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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataataacttctagtgatcacaaaattttcaagttacaactacattgtcattttgaaaattgctgaattgttttctgcattatgtactcttttccatcagGGTTTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGGCGCCATGTGTCATATGACCAAGCCATTGCATGGAAAGTTCTTACTGGGGAAGACA

Basic information

species Glycine max
transcript GLYMA11G20520.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G20520.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv06s0004g02800.t01 (Vitis vinifera), 3'ss of exon 17
-------gtaataataacttctagtgatcacaaaattttcaagttacaactacattgtcattttgaaaattgctgaattgttttctgcattatgtactcttttccatcagGGTTTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGGCGCCATGTGTCATATGACCAAGCCATTGCATGGAAAGTTCTTACTGGGGAAGACA
        |   | |||  | || | || | |     | ||   || || |||||    ||    ||  ||| ||  |   |   ||  ||||      |||   ||||||||||||||||  |||| ||||||||||||||||| || |||||||||||||| |||||||| || ||||| ||||||||||| ||| ||| |||||| |
agaccaaattgaagtaagatata-tcattatatgtcctccagcata-aaatacat--gtatgccaaaccttgatgcctgaatccttggcttat------tttcttatcagGGTTTTGCTTACTTGCCGGCTGGAATCTGCATGTCAACAATGGGGCGCCATGTTTCATATGAACAGGCCATCGCATGGAAAGTCCTTGCTGCGGAAGAGA
















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|7028678|gb|AW458461.1|AW458461
EST:     ATTGTGTACAGACTTTGCCAAGTTAATGCAGCAG                         GGTTTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGGCGCCAT
genomic: ATTGTGTACAGACTTTGCCAAGTTAATGGAGCAGgtaataataa ... tttccatcagGGTTTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGGCGCCAT
EST: gi|254348194|gb|GR851873.1|GR851873
EST:     AGGCTGGACGCAAGGCATTGTGTACAGACTTTGCCAAGTTAATGGAGCAG                         GGTTTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGGCGCCAT
genomic: AGGCTGGACGCAAGGCATTGTGTACAGACTTTGCCAAGTTAATGGAGCAGgtaataataa ... tttccatcagGGTTTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGGCGCCAT
EST: gi|151399697|gb|EV269568.1|EV269568
EST:     AGGCTGGACGCAAGGCATTGTGTACAGACTTTGCCAAGTTAATGGAGCAG                         GGTTTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGGCGCCAT
genomic: AGGCTGGACGCAAGGCATTGTGTACAGACTTTGCCAAGTTAATGGAGCAGgtaataataa ... tttccatcagGGTTTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGGCGCCAT
EST: gi|10252567|gb|BE820333.1|BE820333
EST:     ATTGTGTACAGACTTTGCCAAGTTAATGCAGCAG                         GGTTTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGGCGCCAT
genomic: ATTGTGTACAGACTTTGCCAAGTTAATGGAGCAGgtaataataa ... tttccatcagGGTTTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGGCGCCAT
EST: gi|10232158|gb|BE801046.1|BE801046
EST:     AGGCTGGACGCAAGGCATTGTGTACAGACTTTGCCAAGTTAATGGAGCAG                         GGTTTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGGCGCCAT
genomic: AGGCTGGACGCAAGGCATTGTGTACAGACTTTGCCAAGTTAATGGAGCAGgtaataataa ... tttccatcagGGTTTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGGCGCCAT
EST: gi|31306826|gb|CD392029.1|CD392029
EST:     AGGCTGGACGCAAGGCATTGTGTACAGACTTTGCCAAGTTAATGGAGCAG                         GGTTTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGGCGCCAT
genomic: AGGCTGGACGCAAGGCATTGTGTACAGACTTTGCCAAGTTAATGGAGCAGgtaataataa ... tttccatcagGGTTTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGGCGCCAT
EST: gi|21595122|gb|BQ610375.1|BQ610375
EST:     AGGCTGGACGCAAGGCATTGTGTACAGACTTTGCCAAGTTAATGGAGCAG                         GGTTTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGGCGCCAT
genomic: AGGCTGGACGCAAGGCATTGTGTACAGACTTTGCCAAGTTAATGGAGCAGgtaataataa ... tttccatcagGGTTTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGGCGCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcattttgaaaattgctgaattgttttctgcattatgtactcttttccatcagGGTTTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGGCGCCATGTGTCATATGACCAAGCCATTGCATGGAAAGTTCTTACTGGGGAAGACA
                                       tactcttttccatc  CT-rich tract
     ttttgaaaatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaataataacttctagtgatcacaaaattttcaagttacaactacattgtcattttgaaaattgctgaattgttttctgcattatgtactcttttccatcagGGTTTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGGCGCCATGTGTCATATGACCAAGCCATTGCATGGAAAGTTCTTACTGGGGAAGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA