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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGTTGCCTGTAAAGATTGTTTTTCCTAGAAATTTGTTGGGTGGTGTTGTTCCTGGAGAGAATGCGACAGACTTCATGATGCTTGGTTTAGGAGACATGgtatgacattcttactctctaagatctcttactgtatgagaacatgtccttaactgtttccaagttttagattgtcttttcatttggttactttcatatg...

Basic information

species Glycine max
transcript GLYMA20G29950.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G29950.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv16s0050g00580.t01 (Vitis vinifera), 5'ss of exon 3
AGAGTTGCCTGTAAAGATTGTTTTTCCTAGAAATTTGTTGGGTGGTGTTGTTCCTGGAGAGAATGCGACAGACTTCATGATGCTTGGTTTAGGAGACATGgtatgacattcttactct-ctaagatctcttactgtatgagaacatgtccttaactgtttccaagttttagattgtcttttcatttggttactttcatatg
 |||||||| || ||||| ||||||||||| || ||||| || || ||||||||||| |  ||| |  | |||||||||||||||||| | || |||||||||||| ||| ||  ||| | | ||| |        |||     ||     |  |||||      | |||  |||    || |  ||||  | || | || 
GGAGTTGCCGGTGAAGATCGTTTTTCCTAGGAACTTGTTTGGAGGAGTTGTTCCTGGCGGTAATTCTGCGGACTTCATGATGCTTGGTCTTGGTGACATGgtatgaaattttttttcttccatgatttaacttaccatgcacttatcctggttgctgttattttttgttactttgaaaattgaggtggt-gcattgaaatt
















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|192321496|gb|FK012874.1|FK012874
EST:     GATGCTTGGTTTAGGAGACATG                         GCTATCCCAGGCATGCTACTGGCTTTAGTCCTCTGCTTTGATTATCGCAAG
genomic: GATGCTTGGTTTAGGAGACATGgtatgacatt ... tcttttgtagGCTATCCCAGGCATGCTACTGGCTTTAGTCCTCTGCTTTGATTATCGCAAG
EST: gi|16343545|gb|BI969140.1|BI969140
EST:     TTCCTGGAGAGAATGCGACAGACTTCATGATGCTTGGTTTAGGAGACATG                         GCTATCCCAGGCATGCTACTGGCTTTAGTCCTCTGCTTTGATTATCGCAAG
genomic: TTCCTGGAGAGAATGCGACAGACTTCATGATGCTTGGTTTAGGAGACATGgtatgacatt ... tcttttgtagGCTATCCCAGGCATGCTACTGGCTTTAGTCCTCTGCTTTGATTATCGCAAG
EST: gi|192321497|gb|FK012875.1|FK012875
EST:     TTCCTGGAGAGA-TGCGACAGACTTCATGATGCTTGGTTTAG-AGACATG                         GCTATCC-AGGCATGCTACTGGCTTTAGTC-TCTGCTTTGAT
genomic: TTCCTGGAGAGAATGCGACAGACTTCATGATGCTTGGTTTAGGAGACATGgtatgacatt ... tcttttgtagGCTATCCCAGGCATGCTACTGGCTTTAGTCCTCTGCTTTGAT
EST: gi|209715393|gb|BW684691.1|BW684691
EST:     TTCCTGGAGAGAATGCGACAGACTTCATGATGCTTGGTNTAGGAGACATG                         GCTATCCCAGGCATGCTACTGGCTTTAGTCCTCTGCTTTGATTATCGCAAG
genomic: TTCCTGGAGAGAATGCGACAGACTTCATGATGCTTGGTTTAGGAGACATGgtatgacatt ... tcttttgtagGCTATCCCAGGCATGCTACTGGCTTTAGTCCTCTGCTTTGATTATCGCAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGTTGCCTGTAAAGATTGTTTTTCCTAGAAATTTGTTGGGTGGTGTTGTTCCTGGAGAGAATGCGACAGACTTCATGATGCTTGGTTTAGGAGACATGgtatgacattcttactctctaagatctcttactgtatgagaacatgtccttaactgtttccaagttttagattgtcttttcatttggttactttcatatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA