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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattaattaaacacaatcctttttttttaattataattaagcctgtgtctttaagtatttatttattttcaattgaacttatttgcatgcatgtaaattagaaagcttattaatttgaattaatgaatcgggtcgtattgattattaattaatgctttgttgttgatgtatttatgcaatgcaagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGAATGATCTTTTGAACAGCTCTGATTATGTCCCAACCTATGAGGACAAGGA

Basic information

species Glycine max
transcript GLYMA03G31530.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G31530.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0141g00290.t01 (Vitis vinifera), 3'ss of exon 2
gtaattaattaaacacaatcctttttttttaattataattaagcctgtgtctttaagtatttatttattttcaattgaacttatttgcatgcatgtaaattagaaagcttattaatttgaattaatgaatcgggtcgtattgattattaattaatgctttgttgttgatgtatttatgcaatgcaagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGAATGATCTTTTGAACAGCTCTGATTATGTCCCAACCTATGAGGACAAGGA
                                                                            || ||  |   | |  ||  | || |  ||| |  |   | |  |||||      ||||  ||   ||  |||||||  |  |  || ||  | | |||||    || |||| |||| || ||| ||||||||||||||||||||||||||||||||| |||  |||||||||||  | | |||| |||| ||||| || || ||||| ||
----------------------------------------------------------------------------gatctcgtaatctt--ataaagataatgaagatattgtgtctatattaa------gggttataagcatgtttaattatggtatgattctt--tatttttattttttg-aagGGAATTATGGATCACAAGGAATGAAGGATTTCATGAATGAGAGCAAGTTGATGGATCTTTTGAATGGTTTTGATCATGTTCCAACATACGAAGACAAAGA
















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|193455409|gb|FK419302.1|FK419302
EST:     CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCATAG                         GCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
genomic: CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCATAGgtaattaatt ... gcaatgcaagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
EST: gi|213593271|gb|DB966096.1|DB966096
EST:     CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCATAG                         GCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
genomic: CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCATAGgtaattaatt ... gcaatgcaagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
EST: gi|151394543|gb|EV264414.1|EV264414
EST:     CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCATAG                         GCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
genomic: CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCATAGgtaattaatt ... gcaatgcaagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
EST: gi|31455938|gb|CD397966.1|CD397966
EST:     CCGAGAGCTCTCTGATTCTTTAGGCTAAATGTTCAGCTCCTTCACCATAG                         GCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
genomic: CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCATAGgtaattaatt ... gcaatgcaagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
EST: gi|9987128|gb|BE661236.1|BE661236
EST:     CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTTCTTCACCATAG                         GCAATTGTGAATCC-AAGGAATGAAGGATTTCATGAATGAGAACCAAGCTG
genomic: C-GAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCATAGgtaattaatt ... gcaatgcaagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGC-AAGCTG
EST: gi|207791247|gb|GD760032.1|GD760032
EST:     CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCATAG                         GCAATTGTGAAT
genomic: CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCATAGgtaattaatt ... gcaatgcaagGCAATTGTGAAT
EST: gi|209699150|gb|BW652893.1|BW652893
EST:     CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCATAG                         GCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
genomic: CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCATAGgtaattaatt ... gcaatgcaagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
EST: gi|10255026|gb|BE822792.1|BE822792
EST:     AATGTTCAGCTNNNTCACCATAG                         GCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
genomic: AATGTTCAGCTCCTTCACCATAGgtaattaatt ... gcaatgcaagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
EST: gi|209699149|gb|BW652892.1|BW652892
EST:     CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCATAG                         GCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
genomic: CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCATAGgtaattaatt ... gcaatgcaagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
EST: gi|151406946|gb|EV276761.1|EV276761
EST:     CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCATAG                         GCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAGGCTGA
genomic: CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCATAGgtaattaatt ... gcaatgcaagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
EST: gi|193480258|gb|FK445866.1|FK445866
EST:     CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCATAG                         GCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
genomic: CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCATAGgtaattaatt ... gcaatgcaagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
EST: gi|208084448|gb|GD884930.1|GD884930
EST:     TGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCATAG                         GCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
genomic: TGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCATAGgtaattaatt ... gcaatgcaagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
EST: gi|151394747|gb|EV264618.1|EV264618
EST:     CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCATAG                         GCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
genomic: CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCATAGgtaattaatt ... gcaatgcaagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
EST: gi|6667635|gb|AW279086.1|AW279086
EST:     AATGTTCAGCTCCTTCACCATAG                         GCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
genomic: AATGTTCAGCTCCTTCACCATAGgtaattaatt ... gcaatgcaagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtcgtattgattattaattaatgctttgttgttgatgtatttatgcaatgcaagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGAATGATCTTTTGAACAGCTCTGATTATGTCCCAACCTATGAGGACAAGGA
     tattgattattaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattaattaaacacaatcctttttttttaattataattaagcctgtgtctttaagtatttatttattttcaattgaacttatttgcatgcatgtaaattagaaagcttattaatttgaattaatgaatcgggtcgtattgattattaattaatgctttgttgttgatgtatttatgcaatgcaagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGAATGATCTTTTGAACAGCTCTGATTATGTCCCAACCTATGAGGACAAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC