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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCTTGGAAATCCCTATTCCAAATGACATTGCATTCATTGGTGAAATTGGCCTTGGTGGTGAGCTTCGCATGgtgagcatgttctttaatatgttaatgttgcttttatggcattttaaggtcaatttagagtcttcagttgcataaagttgtgcttaatacaatgttaaat...

Basic information

species Glycine max
transcript GLYMA08G21360.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G21360.1 (Glycine max), 5'ss of exon 14
lower sequence: Vv09s0002g03180.t01 (Vitis vinifera), 5'ss of exon 17
TTGCTTGGAAATCCCTATTCCAAATGACATTGCATTCATTGGTGAAATTGGCCTTGGTGGTGAGCTTCGCATGgtgagcatgttctttaatatgttaatgttgcttttatggcattttaaggtcaatttagagt---cttcagttgcataaagttgtgcttaatacaatgttaaat-
 | ||||||  | |||||||| |||| ||||||||||||||| || || |||||||||||||||||||||| |||  |||| || ||   |          || ||| |        | || |   |||| |||    |||| |||  |       || ||  |  ||  ||  |  
CTTCTTGGAGTTTCCTATTCCCAATGGCATTGCATTCATTGGAGAGATCGGCCTTGGTGGTGAGCTTCGCACGgtatgcatatttttccttgatcctgaactgatttaagaag----tgagctagttttatagtacctttcaattgattccctcactggtttttggaagcttgtaca

upper sequence: GLYMA08G21360.1 (Glycine max), 5'ss of exon 14
lower sequence: Vv09s0002g03190.t01 (Vitis vinifera), 5'ss of exon 14
TTGCTTGGAAATCCCTATTCCAAATGACATTGCATTCATTGGTGAAATTGGCCTTGGTGGTGAGCTTCGCATGgtgagcatgttctttaatatgttaatgttgcttttatggcattttaaggtcaatttagagtcttcagttgcataaagttg-tgcttaatacaatgttaaat
 | ||||||  | |||||||| |||| ||||||||||||||| ||||| |||||||||||||||||||||| |||  |||| || | |   ||        || ||||| |   |      ||   |  ||   |||    |  ||    ||  ||  |  |  ||  ||    
CTTCTTGGAGTTTCCTATTCCCAATGGCATTGCATTCATTGGAGAAATCGGCCTTGGTGGTGAGCTTCGCACGgtatgcatattttctctcattactgaactgattttaagaagtgaactagttt-tgcagtacctttgcctcgattcccttactggcttttggaagcttgtgc
















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|10255430|gb|BE823196.1|BE823196
EST:     GGTGAAATTGGCCTTGGTGGTGAGCTTCGCATG                         GTTCCTAGAATGGAGAAAAGGGTATATACCGTTGCGAAATTGGGTTACAGA
genomic: GGTGAAATTGGCCTTGGTGGTGAGCTTCGCATGgtgagcatgt ... tgatatgcagGTTCCTAGAATGGAGAAAAGGGTATATACCGTTGCGAAATTGGGTTACAGA
EST: gi|51336133|gb|CO979999.1|CO979999
EST:     ATGACATTGCATTCATTGGTGAAATTGGCCTTGGTGGTGAGCTTCGCATG                         GTTCCTAGAATGGAGAAAAGGGTATATACCGTTGCGAAATTGGGTTACAGA
genomic: ATGACATTGCATTCATTGGTGAAATTGGCCTTGGTGGTGAGCTTCGCATGgtgagcatgt ... tgatatgcagGTTCCTAGAATGGAGAAAAGGGTATATACCGTTGCGAAATTGGGTTACAGA
EST: gi|193535081|gb|FK491681.1|FK491681
EST:     ATGACATTGCATTCGTTGGTGAAATTGGCCTTGGTGGTGAGCTTCGCATG                         GTTCCTAGAATGGAGAAAAGGGTATATACCGTTGCGAAATTGGGTTACAGA
genomic: ATGACATTGCATTCATTGGTGAAATTGGCCTTGGTGGTGAGCTTCGCATGgtgagcatgt ... tgatatgcagGTTCCTAGAATGGAGAAAAGGGTATATACCGTTGCGAAATTGGGTTACAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCTTGGAAATCCCTATTCCAAATGACATTGCATTCATTGGTGAAATTGGCCTTGGTGGTGAGCTTCGCATGgtgagcatgttctttaatatgttaatgttgcttttatggcattttaaggtcaatttagagtcttcagttgcataaagttgtgcttaatacaatgttaaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT