAGAATGTAAACCGAAGGCAAAGATTGTTG
genomic: TTCTCCGGAAGTTGTCACCAAGTACAAGAGCGCCGCGGAGATTGTTAACAgtgtgttaca ... aattaaacagGGGCTTTGCAGTTAGTTATTTCAGAATGTAAACCGAAGGCAAAGATTGTTG
EST: gi|192299906|gb|FG991780.1|FG991780
EST:     TTCTCCGGAAGTTGTCACCAAGTACAAGAGCGCCGCGGAGATTGTTAACA                         GGGCTTTGCAGTTAGTTATTTCAGAATGTAAACCGAAGGCAAAGATTGTTG
genomic: TTCTCCGGAAGTTGTCACCAAGTACAAGAGCGCCGCGGAGATTGTTAACAgtgtgttaca ... aattaaacagGGGCTTTGCAGTTAGTTATTTCAGAATGTAAACCGAAGGCAAAGATTGTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGTTACCATGTCGGACGATGAGAGAGAGGAGAAGGAGTTGGATCTCACTTCTCCGGAAGTTGTCACCAAGTACAAGAGCGCCGCGGAGATTGTTAACAgtgtgttacactctcattttttgttaaattcttaatgggtttttggtttttggtacattgggttcattactttgatgggttattgttaatgggttatttgcgtttttatttttcttatgttgatgagttatgttttgttttgttttaattaaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT