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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatgaatttgatttcatttttttgtgttgatcatgtgtattaggttcataaatttcgtcctttgtaacgatttccctttactgcagCGAATGATGACTGAGAGTCCAGAAAAATATCAACACATGCTTCAGAATCTTCTTTTTAAAGCTCAGCAG

Basic information

species Glycine max
transcript GLYMA10G43560.2
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G43560.2 (Glycine max), 3'ss of exon 15
lower sequence: Vv13s0019g00680.t01 (Vitis vinifera), 3'ss of exon 15
gcatgaatttgatttcatttttttgt---------gttgatcatgtgtattaggttca----taaatttcgtcctttgtaacg-atttccctttactgcagCGAATGATGACTGAGAGTCCAGAAAAATATCAACACATGCTTCAGAATCTTCTTTTTAAAGCTCAGCAG
||| |||    |||   | ||              ||||    ||| |||   |||      ||  ||| |     ||    | | ||     |  ||||| |||||||||| ||    || || ||||||||||  ||||||||||||||  |||||| ||||||||||
gcaagaacactattctttcttcccactgcaccaaggttgcaactgtttatccagtttgatgttagtttttgcaaactgacctggagtttggcattttgcagAGAATGATGACAGAAGAACCTGAGAAATATCAACGAATGCTTCAGAATCTCATTTTTAGAGCTCAGCAG
















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|22525503|gb|BU084314.1|BU084314
EST:     ATGACAGAGATTCAAGGGTGGCATATTATTCTTCTGCATTTCTTCTGAAG                         CGAATGATGACTGAGAGTCCAGAAAAATATCAACACATGCTTCAGAATCTT
genomic: ATGACAGAGATTCAAGGGTGGCATATTATTCTTCTGCATTTCTTCTGAAGgcatgaattt ... tttactgcagCGAATGATGACTGAGAGTCCAGAAAAATATCAACACATGCTTCAGAATCTT
EST: gi|4300184|gb|AI443011.1|AI443011
EST:     ATGACAGAGATTCAAGGGTGGCATATTATTCTTCTGCATTTCTTCTGAAG                         CGAATGATGACTGAGAGTCCAGAAAAATATCAACACATGCTTCAGAATCTT
genomic: ATGACAGAGATTCAAGGGTGGCATATTATTCTTCTGCATTTCTTCTGAAGgcatgaattt ... tttactgcagCGAATGATGACTGAGAGTCCAGAAAAATATCAACACATGCTTCAGAATCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgtgtattaggttcataaatttcgtcctttgtaacgatttccctttactgcagCGAATGATGACTGAGAGTCCAGAAAAATATCAACACATGCTTCAGAATCTTCTTTTTAAAGCTCAGCAG
                              ttgtaac  putative branch site (score: 2)
                                       tttccctttactgc  putative PPT
             ttcataaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgaatttgatttcatttttttgtgttgatcatgtgtattaggttcataaatttcgtcctttgtaacgatttccctttactgcagCGAATGATGACTGAGAGTCCAGAAAAATATCAACACATGCTTCAGAATCTTCTTTTTAAAGCTCAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA