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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatgtttatgagtgaatactcactatcacactagaatcaggattgtggccatttaaattgtattttttgtgtgaaatatccatatcttttcacttttcagGCTTTCCTTGAATGGAAGAATGCTAGAAGAGAGGAAGTGTCTGAGTATCAGAAACAGATTGGGGAGCAGTATCTTGCCAATGTTGAGAAGGAATTGGAGA

Basic information

species Glycine max
transcript GLYMA08G19640.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G19640.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv12s0055g00360.t01 (Vitis vinifera), 3'ss of exon 11
-gatgtttatgagtgaatactcactatcacactagaatcaggattgtggccatttaaattgtattttttgtgtgaaatatccatatcttttcacttttcagGCTTTCCTTGAATGGAAGAATGCTAGAAGAGAGGAAGTGTCTGAGTATCAGAAACAGATTGGGGAGCAGTATCTTGCCAATGTTGAGAAGGAATTGGAGA
  ||| |  |  ||      |||   || |  ||        ||  | |    || |  | |            |  ||| |  |    ||  | | |||||  || || |||||||||| |||| | ||||||||| ||||||| ||||||||||| |||| |||||||||| ||||||||||||| ||||| || ||||
gtatgctc-taggtcgcctttcaagctccctttatctaatatatccttgtgtgtttatctatccaaaaaaaaaaatttatactcacaaatttgcatatcagGTATTTCTAGAATGGAAGACTGCTCGGAGAGAGGAACTGTCTGAATATCAGAAACATATTGAGGAGCAGTATATTGCCAATGTTGAAAAGGAGTTAGAGA
















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|193417286|gb|FK384658.1|FK384658
EST:     CTTGAGAAGNGCAAAGAAGAG                         GCTTTCCTTGAATGGAAGAATGCTAGAAGAGAGGAAGTGTCTGAGTATCAG
genomic: CTTGAGAAGCGCAAAGAAGAGgttgtcaaac ... cacttttcagGCTTTCCTTGAATGGAAGAATGCTAGAAGAGAGGAAGTGTCTGAGTATCAG
EST: gi|193448419|gb|FK415958.1|FK415958
EST:     ACAAGCCCTTGGATGAAGATCCTACATTACTTGAGAAGCGCAAAGAAGAG                         GCTTTCCTTGAATGGAAGAATGCTAGAAGAGAGGAAGTGTCTGAGTATCAG
genomic: ACAAGCCCTTGGATGAAGATCCTACATTACTTGAGAAGCGCAAAGAAGAGgttgtcaaac ... cacttttcagGCTTTCCTTGAATGGAAGAATGCTAGAAGAGAGGAAGTGTCTGAGTATCAG
EST: gi|193496460|gb|FK460702.1|FK460702
EST:     ACAAGCCCTTGGATGAAGATCCTACATTACTTGAGAAGCGCAAAGAAGAG                         GCTTTCCTTGAATGGAAGAATGCTAGAAGAGAGGAAGTGTCTGAGTATCAG
genomic: ACAAGCCCTTGGATGAAGATCCTACATTACTTGAGAAGCGCAAAGAAGAGgttgtcaaac ... cacttttcagGCTTTCCTTGAATGGAAGAATGCTAGAAGAGAGGAAGTGTCTGAGTATCAG
EST: gi|207700607|gb|GD683714.1|GD683714
EST:     ACAAGCCCTTGGATGAAGATCCTACATTACTTGAGAAGCGCAAAGAAGAG                         GCTTTCCTTGAATGGAAGAATGCTAGAAGAGAGGAAGTGTCTGAGTATCAG
genomic: ACAAGCCCTTGGATGAAGATCCTACATTACTTGAGAAGCGCAAAGAAGAGgttgtcaaac ... cacttttcagGCTTTCCTTGAATGGAAGAATGCTAGAAGAGAGGAAGTGTCTGAGTATCAG
EST: gi|207731212|gb|GD708869.1|GD708869
EST:     ACAAGCCCTTGGATGAAGATCCTACATTACTTGAGAAGCGCAAAGAAGAG                         GCTTTCCTTGAATGGAAGAATGCTAGAAGAGAGGAAGTGTCTGAGTATCAG
genomic: ACAAGCCCTTGGATGAAGATCCTACATTACTTGAGAAGCGCAAAGAAGAGgttgtcaaac ... cacttttcagGCTTTCCTTGAATGGAAGAATGCTAGAAGAGAGGAAGTGTCTGAGTATCAG
EST: gi|193672521|gb|FK618541.1|FK618541
EST:     ACAAGCCCTTGGATGAAGATCCTACATTACTTGAGAAGCGCAAAGAAGAG                         GCTTTCCTTGAATGGAAGAATGCTAGAAGAGAGGAAGTGTCTTAGTATCAG
genomic: ACAAGCCCTTGGATGAAGATCCTACATTACTTGAGAAGCGCAAAGAAGAGgttgtcaaac ... cacttttcagGCTTTCCTTGAATGGAAGAATGCTAGAAGAGAGGAAGTGTCTGAGTATCAG
EST: gi|193370194|gb|FK336756.1|FK336756
EST:     ACAAGCCCTTGGATGAAGATCCTACATTACTTGAGAAGCGCAAAGAAGAG                         GCTTTCCTTGAATGGAAGAATGCTAGAAGAGAGGAAGTGTCTGAGTATCAG
genomic: ACAAGCCCTTGGATGAAGATCCTACATTACTTGAGAAGCGCAAAGAAGAGgttgtcaaac ... cacttttcagGCTTTCCTTGAATGGAAGAATGCTAGAAGAGAGGAAGTGTCTGAGTATCAG
EST: gi|208084949|gb|GD882785.1|GD882785
EST:     ACAAGCCCTTGGATGAAGATCCTACATTACTTGAGAAGCGCAAAGAAGAG                         GCTTTCCTTGAATGGAAGAATGCTAGAAGAGAGGAAGTGTCTGAGTATCAG
genomic: ACAAGCCCTTGGATGAAGATCCTACATTACTTGAGAAGCGCAAAGAAGAGgttgtcaaac ... cacttttcagGCTTTCCTTGAATGGAAGAATGCTAGAAGAGAGGAAGTGTCTGAGTATCAG
EST: gi|207826946|gb|GD797467.1|GD797467
EST:     AGCGCAAAGAAGAG                         GCTTTCCTTGAATGGAAGAATGCTAGAAGAGAGGAAGTGTCTGAGTATCAG
genomic: AGCGCAAAGAAGAGgttgtcaaac ... cacttttcagGCTTTCCTTGAATGGAAGAATGCTAGAAGAGAGGAAGTGTCTGAGTATCAG
EST: gi|208108322|gb|GD903520.1|GD903520
EST:     ACAAGCCCTTGGATGAAGATCCTACATTACTTGAGAAGCGCAAAGAAGAG                         GCTTTCCTTGAATGGAAGAATGCTAGAAGAGAGGAAGTGTCTGAGTATCAG
genomic: ACAAGCCCTTGGATGAAGATCCTACATTACTTGAGAAGCGCAAAGAAGAGgttgtcaaac ... cacttttcagGCTTTCCTTGAATGGAAGAATGCTAGAAGAGAGGAAGTGTCTGAGTATCAG
EST: gi|208122350|gb|GD920815.1|GD920815
EST:     ACAAGCCCTTGGATGAAGATCCTACATTACTTGAGAAGCGCAAAGAAGAG                         GCTTTCCTTGAATGGAAGAATGCTAGAAGAGAGGAAGTGTCTGAGTATCAG
genomic: ACAAGCCCTTGGATGAAGATCCTACATTACTTGAGAAGCGCAAAGAAGAGgttgtcaaac ... cacttttcagGCTTTCCTTGAATGGAAGAATGCTAGAAGAGAGGAAGTGTCTGAGTATCAG
EST: gi|208239294|gb|GE041782.1|GE041782
EST:     ACAAGCCCTTGGATGAAGATCCTACATTACTTGAGAAGCGCAAAGAAGAG                         GCTTTCCTTGAATGGAAGAATGCTAGAAGAGAGGAAGTGTCTGAGTATCAG
genomic: ACAAGCCCTTGGATGAAGATCCTACATTACTTGAGAAGCGCAAAGAAGAGgttgtcaaac ... cacttttcagGCTTTCCTTGAATGGAAGAATGCTAGAAGAGAGGAAGTGTCTGAGTATCAG
EST: gi|208056996|gb|GD851245.1|GD851245
EST:     ACAAGCCCTTGGATGAAGATCCTACATTACTTGAGAAGCGCAAAGAAGAG                         GCTTTCCTTGAATGGAAGAATGCTAGAAGAGAGGAAGTGTCTGAGTATCAG
genomic: ACAAGCCCTTGGATGAAGATCCTACATTACTTGAGAAGCGCAAAGAAGAGgttgtcaaac ... cacttttcagGCTTTCCTTGAATGGAAGAATGCTAGAAGAGAGGAAGTGTCTGAGTATCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggccatttaaattgtattttttgtgtgaaatatccatatcttttcacttttcagGCTTTCCTTGAATGGAAGAATGCTAGAAGAGAGGAAGTGTCTGAGTATCAGAAACAGATTGGGGAGCAGTATCTTGCCAATGTTGAGAAGGAATTGGAGA
                                     tatcttttcacttttc  CT-rich tract
     atttaaattgtatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatgtttatgagtgaatactcactatcacactagaatcaggattgtggccatttaaattgtattttttgtgtgaaatatccatatcttttcacttttcagGCTTTCCTTGAATGGAAGAATGCTAGAAGAGAGGAAGTGTCTGAGTATCAGAAACAGATTGGGGAGCAGTATCTTGCCAATGTTGAGAAGGAATTGGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA