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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actaatttattggtcttaatgaattaggtatttgtttcttatatataggaactatagtaattttaattttttttaaaaaaaattcttgaattttttctagCTTGATTCCCTGAAGCCAAAGGAGAGCCTAGTGATCAGGCAGAGATATGGACTTGATGGCAAGGGTGACAGAACATTGGGAGAAATTGCTGGGAACTTGA

Basic information

species Glycine max
transcript GLYMA13G08390.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G08390.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv16s0050g02520.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------------------------------------actaatttattggtcttaatgaattaggtatttgtttct-tatatataggaactatagtaattttaattttttttaaaaaaaattcttgaattttttc---tagCTTGATTCCCTGAAGCCAAAGGAGAGCCTAGTGATCAGGCAGAGATATGGACTTGATGGCAAGGGTGACAGAACATTGGGAGAAATTGCTGGGAACTTGA
                                                           | | |  | |  |  |||| || |     ||| | | | | |  ||   | || |  | |    ||||   |    ||  | ||||| || | |||     |||| ||||| |||||||||||||||||| | ||||| || ||||||||||| |||||||| ||||||||  | ||| |||| || ||||| || ||| | |
gtaattcttcgcctccttcaactagagtcgaaccatatagtccctataatgatgggtttccattcgaattctactaataaacttaccctttttgtttgtctgaattccatctttgttcaaacaaattagctaatgaactatttcttaaactcttttatgcagCTCGATTCTCTGAAGCCAAAGGAGAGCTTGGTGATGAGACAGAGATATGGTCTTGATGGTAAGGGTGATCGGACACTGGGGGAGATTGCAGGAAACCTAA
















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|14258518|gb|BG881426.1|BG881426
EST:     GTGATAATAGGAGGCAACTTGCTGTTCTAAGACTTGCTCTTGATGATGTG                         CTTGATTCCCTGAAGCCAAAAGAGAGCCTAGTGATCAGGCAGAGATATGGA
genomic: GTGATAATAGGAGGCAACTTGCTGTTCTAAGACTTGCTCTTGATGATGTGgtaattactc ... ttttttctagCTTGATTCCCTGAAGCCAAAGGAGAGCCTAGTGATCAGGCAGAGATATGGA
EST: gi|192319336|gb|FK009878.1|FK009878
EST:     GTGATAATAGGAGGCAACTTGCTGTTCTAAGACTTGCTCTTGATGATGTG                         CTTGATTCCCTGAAGCCAAAGGACAGCCTAGTGATCAGGCAGAGATATGGA
genomic: GTGATAATAGGAGGCAACTTGCTGTTCTAAGACTTGCTCTTGATGATGTGgtaattactc ... ttttttctagCTTGATTCCCTGAAGCCAAAGGAGAGCCTAGTGATCAGGCAGAGATATGGA
EST: gi|7693160|gb|AW761257.1|AW761257
EST:     GTGATAATANGAGGCAACTTGCTGTTCTAAGACTTGCTCTTGATGATGTG                         CTTGATTCCCTGAAGCCAAAAGAGAGCCTAGTGATCAGGCAGAGATATGGA
genomic: GTGATAATAGGAGGCAACTTGCTGTTCTAAGACTTGCTCTTGATGATGTGgtaattactc ... ttttttctagCTTGATTCCCTGAAGCCAAAGGAGAGCCTAGTGATCAGGCAGAGATATGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taggaactatagtaattttaattttttttaaaaaaaattcttgaattttttctagCTTGATTCCCTGAAGCCAAAGGAGAGCCTAGTGATCAGGCAGAGATATGGACTTGATGGCAAGGGTGACAGAACATTGGGAGAAATTGCTGGGAACTTGA
               ttttaat  putative branch site (score: 3)
                                             ttttttct  putative PPT
            taattttaattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actaatttattggtcttaatgaattaggtatttgtttcttatatataggaactatagtaattttaattttttttaaaaaaaattcttgaattttttctagCTTGATTCCCTGAAGCCAAAGGAGAGCCTAGTGATCAGGCAGAGATATGGACTTGATGGCAAGGGTGACAGAACATTGGGAGAAATTGCTGGGAACTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa