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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggacaatgttttacatactgcatggaagtgattcaagtgaagtaactctgatgtatgtcatgacaaatgactttttatccttctaattaattgtgtgaagGCTGCATCTAAGAAACTGATAACAAGAGAAGAGTGGGAGAAGAAGCTTAGTGATGTGAAGATTAGAAAAGAAGACATGAATAAGTTGGTAATGAATTTCC

Basic information

species Glycine max
transcript GLYMA15G07570.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G07570.3 (Glycine max), 3'ss of exon 2
lower sequence: AT1G61150.3 (Arabidopsis thaliana), 3'ss of exon 2
--------------------------ggacaatgttttac---atactgcatggaagtgattcaagtgaagtaactctgatgtatgt-catgacaaatgactttttatccttctaattaattgtgtgaagGCTGCATCTAAGAAACTGATAACAAGAGAAGAGTGGGAGAAGAAGCTTAGTGATGTGAAGATTAGAAAAGAAGACATGAATAAGTTGGTAATGAATTTCC
                          |  |  ||| |||    ||||  | ||    ||  |     |||  |||| | || | | | || |     |||| |    |  |  |  |   ||||  | ||||| | || |||||| |||| ||| | ||||| ||||||||||| || | || ||||||| |||| |||||||| |||||||  ||||| |||||||| |
gtaattttgactcctcttatgagtctgttctttgtgttatttgatacaacttgatgatgggtttttggaa--aactttaatctttatgcacgttgtgtgacct--agttttaatcgtggcttgt-cgcagGCTACTTCGAAGAAAATGATCACACGTGAAGAATGGGAGAAGAAACTAAATGCTGTGAAGCTTAGGAAAGAAGATATGAATACTTTGGTGATGAATTTTC

upper sequence: GLYMA15G07570.3 (Glycine max), 3'ss of exon 2
lower sequence: AT1G61150.5 (Arabidopsis thaliana), 3'ss of exon 1
-ggacaatgttttac---atactgcatggaagtgattcaagtgaagtaactctgatgtatgt-catgacaaatgactttttatccttctaattaattgtgtgaagGCTGCATCTAAGAAACTGATAACAAGAGAAGAGTGGGAGAAGAAGCTTAGTGATGTGAAGATTAGAAAAGAAGACATGAATAAGTTGGTAATGAATTTCC
 |  |  ||| |||    ||||  | ||    ||  |     |||  |||| | || | | | || |     |||| |    |  |  |  |   ||||  | ||||| | || |||||| |||| ||| | ||||| ||||||||||| || | || ||||||| |||| |||||||| |||||||  ||||| |||||||| |
tgttctttgtgttatttgatacaacttgatgatgggtttttggaa--aactttaatctttatgcacgttgtgtgacct--agttttaatcgtggcttgt-cgcagGCTACTTCGAAGAAAATGATCACACGTGAAGAATGGGAGAAGAAACTAAATGCTGTGAAGCTTAGGAAAGAAGATATGAATACTTTGGTGATGAATTTTC
















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|151408269|gb|EV278077.1|EV278077
EST:     TGTCATTGTTGTGGCTTGTGATTCGTCAACTTGCAGAAATCGAGGCAATG                         GCTGCATCTAAGAAACTGATAACAAGAGAAGAGTGGGAGAAGAAGCTTAGT
genomic: TGTCATTGTTGTGGCTTGTGATTCGTCAACTTGCAGAAATCGAGGCAATGgtatttgact ... ttgtgtgaagGCTGCATCTAAGAAACTGATAACAAGAGAAGAGTGGGAGAAGAAGCTTAGT
EST: gi|298181140|gb|HO022579.1|HO022579
EST:     TGTCATTGTTGTGGCTTGTGACTCGTCAACTTGCAGAAATCGAGGCAATG                         GCTGCATCTAAGAAACTGATAACAAGAGAAGAGTGGGAGAAGAAGCTTAGT
genomic: TGTCATTGTTGTGGCTTGTGATTCGTCAACTTGCAGAAATCGAGGCAATGgtatttgact ... ttgtgtgaagGCTGCATCTAAGAAACTGATAACAAGAGAAGAGTGGGAGAAGAAGCTTAGT
EST: gi|9819896|gb|BE555339.1|BE555339
EST:     TGTCATTGTTGTGGCTTGTGATTCGTCAACTTGCAGAAATCGAGGCAATG                         GCTGCATCTAAGAAACTGATAACAAGAGAAGAGTGGGAGAAGAAGCTTAGT
genomic: TGTCATTGTTGTGGCTTGTGATTCGTCAACTTGCAGAAATCGAGGCAATGgtatttgact ... ttgtgtgaagGCTGCATCTAAGAAACTGATAACAAGAGAAGAGTGGGAGAAGAAGCTTAGT
EST: gi|8283127|gb|BE020688.1|BE020688
EST:     TGTCATTGTTGTGGCTTGTGATTCGTCAACTTGCAGAAATCGAGGCAATG                         GCTGCATCTAAGAAACTGATAACAAGAGAAGAGTGGGAGAAGAAGCTTAGT
genomic: TGTCATTGTTGTGGCTTGTGATTCGTCAACTTGCAGAAATCGAGGCAATGgtatttgact ... ttgtgtgaagGCTGCATCTAAGAAACTGATAACAAGAGAAGAGTGGGAGAAGAAGCTTAGT
EST: gi|7588045|gb|AW703849.1|AW703849
EST:     GTCATTGTTGTGGCTTGTGATTCGTCAACTTGCAGAAATCGAGGCAATG                         GCTGCATCTAAGAAACTGATATCAAGAGAAGAGTGGGAGAAGAAGCTTAGT
genomic: GTCATTGTTGTGGCTTGTGATTCGTCAACTTGCAGAAATCGAGGCAATGgtatttgact ... ttgtgtgaagGCTGCATCTAAGAAACTGATAACAAGAGAAGAGTGGGAGAAGAAGCTTAGT
EST: gi|15812571|gb|BI784846.1|BI784846
EST:     TGTCATTGTTGTGGCTTGTGATTCGTCAACTTGCAGAAATCGAGGCAATG                         GCTGCATCTAAGAAACTGATAACAAGAGAAGAGTGGGAGAAGAAGCTTAGT
genomic: TGTCATTGTTGTGGCTTGTGATTCGTCAACTTGCAGAAATCGAGGCAATGgtatttgact ... ttgtgtgaagGCTGCATCTAAGAAACTGATAACAAGAGAAGAGTGGGAGAAGAAGCTTAGT
EST: gi|192297765|gb|FG989971.1|FG989971
EST:     TGTCATTGTTGTGGCTTGTGATTCGTCAACTTGCAGAAATCGAGGCAATG                         GCTGCATCTAAGAAACTGATAACAAGAGAAGAGTGGGAGAAGAAGCTTAGT
genomic: TGTCATTGTTGTGGCTTGTGATTCGTCAACTTGCAGAAATCGAGGCAATGgtatttgact ... ttgtgtgaagGCTGCATCTAAGAAACTGATAACAAGAGAAGAGTGGGAGAAGAAGCTTAGT
EST: gi|207765821|gb|GD735462.1|GD735462
EST:     CAACTTGCAGAAATCGAGGCAATG                         GCTGCATCTAAGAAACTGATAACAAGAGAAGAGTGGGAGAAGAAGCTTAGT
genomic: CAACTTGCAGAAATCGAGGCAATGgtatttgact ... ttgtgtgaagGCTGCATCTAAGAAACTGATAACAAGAGAAGAGTGGGAGAAGAAGCTTAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctgatgtatgtcatgacaaatgactttttatccttctaattaattgtgtgaagGCTGCATCTAAGAAACTGATAACAAGAGAAGAGTGGGAGAAGAAGCTTAGTGATGTGAAGATTAGAAAAGAAGACATGAATAAGTTGGTAATGAATTTCC
                          tttttatccttctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggacaatgttttacatactgcatggaagtgattcaagtgaagtaactctgatgtatgtcatgacaaatgactttttatccttctaattaattgtgtgaagGCTGCATCTAAGAAACTGATAACAAGAGAAGAGTGGGAGAAGAAGCTTAGTGATGTGAAGATTAGAAAAGAAGACATGAATAAGTTGGTAATGAATTTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG