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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCGGCGTTGGAGCTGACGGAGTTATCTTTGTATTGCCTGGCATCAATGGCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAGgtagttcttcttacgaactgttattcctgcatgcttttgattgattggacttgggccctgtttggataaatctctctataagtagttacaagaaaagaaa...

Basic information

species Glycine max
transcript GLYMA19G35780.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G35780.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv08s0040g02540.t01 (Vitis vinifera), 5'ss of exon 2
CTTCGGCGTTGGAGCTGACGGAGTTATCTTTGTATTGCCTGGCATCAATGGCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAGgtagttcttcttacgaactgttattcctgcatgcttttgattgattggacttgggccctgtttggataaatctctctataagt---agttacaagaaaagaaa------
||| ||  |||| |||||||| || ||||| |   |||| || ||||||||||| |||||||| ||||||||||| || |||||||| ||||||||||||||| ||      |  || |   |  | | |||| |||   |||| ||||        |||||||  | | |  | ||  || |   || || ||     ||||      
CTTTGGGATTGGTGCTGACGGTGTGATCTTCGCCATGCCGGGGATCAATGGCACTGATTATACAATGAGGATTTTCAATTCTGATGGCAGTGAGCCTGAGgtaatt------aacaatttcca--cgtacatgttttctgttgagtggatcgtcagtctgtttgt-tgagtagccctgaaaatttgagctaaaaatgtggaaagtaatt
















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|192307888|gb|FG999367.1|FG999367
EST:     GCACCGATTATACCATGAGGATTTTTAACTCTGATAGTAGTGAGCCTGAG                         ATGTGTGGCAATGGAGTTCGATGCTTTGCCAAATTTGTTTCTCAGCTTGAG
genomic: GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAGgtagttcttc ... ttcttcatagATGTGTGGCAATGGAGTTCGATGCTTTGCCAAATTTGTTTCTCAGCTTGAG
EST: gi|6951840|gb|AW423908.1|AW423908
EST:     TTAACTCTGATGGTAGTGAGCCTGAG                         ATGTGTGGCAATGGAGTTCGATGCTTTGCCAAATTTGTTTCTCAGCTTGAG
genomic: TTAACTCTGATGGTAGTGAGCCTGAGgtagttcttc ... ttcttcatagATGTGTGGCAATGGAGTTCGATGCTTTGCCAAATTTGTTTCTCAGCTTGAG
EST: gi|12774729|gb|BG239656.1|BG239656
EST:     GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAG                         ATGTGTGGCAATGGAGTTCGATGCTTTGCCAAATTT
genomic: GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAGgtagttcttc ... ttcttcatagATGTGTGGCAATGGAGTTCGATGCTTTGCCAAATTT
EST: gi|8827787|gb|BE211517.1|BE211517
EST:     GCACCGATTATACCATGAGGATTATTAACTCTGATGGTAGTGAGCCTGAG                         ATGTGTGGCAATGGAGTTCGATGCTTTGCCCAAATT-GTATCTTAGCTTGA
genomic: GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAGgtagttcttc ... ttcttcatagATGTGTGGCAATGGAGTTCGATGCTTTGCC-AAATTTGTTTCTCAGCTTGA
EST: gi|213600981|gb|DB968861.1|DB968861
EST:     GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAG                         ATGTGTGGCAATGGAGTTCGATGCTTTGCCAAATTTGTTTCTCAGCTTGAG
genomic: GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAGgtagttcttc ... ttcttcatagATGTGTGGCAATGGAGTTCGATGCTTTGCCAAATTTGTTTCTCAGCTTGAG
EST: gi|21888052|gb|BQ741265.1|BQ741265
EST:     GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAG                         ATGTGTGGCAATGGAGTT
genomic: GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAGgtagttcttc ... ttcttcatagATGTGTGGCAATGGAGTT
EST: gi|18039712|gb|BM308006.1|BM308006
EST:     GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAG                         ATGTGTGGCAATGGAGTTCGATGCTTTGCCAAATTTGTTTCTCAGCTTGAG
genomic: GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAGgtagttcttc ... ttcttcatagATGTGTGGCAATGGAGTTCGATGCTTTGCCAAATTTGTTTCTCAGCTTGAG
EST: gi|151406971|gb|EV276786.1|EV276786
EST:     GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAG                         ATGTGTGGCAATGGAGTTCGATGCTTTGCCAAATTTGTTTCTCAGCTTGAG
genomic: GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAGgtagttcttc ... ttcttcatagATGTGTGGCAATGGAGTTCGATGCTTTGCCAAATTTGTTTCTCAGCTTGAG
EST: gi|9258643|gb|BE346790.1|BE346790
EST:     GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAG                         ATGTGTGGCAATGGAGTTCGATGCTTTGCCAAATTTGTTTCTCAGCTTGAG
genomic: GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAGgtagttcttc ... ttcttcatagATGTGTGGCAATGGAGTTCGATGCTTTGCCAAATTTGTTTCTCAGCTTGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCGGCGTTGGAGCTGACGGAGTTATCTTTGTATTGCCTGGCATCAATGGCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAGgtagttcttcttacgaactgttattcctgcatgcttttgattgattggacttgggccctgtttggataaatctctctataagtagttacaagaaaagaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaagaa