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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTAAAAGAGAGATATCCATTATGAAGATTGTCAGGCATCCTAATATAGTTAGATTGCACGAGgtatgtttagatatcctaatatgccaggaattataccatatttctttcttttctatttctcacattgttttcaaattttag

Basic information

species Glycine max
transcript GLYMA17G12250.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G12250.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os06g40370.1 (Oryza sativa), 5'ss of exon 2
ATTAAAAGAGAGATATCCATTATGAAGATTGTCAGGCATCCTAATATAGTTAGATTGCACGAGgtatgtttagatatcctaatatgccaggaattataccatatttctttcttttctat-ttctcacattgt---tttcaaattttag------------------------------------
|| ||||| |||||||| || ||||||||||| || || || |||||||||||| |  |||||||||| | | ||||     |       |   ||||  |  |||| || ||  | |   ||  |  |||    | | || ||   |                                    
ATCAAAAGGGAGATATCAATAATGAAGATTGTAAGACACCCCAATATAGTTAGACTAAACGAGgtatgct-aaatatttacttgccatctgtcctatataacttttcattattaacaaaactcctatgttggctatcttaacttcctgtgtcactactttgttaccattactatgattttgtag

upper sequence: GLYMA17G12250.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv11s0016g05420.t01 (Vitis vinifera), 5'ss of exon 3
ATTAAAAGAGAGATATCCATTATGAAGATTGTCAGGCATCCTAATATAGTTAGATTGCACGAGgtatgtttagatatcctaatatgccaggaattataccat---atttctttcttttc--tatttctcacattgtttt---caaattttag-----------
||||||  |||||||||||| ||||||||||||||||| ||||| |||||||||||||| |||||||||||| || |  |   |||      || | |   |   ||||| |||| |    || || | | | ||  |     | ||| | |           
ATTAAACAAGAGATATCCATAATGAAGATTGTCAGGCACCCTAACATAGTTAGATTGCATGAGgtatgtttacattttttgtaatgtataatatgacattttgaaatttccttctatctagtaattgttagagtgcatgatatatattgtgggcttaaactta
















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|254322068|gb|GR837482.1|GR837482
EST:     TATCCATTATGAAGATTGTCAGGCATCCTAATATAGTTAGATTGCACGAG                         GTTTTGGCTAGCCAGACCAAGATCTACATAATCCTTGAATTTGTAATGGGA
genomic: TATCCATTATGAAGATTGTCAGGCATCCTAATATAGTTAGATTGCACGAGgtatgtttag ... caaattttagGTTTTGGCTAGCCAGACCAAGATCTACATAATCCTTGAATTTGTAATGGGA
EST: gi|213603671|gb|DB962761.1|DB962761
EST:     TATCCATTATGAAGATTGTCAGGCATCCTAATATAGTTAGATTGCACGAG                         GTTTTGGCTAGCCAGACCAAGATCTACATAATCCTTGAAT
genomic: TATCCATTATGAAGATTGTCAGGCATCCTAATATAGTTAGATTGCACGAGgtatgtttag ... caaattttagGTTTTGGCTAGCCAGACCAAGATCTACATAATCCTTGAAT
EST: gi|209718606|gb|BW674732.1|BW674732
EST:     TATCCATTATGAAGATTGTCAGGCATCCTAATATAGTTAGATTGCACGAG                         GTTTTGGCTAGCCAGACCAAGATCTACATAATCCTTGAATTTGTAATGGGA
genomic: TATCCATTATGAAGATTGTCAGGCATCCTAATATAGTTAGATTGCACGAGgtatgtttag ... caaattttagGTTTTGGCTAGCCAGACCAAGATCTACATAATCCTTGAATTTGTAATGGGA
EST: gi|209698841|gb|BW675769.1|BW675769
EST:     TATCCATTATGAAGATTGTCAGGCATCCTAATATAGTTAGATTGCACGAG                         GTTTTGGCTAGCCAGACCAAGATCTACATAATCC
genomic: TATCCATTATGAAGATTGTCAGGCATCCTAATATAGTTAGATTGCACGAGgtatgtttag ... caaattttagGTTTTGGCTAGCCAGACCAAGATCTACATAATCC
EST: gi|213594834|gb|DB959861.1|DB959861
EST:     TATCCATTATGAAGATTGTCAGGCATCCTAATATAGTTAGATTGCACGAG                         GTTTTGGCTAGCCAGACCAAGATCTACATAATCCTTGAATTTGTA
genomic: TATCCATTATGAAGATTGTCAGGCATCCTAATATAGTTAGATTGCACGAGgtatgtttag ... caaattttagGTTTTGGCTAGCCAGACCAAGATCTACATAATCCTTGAATTTGTA
EST: gi|151394038|gb|EV263909.1|EV263909
EST:     TATCCATTATGAAGATTGTCAGGCATCCTAATATAGTTAGATTGCACGAG                         GTTTTGGCTAGCCAGACCAAGATCTACATAATCCTTGAATTTGTAATGGGA
genomic: TATCCATTATGAAGATTGTCAGGCATCCTAATATAGTTAGATTGCACGAGgtatgtttag ... caaattttagGTTTTGGCTAGCCAGACCAAGATCTACATAATCCTTGAATTTGTAATGGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTAAAAGAGAGATATCCATTATGAAGATTGTCAGGCATCCTAATATAGTTAGATTGCACGAGgtatgtttagatatcctaatatgccaggaattataccatatttctttcttttctatttctcacattgttttcaaattttag

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