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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatttcttggattatttttttatagttgtttgtttcccttttttttttattatttttcttaaagcaactgtttccaacatttgccttctttgtttgcagGGATTCTTACCACCAGATGAAGTTCATATTTTTGGCTATGCAAGGACAAAAATCTCTGATGATGAATTGAGAAACCGGTTGCGCGG

Basic information

species Glycine max
transcript GLYMA16G06850.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G06850.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G27300.2 (Arabidopsis thaliana), 3'ss of exon 3
aaatttcttggattatttttttatagttgtt-tgtttcccttttttttttattatttttcttaaagcaactgtttccaacatttgccttctttgtttgcagGGATTCTTACCACCAGATGAAGTTCATATTTTTGGCTATGCAAGGACAAAAATCTCTGATGATGAATTGAGAAACCGGTTGCGCGG
   ||| ||  |  |       ||  || || | |||   | ||||   | | | || | || |   |  || |      ||| |  ||   ||    ||||||||  |    ||||||||||||||||| ||||| ||||||||||  || ||  ||||||| ||  | ||| |     | |||||
--gtttttttaaacaaacaagaatcttttttatcttttattgttttcaatgtcacttgtttttatttatttgatgtgtttattggttttacatgagcacagGGATTTCTTAATCCAGATGAAGTTCATATATTTGGATATGCAAGGAGTAAGATTACTGATGAGGAGCTTAGAGATAAAATCCGCGG

upper sequence: GLYMA16G06850.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 2
aaatttcttggattatttttttatagttgtttgtttcccttttttttttattatttttcttaaagcaactgtttccaacattt--gccttctttgtttg-cagGGATTCTTACCACCAGATGAAGTTCATATTTTTGGCTATGCAAGGACAAAAATCTCTGATGATGAATTGAGAAACCGGTTGCGCGG
            ||  ||   |||    | | ||     | ||    | | |  | |  ||||      |  ||      |||  |  || | || | | ||||||||  |    |||||||||||||||||||| || ||||| ||||| || || |||||||| ||  ||||| |  || | || ||
-----------gtttgttccatatcagagctggtgcatgtgttagaatcaatcctctggttaattgtgttagttatggtttttttggtttgtatgatggtcagGGATTTCTCAATCCAGATGAAGTTCATATTTTCGGGTATGCGAGGACTAAGATTTCTGATGAAGAGCTGAGAGATAGGATTCGTGG
















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|21637841|gb|BM107996.1|BM107996
EST:     TCTTGCTAAGAAAGAAGACATTTCCTGCACTTTTCCACCTATACCTGCAG                         GGATTCTTACCACCAGATGAAGTTCATATTTTTGGCTATGCAAGGACAAAA
genomic: TCTTGCTAAG-AAGAAGACATTTCCTGCACTTTTCCACCTATACCTGCAGgtaaagcaga ... ttgtttgcagGGATTCTTACCACCAGATGAAGTTCATATTTTTGGCTATGCAAGGACAAAA
EST: gi|213607767|gb|DB959106.1|DB959106
EST:     ATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCACCTATACCTGCAG                         GGATTCTTACCACCAGATGAAGTTCATATTTTTGGCTATGCAAGGACAAAA
genomic: ATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCACCTATACCTGCAGgtaaagcaga ... ttgtttgcagGGATTCTTACCACCAGATGAAGTTCATATTTTTGGCTATGCAAGGACAAAA
EST: gi|213608230|gb|DB970827.1|DB970827
EST:     ATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCACCTATACCTGCAG                         GGATTCTTACCACCAGATGAAGTTCATATTTTTGGCTATGCAAGGACAAAA
genomic: ATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCACCTATACCTGCAGgtaaagcaga ... ttgtttgcagGGATTCTTACCACCAGATGAAGTTCATATTTTTGGCTATGCAAGGACAAAA
EST: gi|19453077|gb|BM954487.1|BM954487
EST:     ATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCACCTATACCTGCAG                         GGATTCTTACCACCAGATGAAGTTCATATTTTTGGCTATGCAAGGACAAAA
genomic: ATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCACCTATACCTGCAGgtaaagcaga ... ttgtttgcagGGATTCTTACCACCAGATGAAGTTCATATTTTTGGCTATGCAAGGACAAAA
EST: gi|19268946|gb|BM885202.1|BM885202
EST:     ATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCACCTATACCTGCAG                         GGATTCTTACCACCAGATGAAGTTCATATTTTTGGCTATGCAAGGACAAAA
genomic: ATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCACCTATACCTGCAGgtaaagcaga ... ttgtttgcagGGATTCTTACCACCAGATGAAGTTCATATTTTTGGCTATGCAAGGACAAAA
EST: gi|9986040|gb|BE660148.1|BE660148
EST:     ATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCACCTATACCTGCAG                         GGATTCTTACCACCAGATGAAGTTCATATTTTTGGCTATGCAAGGACAAAA
genomic: ATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCACCTATACCTGCAGgtaaagcaga ... ttgtttgcagGGATTCTTACCACCAGATGAAGTTCATATTTTTGGCTATGCAAGGACAAAA
EST: gi|37995559|gb|CF807148.1|CF807148
EST:     ATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCACCTATACCTGCAG                         GGATTCTTACCACCAGATGAAGTTCATATTTTTGGCTATGCAAGGACAAAA
genomic: ATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCACCTATACCTGCAGgtaaagcaga ... ttgtttgcagGGATTCTTACCACCAGATGAAGTTCATATTTTTGGCTATGCAAGGACAAAA
EST: gi|15663680|gb|BI701051.1|BI701051
EST:     ATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCACCTATACCTGCAG                         GGATTCTTACCACCAGATGAAGTTCATATTTTTGGCTATGCAAGGACAAAA
genomic: ATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCACCTATACCTGCAGgtaaagcaga ... ttgtttgcagGGATTCTTACCACCAGATGAAGTTCATATTTTTGGCTATGCAAGGACAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttattatttttcttaaagcaactgtttccaacatttgccttctttgtttgcagGGATTCTTACCACCAGATGAAGTTCATATTTTTGGCTATGCAAGGACAAAAATCTCTGATGATGAATTGAGAAACCGGTTGCGCGG
                                   tttgccttctttgttt  CT-rich tract
     ttatttttcttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatttcttggattatttttttatagttgtttgtttcccttttttttttattatttttcttaaagcaactgtttccaacatttgccttctttgtttgcagGGATTCTTACCACCAGATGAAGTTCATATTTTTGGCTATGCAAGGACAAAAATCTCTGATGATGAATTGAGAAACCGGTTGCGCGG

- - - - - - - - - - - - - - - - gtttccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcaactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gccttct