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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgataatttctagtgatcacaaagttttcaagttacaactacattctcattttgaaaagggctgaatttttttctgcattgtgtattcttccatcagGGATTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGACGCCATGTGTCATATGACCAAGCCATCGCATGGAAAGTGCTTACTGGAGAAGACA

Basic information

species Glycine max
transcript GLYMA12G08080.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv06s0004g02800.t01 (Vitis vinifera), 3'ss of exon 17
gtgataatttctagtgatcacaaagttttcaagt--tacaactacattctcattttgaaaagggctgaatttttttctgcattgtgtattcttccatcagGGATTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGACGCCATGTGTCATATGACCAAGCCATCGCATGGAAAGTGCTTACTGGAGAAGACA
     || ||  ||| |     |   ||  | ||  | || |   |    ||| |     |   ||  ||   |   | | | |  |||| |   ||||||| ||||||||  |||| ||||||||||||||||| || ||||| |||||||| |||||||| || ||||||||||||||||| ||| |||  ||||| |
agaccaaattgaagtaagatatatcattatatgtcctccagcataaaatacatgtatgccaaaccttgatgcctgaatccttggcttattttcttatcagGGTTTTGCTTACTTGCCGGCTGGAATCTGCATGTCAACAATGGGGCGCCATGTTTCATATGAACAGGCCATCGCATGGAAAGTCCTTGCTGCGGAAGAGA
















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|151412482|gb|EV282294.1|EV282294
EST:     AGGCTGGACGCAAGGCATTGTGTACAGACTTTGCCAAGTTAATGGAGCAG                         GGATTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGACGCCAT
genomic: AGGCTGGACGCAAGGCATTGTGTACAGACTTTGCCAAGTTAATGGAGCAGgtgataattt ... cttccatcagGGATTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGACGCCAT
EST: gi|15201671|gb|BI424995.1|BI424995
EST:     AGGCTGGACGCAAGGCATTGTGTACAGACTTTGCCAAGTTAATGGAGCAG                         GGATTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGACGCCAT
genomic: AGGCTGGACGCAAGGCATTGTGTACAGACTTTGCCAAGTTAATGGAGCAGgtgataattt ... cttccatcagGGATTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGACGCCAT
EST: gi|209726555|gb|BW662869.1|BW662869
EST:     AGGCTGGACGCAAGGCATTGTGTACAGACTTTGCCAAGTTAATGGAGCAG                         GGATTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGACGCCAT
genomic: AGGCTGGACGCAAGGCATTGTGTACAGACTTTGCCAAGTTAATGGAGCAGgtgataattt ... cttccatcagGGATTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGACGCCAT
EST: gi|16343673|gb|BI969268.1|BI969268
EST:     AGGCTGGACGCAAGGCATTGTGTACAGACTTTGCCAAGTTAATGGAGCAG                         GGATTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGACGCCAT
genomic: AGGCTGGACGCAAGGCATTGTGTACAGACTTTGCCAAGTTAATGGAGCAGgtgataattt ... cttccatcagGGATTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGACGCCAT
EST: gi|31463153|gb|CD405181.1|CD405181
EST:     AGGCTGGACGCAAGGCATTGTGTACAGACTTTGCCAAGTTAATGGAGCAG                         GGATTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGACGCCAT
genomic: AGGCTGGACGCAAGGCATTGTGTACAGACTTTGCCAAGTTAATGGAGCAGgtgataattt ... cttccatcagGGATTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGACGCCAT
EST: gi|51342397|gb|CO983472.1|CO983472
EST:     AGGCTGGACGCAAGGCATTGTGTACAGACTTTGCCAAGTTAATGGAGCAG                         GGATTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGACGCCAT
genomic: AGGCTGGACGCAAGGCATTGTGTACAGACTTTGCCAAGTTAATGGAGCAGgtgataattt ... cttccatcagGGATTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGACGCCAT
EST: gi|209705017|gb|BW667715.1|BW667715
EST:     GCCAAGTTAATGGAGCAG                         GGATTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGACGCCAT
genomic: GCCAAGTTAATGGAGCAGgtgataattt ... cttccatcagGGATTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGACGCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctcattttgaaaagggctgaatttttttctgcattgtgtattcttccatcagGGATTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGACGCCATGTGTCATATGACCAAGCCATCGCATGGAAAGTGCTTACTGGAGAAGACA
                                           ttcttccatc  CT-rich tract
                    tgaattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgataatttctagtgatcacaaagttttcaagttacaactacattctcattttgaaaagggctgaatttttttctgcattgtgtattcttccatcagGGATTTGCTTATCTGCCAGCTGGAATCTGCATGTCGACGATGGGACGCCATGTGTCATATGACCAAGCCATCGCATGGAAAGTGCTTACTGGAGAAGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA