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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctgttatatcactactttgatagacacccccatatcaatttcaaagattctgaacctatttctgtgataactgaaactttgtttgcactggcatccagATTGTGAAACATCATAAACAAGAAATTGGACTTCAAAGGCGAGTTTTTGTTGATTTCTTCTGCAATCCTGAGCGATTAAGGAGCCAAGTTAGGGATCTGA

Basic information

species Glycine max
transcript GLYMA17G15510.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G15510.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv00s0333g00070.t01 (Vitis vinifera), 3'ss of exon 13
-ttctgttatatcactactttgatagacacccccatatcaatttcaaagattctgaacctatttctgtgataactgaaactttgtttgcactggcatccagATTGTGAAACATCATAAACAAGAAATTGGACTTCAAAGGCGAGTTTTTGTTGATTTCTTCTGCAATCCTGAGCGATTAAGGAGCCAAGTTAGGGATCTGA
 | | |    || | | |  | || |         |||  |  |   |     |  |||  |   | |   | ||   |  |   || |  |      |||||||| |||||||||  ||| ||| | || ||||| ||||| ||||||||||||||||||||||||||||| ||  | |||| ||||||||| ||  |||
atacggcctcataattgcggtcattgttgttggt-tattgaagttggattcattctaccattgcatatacaagctctcatctgaatttctttttggaacagATTGTAAAACATCATTCACAGGAAGTGGGGCTTCAGAGGCGGGTTTTTGTTGATTTCTTCTGCAATCCTGAACGTCTGAGGAACCAAGTTAGAGAATTGA
















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|57574285|gb|CX547260.1|CX547260
EST:     TGTCTGTTGCTGTTGAAGAGGTGACACTAGAGCATGTAAAGAAGAATGAG                         ATTGTGAAACATCATAAACAAGAAATTGGACTTCAAAGGCGAGTTTTTGTT
genomic: TGTCTGTTGCTGTTGAAGAGGTGACACTAGAGCATGTAAAGAAGAATGAGgtaatgtaac ... tggcatccagATTGTGAAACATCATAAACAAGAAATTGGACTTCAAAGGCGAGTTTTTGTT
EST: gi|214010096|gb|DB989468.1|DB989468
EST:     CT-TAGGTGCTGATGAAGAGTTTACACTAGAGCATGTAAAGAAGAATGAG                         ATTGTGAAACATCATAAACGAGAAATTGGACTTCAAAGGCGAGTTTTTGTT
genomic: GTCT-GTTGCTGTTGAAGAGGTGACACTAGAGCATGTAAAGAAGAATGAGgtaatgtaac ... tggcatccagATTGTGAAACATCATAAACAAGAAATTGGACTTCAAAGGCGAGTTTTTGTT
EST: gi|213605084|gb|DB982348.1|DB982348
EST:     TAGAGCATGTAAAGAAGAATGAG                         ATAGTGAAACATCATAAACAAGAAATTGGACTTCAAAGGCGAGTTTTTGTT
genomic: TAGAGCATGTAAAGAAGAATGAGgtaatgtaac ... tggcatccagATTGTGAAACATCATAAACAAGAAATTGGACTTCAAAGGCGAGTTTTTG-T
EST: gi|58014978|gb|CX701720.1|CX701720
EST:     TGTCTGTTGCTGTTGAAGAGGTGACACTAGAGCATGTAAAGAAGAATGAG                         ATTGTGAAACATCATAAACAAGAAATTGGACTTCAAAGGCGAGTTTTTGTT
genomic: TGTCTGTTGCTGTTGAAGAGGTGACACTAGAGCATGTAAAGAAGAATGAGgtaatgtaac ... tggcatccagATTGTGAAACATCATAAACAAGAAATTGGACTTCAAAGGCGAGTTTTTGTT
EST: gi|214006531|gb|DB986338.1|DB986338
EST:     ACACTAGAGCATGTAAAGAAGAATGAG                         ATTGTGAAACATCATAAACAAGAAATAGGACTTCAAAGGCGAGTTTTTGTT
genomic: ACACTAGAGCATGTAAAGAAGAATGAGgtaatgtaac ... tggcatccagATTGTGAAACATCATAAACAAGAAATTGGACTTCAAAGGCGAGTTTTTGTT
EST: gi|209729309|gb|BW660355.1|BW660355
EST:     TGTCTGTTGCTGTTGAAGAGGTGACACTAGAGCATGTAAAGAAGAATGAG                         ATTGTGAAACATCATAAACAAGAAATTGGACTTCAAAGGCGAGTTTTTGTT
genomic: TGTCTGTTGCTGTTGAAGAGGTGACACTAGAGCATGTAAAGAAGAATGAGgtaatgtaac ... tggcatccagATTGTGAAACATCATAAACAAGAAATTGGACTTCAAAGGCGAGTTTTTGTT
EST: gi|22933194|gb|BU550333.1|BU550333
EST:     TGTCTGTTGCTGTTGAAGAGGTGACACTAGAGCATGTAAAGAAGAATGAG                         ATTGTGAAACATCATAAACAAGAAATTGGACTTCAAAGGCGAGTTTTTGTT
genomic: TGTCTGTTGCTGTTGAAGAGGTGACACTAGAGCATGTAAAGAAGAATGAGgtaatgtaac ... tggcatccagATTGTGAAACATCATAAACAAGAAATTGGACTTCAAAGGCGAGTTTTTGTT
EST: gi|15815108|gb|BI787383.1|BI787383
EST:     TGTCTGTTGCTGTTGAAGAGGTGACACTAGAGCATGTAAAGAAGAATGAG                         ATTGTGAAACATCATAAACAAGAAATTGGACTTCAAAGGCGAGTTTTTGTT
genomic: TGTCTGTTGCTGTTGAAGAGGTGACACTAGAGCATGTAAAGAAGAATGAGgtaatgtaac ... tggcatccagATTGTGAAACATCATAAACAAGAAATTGGACTTCAAAGGCGAGTTTTTGTT
EST: gi|17401211|gb|BM177993.1|BM177993
EST:     TGTCTGTTGCTGTTGAAGAGGTGACACTAGAGCATGTAAAGAAGAATGAG                         ATTGTGAAACATCATAAACAAGAAATTGGACTTCAAAGGCGAGTTTTTGTT
genomic: TGTCTGTTGCTGTTGAAGAGGTGACACTAGAGCATGTAAAGAAGAATGAGgtaatgtaac ... tggcatccagATTGTGAAACATCATAAACAAGAAATTGGACTTCAAAGGCGAGTTTTTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagattctgaacctatttctgtgataactgaaactttgtttgcactggcatccagATTGTGAAACATCATAAACAAGAAATTGGACTTCAAAGGCGAGTTTTTGTTGATTTCTTCTGCAATCCTGAGCGATTAAGGAGCCAAGTTAGGGATCTGA
                     tgataac  putative branch site (score: 2)
             tatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctgttatatcactactttgatagacacccccatatcaatttcaaagattctgaacctatttctgtgataactgaaactttgtttgcactggcatccagATTGTGAAACATCATAAACAAGAAATTGGACTTCAAAGGCGAGTTTTTGTTGATTTCTTCTGCAATCCTGAGCGATTAAGGAGCCAAGTTAGGGATCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
ttctgtt
- - - - - - - - - - - - - caccccc
- - - - - - - - - - - - - - - - - - - - - - - -gattctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgc