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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactaatattgttatatttccaaaggacaaaaaaaagatttttttttttcaaatatcacctttgagcaatttgttaatgtaacttgattaaatatttcagGTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAATCGGGTCTTATCAAG

Basic information

species Glycine max
transcript GLYMA03G33000.6
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G33000.6 (Glycine max), 3'ss of exon 5
lower sequence: AT3G53620.1 (Arabidopsis thaliana), 3'ss of exon 3
tactaatatt-gttatatttccaaaggacaaaaaaaagatttttttttttcaaatatcacctttgagcaatttgttaatgtaacttgattaaatatttcagGTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAATCGGGTCTTATCAAG
 | | || ||  |    |    |    || |    | |  |||  | ||| | ||||     | |      ||    | | |    ||   | |||| |||||| ||||||| || |||||||||||||||||||||||||| |||||||   ||||||| || |||
-aatgatgttcatcgcctgattaggaaaccattttatgggtttaatctttgagatattgttgtgggaatcattaaccaagcatacggaggcattattacagGTGGTTGAGATAGGAAAAGGGAGCAAGGTGAAATATGAACTCGACAAAACTACGGGTCTCATTAAG

upper sequence: GLYMA03G33000.6 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0040g02470.t01 (Vitis vinifera), 3'ss of exon 3
--tactaatatt--gttatatttccaaaggacaaaaaaaagatttttttttttcaaatatcacctttgagcaatttgttaatgtaacttgattaaatatttcagGTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAATCGGGTCTTATCAAG
  || | | |||     | |||| || |    ||     |||    ||   |||  | |||| |   |     | | | ||  ||   ||  ||| | || |||||| |||| || ||||||||||||||||||||||||||||| ||||| ||| | || || ||||||
actagtgaaatttgacaaaattttcataaataaattgttagaaaccttgccttctta-atcaaccaaggttcttatttgaacata---tgtctaatttttgcagGTGGTTGAAATAGGGAAAGGGAGCAAGGTGAAATATGAACTTGACAAGAAAACTGGACTGATCAAG
















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|207840938|gb|GD810193.1|GD810193
EST:     GGCCTGGTGCTCCAACGATCTTCAATTGT                         GTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAA
genomic: GGCCTGGTGCTCCAACGATCTTCAATTGTgtaagtctgc ... aatatttcagGTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAA
EST: gi|207831666|gb|GD801720.1|GD801720
EST:     CTGGTGCTCCTAACGATTCTTTCAATTGT                         GTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAA
genomic: CTGGTGCTCC-AACGA-TC-TTCAATTGTgtaagtctgc ... aatatttcagGTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAA
EST: gi|193320747|gb|FK283132.1|FK283132
EST:     GGCCTGGTGCTCCAACGATCTTCAATCGT                         GTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAA
genomic: GGCCTGGTGCTCCAACGATCTTCAATTGTgtaagtctgc ... aatatttcagGTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAA
EST: gi|151404690|gb|EV274504.1|EV274504
EST:     GGCCTGGTGCTCCAACGATCTTCAATTGT                         GTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAA
genomic: GGCCTGGTGCTCCAACGATCTTCAATTGTgtaagtctgc ... aatatttcagGTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAA
EST: gi|298199436|gb|HO042799.1|HO042799
EST:     GGCCTGGTGCTCCAACGATCTTCAATTGT                         GTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAA
genomic: GGCCTGGTGCTCCAACGATCTTCAATTGTgtaagtctgc ... aatatttcagGTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAA
EST: gi|7925031|gb|AW831057.1|AW831057
EST:     GGCCTGGTGCTCCAACGATCTTCAATTGT                         GTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAA
genomic: GGCCTGGTGCTCCAACGATCTTCAATTGTgtaagtctgc ... aatatttcagGTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAA
EST: gi|8827754|gb|BE211484.1|BE211484
EST:     GGCCTGGTGCTCCAACGATCTTCAATTGT                         GTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAA
genomic: GGCCTGGTGCTCCAACGATCTTCAATTGTgtaagtctgc ... aatatttcagGTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAA
EST: gi|27446381|gb|CA953504.1|CA953504
EST:     GGCCTGGTGCTCCAACGATCTTCAATTGT                         GTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAA
genomic: GGCCTGGTGCTCCAACGATCTTCAATTGTgtaagtctgc ... aatatttcagGTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAA
EST: gi|192324459|gb|FK015810.1|FK015810
EST:     GGCCTGGTGCTCCAACGATCTTCAATTGT                         GTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAA
genomic: GGCCTGGTGCTCCAACGATCTTCAATTGTgtaagtctgc ... aatatttcagGTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAA
EST: gi|5510301|gb|AI856743.1|AI856743
EST:     GGCCTGGTGCTCCAACGATCTTCAATTGT                         GTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAA
genomic: GGCCTGGTGCTCCAACGATCTTCAATTGTgtaagtctgc ... aatatttcagGTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAA
EST: gi|10236851|gb|BE805739.1|BE805739
EST:     GGCCTGGTGCTCCAACGATCTTCAATTGT                         GTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAA
genomic: GGCCTGGTGCTCCAACGATCTTCAATTGTgtaagtctgc ... aatatttcagGTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAA
EST: gi|208275603|gb|GE078223.1|GE078223
EST:     GGCCTGGTGCTCCAACGATCTTCAATTGT                         GTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAA
genomic: GGCCTGGTGCTCCAACGATCTTCAATTGTgtaagtctgc ... aatatttcagGTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAA
EST: gi|16105384|gb|BI893124.1|BI893124
EST:     GGCCTGGTGCTCCAACGATCTTCAATTGT                         GTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAA
genomic: GGCCTGGTGCTCCAACGATCTTCAATTGTgtaagtctgc ... aatatttcagGTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAA
EST: gi|192296495|gb|FG989111.1|FG989111
EST:     GGCCTGGTGCTCCAACGATCTTCAATTGT                         GTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAA
genomic: GGCCTGGTGCTCCAACGATCTTCAATTGTgtaagtctgc ... aatatttcagGTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAA
EST: gi|207702226|gb|GD682981.1|GD682981
EST:     GGCCTGGTGCTCCAACGATCTTCAATTGT                         GTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAA
genomic: GGCCTGGTGCTCCAACGATCTTCAATTGTgtaagtctgc ... aatatttcagGTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAA
EST: gi|9986811|gb|BE660919.1|BE660919
EST:     GGCCTGGTGCTCCAACGATCTTCAATTGT                         GTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAA
genomic: GGCCTGGTGCTCCAACGATCTTCAATTGTgtaagtctgc ... aatatttcagGTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAA
EST: gi|17022987|gb|BM094021.1|BM094021
EST:     GGCCTGGTGCTCCAACGATCTTCAATTGT                         GTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAA
genomic: GGCCTGGTGCTCCAACGATCTTCAATTGTgtaagtctgc ... aatatttcagGTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcaaatatcacctttgagcaatttgttaatgtaacttgattaaatatttcagGTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAATCGGGTCTTATCAAG
                      aatttgttaatgtaac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tactaatattgttatatttccaaaggacaaaaaaaagatttttttttttcaaatatcacctttgagcaatttgttaatgtaacttgattaaatatttcagGTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAATCGGGTCTTATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG