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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccttcagttattttttgtagcattttgcataaacgcctgcgataaggatatatttttgttttagtttttgccatcttaatggatatttacatgattgcagCAAGGTGATCCAATTGAAGAGCGTTACAAGGAATACATGGAGAGGGGTACAGTAATTGATCAACTTGCCTATTGTATAAATAGTTATAGAGAAGCTGCAA

Basic information

species Glycine max
transcript GLYMA13G43630.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G43630.2 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0002g04680.t01 (Vitis vinifera), 3'ss of exon 6
ccttcagttattttttgtagcattttgcataaacgcctgcgataaggatatatttttgttttagtttttgccatcttaatggatatttacatgattgcagCAAGGTGATCCAATTGAAGAGCGTTACAAGGAATACATGGAGAGGGGTACAGTAATTGATCAACTTGCCTATTGTATAAATAGTTATAGAGAAGCTGCAA
              |  |  || ||| | |||   |    | |     ||  ||  | || |   ||||    |     || | | | | |  ||||||||||||||| |||||||| ||||| |||||||| |||   ||| |||| |||||  ||||||||||||  |||||||| |||||||| ||||| || ||||
-------------gtaattacacttt-cttaactccaaatggtttctttagtttgatcttcttagttttatggttgacgtgaaaaataaaa--attgcagCAAGGTGACCCAATTGAGGAGCGCTACAAGGAGTACTCTGAGCGGGGAACAGTGGTTGATCAACTTGTTTATTGTATCAATAGTTACAGAGAGGCAGCAA
















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|254322029|gb|GR837443.1|GR837443
EST:     AAGATGAAACTAAAGGCGTATACATTGCCAAGCTAGAAGAGCTCAAGAAG                         CAAGGTGATCCAATTGAAGAGCGTTACAAGGAATACATGGAGAGGGGTACA
genomic: AAGATGAAACTAAAGGCGTATACATTGCCAAGCTAGAAGAGCTCAAGAAGgtaagaaatt ... atgattgcagCAAGGTGATCCAATTGAAGAGCGTTACAAGGAATACATGGAGAGGGGTACA
EST: gi|192294395|gb|FG987324.1|FG987324
EST:     AAGATGAAACTAAAGGCGTATACATTGCCAAGCTAGAAGAGCTCAAGAAG                         CAAGGTGATCCAATTGAAGAGCGTTACAAGGAATACATGGAGAGGGGTACA
genomic: AAGATGAAACTAAAGGCGTATACATTGCCAAGCTAGAAGAGCTCAAGAAGgtaagaaatt ... atgattgcagCAAGGTGATCCAATTGAAGAGCGTTACAAGGAATACATGGAGAGGGGTACA
EST: gi|207735431|gb|GD710274.1|GD710274
EST:     CTAAAGGCGTATACTATTTGTCCAAGCTAGAAGAGCTCAAGAAG                         CAAGGTGATCCAATTGAAGAGCGTTACAAGGAATACATGGAGAGGGGTACA
genomic: CTAAAGGCGTATAC-A-TTG-CCAAGCTAGAAGAGCTCAAGAAGgtaagaaatt ... atgattgcagCAAGGTGATCCAATTGAAGAGCGTTACAAGGAATACATGGAGAGGGGTACA
EST: gi|11687354|gb|BF595030.1|BF595030
EST:     CAAGCTAGAAGAGCTCAAGAAG                         CAAGGTGATCCAATTGAAGAGCGTTACAAGGAATACATGGAGAGGGGTACA
genomic: CAAGCTAGAAGAGCTCAAGAAGgtaagaaatt ... atgattgcagCAAGGTGATCCAATTGAAGAGCGTTACAAGGAATACATGGAGAGGGGTACA
EST: gi|298188653|gb|HO035346.1|HO035346
EST:     AAGATGAAACTAAAGGCGTATACATTGCCAAGCTAGAAGAGCTCAAAAAG                         CAAGGTGATCCAATTGAAGAGCGTTACTAAG-AATACATGGAGAGGGGTAC
genomic: AAGATGAAACTAAAGGCGTATACATTGCCAAGCTAGAAGAGCTCAAGAAGgtaagaaatt ... atgattgcagCAAGGTGATCCAATTGAAGAGCGTTAC-AAGGAATACATGGAGAGGGGTAC
EST: gi|298183420|gb|HO028633.1|HO028633
EST:     GAGCTCAAGAAG                         CAAGGTGATCCAATTGAAGAGCGTTACAAGGAATACATGGAGAGGGGTACA
genomic: GAGCTCAAGAAGgtaagaaatt ... atgattgcagCAAGGTGATCCAATTGAAGAGCGTTACAAGGAATACATGGAGAGGGGTACA
EST: gi|192301840|gb|FG997698.1|FG997698
EST:     AAGATGAAACTAAAGGCGTATACATTGCCAAGCTAGAAGAGCTCAAGAAG                         CAAGGTGATCCAATTGAAGAGCGTTACAAGGAATACATGGAGAGGGGTACA
genomic: AAGATGAAACTAAAGGCGTATACATTGCCAAGCTAGAAGAGCTCAAGAAGgtaagaaatt ... atgattgcagCAAGGTGATCCAATTGAAGAGCGTTACAAGGAATACATGGAGAGGGGTACA
EST: gi|298166695|gb|HO010134.1|HO010134
EST:     AAGATGAAACTAAAGGCGTATACATTGCCAAGCTAGAAGAGCTCAAGAAG                         CAAGGTGATCCAATTGAAGAGCGTTACAAGGAATACATGGAGAGGGGTACA
genomic: AAGATGAAACTAAAGGCGTATACATTGCCAAGCTAGAAGAGCTCAAGAAGgtaagaaatt ... atgattgcagCAAGGTGATCCAATTGAAGAGCGTTACAAGGAATACATGGAGAGGGGTACA
EST: gi|8827941|gb|BE211671.1|BE211671
EST:     AAGATGAAACTAAAGGCGTATACATTGCCAAGCTAGAAGAGCTCAAGAAG                         CAAGGTGATCCAATTGAAGAGCGTTACAAGGAATACATGGAGAGGGGTACA
genomic: AAGATGAAACTAAAGGCGTATACATTGCCAAGCTAGAAGAGCTCAAGAAGgtaagaaatt ... atgattgcagCAAGGTGATCCAATTGAAGAGCGTTACAAGGAATACATGGAGAGGGGTACA
EST: gi|6963487|gb|AW432180.1|AW432180
EST:     AACTAAAGGCGTATACATTGCCAAGCTAGAAGAGCTCAAGAAG                         CAAGGTGATCCAATTGAAGAGCGTTACAAGGAATACATGGAGAGGGGTACA
genomic: AACTAAAGGCGTATACATTGCCAAGCTAGAAGAGCTCAAGAAGgtaagaaatt ... atgattgcagCAAGGTGATCCAATTGAAGAGCGTTACAAGGAATACATGGAGAGGGGTACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatatatttttgttttagtttttgccatcttaatggatatttacatgattgcagCAAGGTGATCCAATTGAAGAGCGTTACAAGGAATACATGGAGAGGGGTACAGTAATTGATCAACTTGCCTATTGTATAAATAGTTATAGAGAAGCTGCAA
                            tcttaat  putative branch site (score: 3)
     tatttttgttttagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccttcagttattttttgtagcattttgcataaacgcctgcgataaggatatatttttgttttagtttttgccatcttaatggatatttacatgattgcagCAAGGTGATCCAATTGAAGAGCGTTACAAGGAATACATGGAGAGGGGTACAGTAATTGATCAACTTGCCTATTGTATAAATAGTTATAGAGAAGCTGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
ccttcag
- - - - - - - - - - - - -tgcataa
- - - - - - - - - - - - - - - - -cgcctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgccatc