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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcattctggataatgcgtttggaaacatcaatttctctttactctcattcttgttatccatgggaccagATAGGTACAGATATTGAAGATTTCAAGTGCTCTTGGTTAGTTGTGAAAGCCTTGGAACTTAGTAATGAACAACAAAAGAAAGTTCTACAC

Basic information

species Glycine max
transcript GLYMA15G12780.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G12780.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G47770.1 (Arabidopsis thaliana), 3'ss of exon 9
-----------gtgagcattctggataatgcgtttggaaacatcaatttctctttactct-cattcttgttatccatgggaccagATAGGTACAGATATTGAAGATTTCAAGTGCTCTTGGTTAGTTGTGAAAGCCTTGGAACTTAGTAATGAACAACAAAAGAAAGTTCTACAC
           |  | || | ||| |  |  |  ||     |     ||| |||   ||  |||  | ||| |  ||    | ||||||| |||||||| ||||||||||| ||||| ||||| || || || || || || |   | |  ||| ||||||  ||  |  || | 
gtttcactcgtgctaacact-tggtttctcaggctgatgtgaatgtattcacttggttcagcatattggttttttataatgc-agATAGGAACAGATATAGAAGATTTCAAATGCTCGTGGTTGGTGGTTAAGGCATTAGAGCGCTGCAGCGAAGAACAAACTAAGATATTATAT

upper sequence: GLYMA15G12780.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv19s0015g01010.t01 (Vitis vinifera), 3'ss of exon 9
----------------------------------------gtgagcattctggataatgcgtttggaaaca--tcaatttctctttac---tctcattcttgttatccatgggaccagATAGGTACAGATATTGAAGATTTCAAGTGCTCTTGGTTAGTTGTGAAAGCCTTGGAACTTAGTAATGAACAACAAAAGAAAGTTCTACAC
                                        || |   |  |  || ||   | |  || ||  |  |        ||    ||| | | ||    | ||||  ||||||| || || |||||||||||||| |||||||||||||| |||||||||||  | ||  || |||||||  |||| || |||    || | 
gtaagtttcagggttactacactcatttggtttgtggaatgtaattgtatta-atcatcaatatataaccagtttgagcaaagaatatggatcttagtgttacctttcatgctaccagATCGGAACGGATATTGAAGATTTTAAGTGCTCTTGGTTGGTTGTGAAAGCACTAGAGATTTGTAATGAGGAACAGAAAAAAACCTTATAT
















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|7233280|gb|AW568628.1|AW568628
EST:     GATGATTATTTGGATTGTTTTGGTGATCCTCANACAATTGGANAG                         ATAGGTACAGATATTGAAGAT
genomic: GATGATTATTTGGATTGTTTTGGTGATCCTCAAACAATTGGAAAGgtgagcattc ... atgggaccagATAGGTACAGATATTGAAGAT
EST: gi|7926518|gb|AW832544.1|AW832544
EST:     GATGATTATTTGGATTGTTTTGGTGATCCTCAAACAATTGGAAAG                         ATAGGTACAGATATTGAAGATTTCAAGTGCTCTTGGTTAGTTGTGAAAGCC
genomic: GATGATTATTTGGATTGTTTTGGTGATCCTCAAACAATTGGAAAGgtgagcattc ... atgggaccagATAGGTACAGATATTGAAGATTTCAAGTGCTCTTGGTTAGTTGTGAAAGCC
EST: gi|9565120|gb|BE474629.1|BE474629
EST:     GATGATTATTTGGATTGTTNTGGTGATCCTCAAACAATTGGAAAG                         ATAGGTACAGATATTGAAGATTTCAAGTGCTCTTGGTTAGTTGTGAAAGCC
genomic: GATGATTATTTGGATTGTTTTGGTGATCCTCAAACAATTGGAAAGgtgagcattc ... atgggaccagATAGGTACAGATATTGAAGATTTCAAGTGCTCTTGGTTAGTTGTGAAAGCC
EST: gi|193615774|gb|FK561987.1|FK561987
EST:     GATGATTATTTGGATTGTTTTGGTGATCCTCAAACAATTGGAAAG                         ATAGGTACAGATATTGAAGATTTCAAGTGCTCTTGGTTAGTTGTGAAAG
genomic: GATGATTATTTGGATTGTTTTGGTGATCCTCAAACAATTGGAAAGgtgagcattc ... atgggaccagATAGGTACAGATATTGAAGATTTCAAGTGCTCTTGGTTAGTTGTGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgtttggaaacatcaatttctctttactctcattcttgttatccatgggaccagATAGGTACAGATATTGAAGATTTCAAGTGCTCTTGGTTAGTTGTGAAAGCCTTGGAACTTAGTAATGAACAACAAAAGAAAGTTCTACAC
            atcaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcattctggataatgcgtttggaaacatcaatttctctttactctcattcttgttatccatgggaccagATAGGTACAGATATTGAAGATTTCAAGTGCTCTTGGTTAGTTGTGAAAGCCTTGGAACTTAGTAATGAACAACAAAAGAAAGTTCTACAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA