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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttattcttggttttgttttatcatggaaaattgttttaaatagccggttaatgtggaaattgttcgttataattatatatacaattttgtttactgtagTTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGTACAACGCCGAGAAACGGGGGAAGCGCCAAGTCATGATTAGGCCGTCCTC

Basic information

species Glycine max
transcript GLYMA01G45060.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G45060.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv13s0019g00530.t01 (Vitis vinifera), 3'ss of exon 2
------tttattcttggttttgttttatcatggaaaattgttttaaatagccggttaa-----tgtggaaattgttcgttataattatatatacaattttgtttactgtagTTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGTACAACGCCGAGAAACGGGGGAAGCGCCAAGTCATGATTAGGCCGTCCTC
       || | |||| |||   ||| |  |     ||  | |   ||  |  || ||     |||| || | ||| |  | |    | ||||   | | |    ||    | ||||  |||||||| ||||||||  ||||||||||||| |||||||||||||| || ||||| || |||||||| || || ||||| |          
gtttctgttctgcttgatttctattttttcttatttatcatgtgggatttcatgtcaaagttttgtgcaagtagtttgaca-acccttttatattttgtagCGGCCTTGTTTAGTGAAGATGGTGAGAGTTAGTGTCCTGAATGATGCTCTCAAGAGCATGTACAATGCAGAGAAGCGTGGGAAGCGACAGGTGATGATCA----------

upper sequence: GLYMA01G45060.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0040g02460.t01 (Vitis vinifera), 3'ss of exon 1
------------------tttat-tcttggttttgttttatcatggaaaattgttttaaatagccggttaatgtggaaattgttcgttataattatatatacaattttgtttactgtagTTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGTACAACGCCGAGAAACGGGGGAAGCGCCAAGTCATGATTAGGCCGTCCTC
                   |||| |||   |       |  |   ||||  ||| || || |   ||||        || |  | | | ||  | |  |  ||   ||  |        |||  |  |||||||| || ||||| |||||||||||||| ||||||||||| || || ||||| ||||| ||||| || || ||||| |          
catctgtgttggctgatagttatatctccctccctccctccctctgaaatatgtcttgaagacatggttttcaattgaacttcttgctttacctttgca-gCAGCCTTTCT--------TTGCAAGGATGGTGAGAGTCAGTGTCTTGAATGATGCTCTAAAGAGCATGTATAATGCAGAGAAGCGGGGAAAGCGACAGGTTATGATCA----------
















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|12773918|gb|BG238845.1|BG238845
EST:     CAGAGCTCGCTCTCCTCGCCGTTTCTCTCATCGCTAGTTTCAAGTCTCC                         TTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
genomic: CAGAGCTCGCTCTCCTCGCCGTTTCTCTCATCGCTAGTTTCAAGTCTCCgtaagatctt ... tttactgtagTTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
EST: gi|193399833|gb|FK369980.1|FK369980
EST:     TCAGAGCTCGCTCTCCTCGCCGTTTCTCTCATCGCTAGTTTCAAGTCTCC                         TTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
genomic: TCAGAGCTCGCTCTCCTCGCCGTTTCTCTCATCGCTAGTTTCAAGTCTCCgtaagatctt ... tttactgtagTTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
EST: gi|7233861|gb|AW569204.1|AW569204
EST:     TCAGAGCTCGCTCTCCTCGCCGTTTCTCTCATCGCTAGTTTCAAGTCTCC                         TTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
genomic: TCAGAGCTCGCTCTCCTCGCCGTTTCTCTCATCGCTAGTTTCAAGTCTCCgtaagatctt ... tttactgtagTTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
EST: gi|192330019|gb|FK020835.1|FK020835
EST:     TCAGAGCTCGCTCTCCTCGCCGTTTCTCTCATCGCTAGTTTCAAGTCTCC                         TTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
genomic: TCAGAGCTCGCTCTCCTCGCCGTTTCTCTCATCGCTAGTTTCAAGTCTCCgtaagatctt ... tttactgtagTTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
EST: gi|6846271|gb|AW348561.1|AW348561
EST:     TCAGAGCTCGCTCTCCTCNCNGTTTCTCTCATCGCTAGTTTCAAGTCTCC                         TTGTGACAATGGTNNGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
genomic: TCAGAGCTCGCTCTCCTCGCCGTTTCTCTCATCGCTAGTTTCAAGTCTCCgtaagatctt ... tttactgtagTTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
EST: gi|213591764|gb|DB973371.1|DB973371
EST:     TCAGAGTTCGCTCTCCTCGCCGTTTCTCTCATCGCTAGTTTCAAGTCTCC                         TTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
genomic: TCAGAGCTCGCTCTCCTCGCCGTTTCTCTCATCGCTAGTTTCAAGTCTCCgtaagatctt ... tttactgtagTTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
EST: gi|192334186|gb|FK026567.1|FK026567
EST:     TCAGAGCTCGCTCTCCTCGCCGTTTCTCTCATCGCTAGTTTCAAGTCTCC                         TTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
genomic: TCAGAGCTCGCTCTCCTCGCCGTTTCTCTCATCGCTAGTTTCAAGTCTCCgtaagatctt ... tttactgtagTTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
EST: gi|209726482|gb|BW662834.1|BW662834
EST:     TCAGAGTTCGCTCTCCTCGCCGTTTCTCTCATCGCTAGTTTCAAGTCTCC                         TTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
genomic: TCAGAGCTCGCTCTCCTCGCCGTTTCTCTCATCGCTAGTTTCAAGTCTCCgtaagatctt ... tttactgtagTTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
EST: gi|192298113|gb|FG991393.1|FG991393
EST:     TCAGAGCTCGCTCTCCTCGCCGTTTCTCTCATCGCTAGTTTCAAGTCTCC                         TTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
genomic: TCAGAGCTCGCTCTCCTCGCCGTTTCTCTCATCGCTAGTTTCAAGTCTCCgtaagatctt ... tttactgtagTTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
EST: gi|193385152|gb|FK351984.1|FK351984
EST:     TCAGAGCTCGCTCTCCTCGCCGTTTCTCTCATCGCTAGTTTCAAGTCTCC                         TTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
genomic: TCAGAGCTCGCTCTCCTCGCCGTTTCTCTCATCGCTAGTTTCAAGTCTCCgtaagatctt ... tttactgtagTTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
EST: gi|209726497|gb|BW662835.1|BW662835
EST:     CATCGCTAGTTTCAAGTCTCC                         TTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
genomic: CATCGCTAGTTTCAAGTCTCCgtaagatctt ... tttactgtagTTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
EST: gi|31469585|gb|CD411613.1|CD411613
EST:     CGTTTCTCTCATCGCTAGTTTCAAGTCTCC                         TTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
genomic: CGTTTCTCTCATCGCTAGTTTCAAGTCTCCgtaagatctt ... tttactgtagTTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
EST: gi|7686423|gb|AW757071.1|AW757071
EST:     TCAGAGCTCGCTCTCCTCGCCGTTTCTCTCATCGCTAGTTTCAAGTCTCC                         TTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
genomic: TCAGAGCTCGCTCTCCTCGCCGTTTCTCTCATCGCTAGTTTCAAGTCTCCgtaagatctt ... tttactgtagTTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
EST: gi|192334185|gb|FK026566.1|FK026566
EST:     TCAGAGCTCGCTCTCCTCGCCGTTTCTCTCATCGCTAGTTTCAAGTCTCC                         TTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
genomic: TCAGAGCTCGCTCTCCTCGCCGTTTCTCTCATCGCTAGTTTCAAGTCTCCgtaagatctt ... tttactgtagTTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
EST: gi|193374772|gb|FK341614.1|FK341614
EST:     TCAGAGCTCGCTCTCCTCGCCGTTTCTCTCATCGCTAGTTTCAAGTCTCC                         TTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
genomic: TCAGAGCTCGCTCTCCTCGCCGTTTCTCTCATCGCTAGTTTCAAGTCTCCgtaagatctt ... tttactgtagTTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
EST: gi|213587877|gb|DB959701.1|DB959701
EST:     GCTCTCCTCGCCGTTTCTCTCATCGCTAGTTTCAAGTCTCC                         TTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
genomic: GCTCTCCTCGCCGTTTCTCTCATCGCTAGTTTCAAGTCTCCgtaagatctt ... tttactgtagTTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
EST: gi|193304006|gb|FK269811.1|FK269811
EST:     TCAGAGCTCGCTCTCCTCGCCGTTTCTCTCATCGCTAGTTTCAAGTCTCC                         TTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
genomic: TCAGAGCTCGCTCTCCTCGCCGTTTCTCTCATCGCTAGTTTCAAGTCTCCgtaagatctt ... tttactgtagTTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
EST: gi|4292212|gb|AI437730.1|AI437730
EST:     GAGCTCGCTCTCCTCGCCGTTTCTCTCATCGCTAGTTTCAAGTCTCC                         TTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
genomic: GAGCTCGCTCTCCTCGCCGTTTCTCTCATCGCTAGTTTCAAGTCTCCgtaagatctt ... tttactgtagTTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
EST: gi|151408384|gb|EV278192.1|EV278192
EST:     TCAGAGCTCGCTCTCCTCGCCGTTTCTCTCATCGCTAGTTTCAAGTCTCC                         TTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT
genomic: TCAGAGCTCGCTCTCCTCGCCGTTTCTCTCATCGCTAGTTTCAAGTCTCCgtaagatctt ... tttactgtagTTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggttaatgtggaaattgttcgttataattatatatacaattttgtttactgtagTTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGTACAACGCCGAGAAACGGGGGAAGCGCCAAGTCATGATTAGGCCGTCCTC
 ggttaat  putative branch site (score: 4)
                                        ttttgttt  putative PPT
            aaattgttcgttataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttattcttggttttgttttatcatggaaaattgttttaaatagccggttaatgtggaaattgttcgttataattatatatacaattttgtttactgtagTTGTGACAATGGTGAGGGTTAGTGTGTTGAATGATGCTCTGAAGAGCATGTACAACGCCGAGAAACGGGGGAAGCGCCAAGTCATGATTAGGCCGTCCTC

- - - - -ggttttg
- - - - - - - - - - - catggaa