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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttttcttcgtcttggcttgaagatcttgtttttattctttaatggcatctctccgtaccttggtgcacatgtaatgtgactgcacttttttgtgtgcagATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAA

Basic information

species Glycine max
transcript GLYMA06G42900.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G42900.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv12s0028g02020.t01 (Vitis vinifera), 3'ss of exon 2
cttttcttcgtcttg-gcttgaagatcttgtttttattctttaatggcatctctccgtac-cttggtgcacatgtaatgtgactgcacttttttgtgtgcagATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAA
  ||| || ||   |   ||     | |||     ||  ||   |  ||| | |  | |   |||        || |||   |  |   |||||| ||||||||||    ||||||||||| || |||||    || ||||||||| | ||||||||||||||||| |||||||| |||||||| 
--tttgtttgttgcgcaattatttttgttggaaaaatatttcttttacatgtatttgcatatttgacattgtagttatggatcatctaatttttgcgtgcagATGATCGAGTACCAACTGAGCTGAAGAAAAGTATCATGCAAGCTCGAATGGACAAGAAACTTACCCAGTCTCAACTTGCTCAG
















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|208201272|gb|GD996629.1|GD996629
EST:     CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTC                         ATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
genomic: CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTCgtgagtatta ... ttgtgtgcagATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
EST: gi|10237885|gb|BE806773.1|BE806773
EST:     CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTC                         ATGAGAAGGTACCGACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
genomic: CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTCgtgagtatta ... ttgtgtgcagATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
EST: gi|120492194|gb|EH220361.1|EH220361
EST:     CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTC                         ATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
genomic: CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTCgtgagtatta ... ttgtgtgcagATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
EST: gi|192316373|gb|FK008162.1|FK008162
EST:     CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTC                         ATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
genomic: CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTCgtgagtatta ... ttgtgtgcagATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
EST: gi|192302097|gb|FG993467.1|FG993467
EST:     CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTC                         ATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
genomic: CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTCgtgagtatta ... ttgtgtgcagATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
EST: gi|254337318|gb|GR845101.1|GR845101
EST:     CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTC                         ATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
genomic: CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTCgtgagtatta ... ttgtgtgcagATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
EST: gi|192329167|gb|FK019754.1|FK019754
EST:     CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTC                         ATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
genomic: CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTCgtgagtatta ... ttgtgtgcagATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
EST: gi|192302223|gb|FG996617.1|FG996617
EST:     CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTC                         ATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
genomic: CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTCgtgagtatta ... ttgtgtgcagATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
EST: gi|18735226|gb|BM528641.1|BM528641
EST:     CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTC                         ATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
genomic: CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTCgtgagtatta ... ttgtgtgcagATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
EST: gi|192315428|gb|FK007774.1|FK007774
EST:     CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTC                         ATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
genomic: CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTCgtgagtatta ... ttgtgtgcagATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
EST: gi|21888229|gb|BQ741433.1|BQ741433
EST:     CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTC                         ATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
genomic: CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTCgtgagtatta ... ttgtgtgcagATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
EST: gi|7638872|gb|AW733264.1|AW733264
EST:     CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTC                         ATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
genomic: CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTCgtgagtatta ... ttgtgtgcagATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
EST: gi|193318238|gb|FK287482.1|FK287482
EST:     GATGATACTGAGAGTCTAGCTC                         ATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
genomic: GATGATACTGAGAGTCTAGCTCgtgagtatta ... ttgtgtgcagATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
EST: gi|10231268|gb|BE800165.1|BE800165
EST:     CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTC                         ATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
genomic: CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTCgtgagtatta ... ttgtgtgcagATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
EST: gi|7638873|gb|AW733265.1|AW733265
EST:     CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTC                         ATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
genomic: CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTCgtgagtatta ... ttgtgtgcagATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
EST: gi|192316374|gb|FK008163.1|FK008163
EST:     CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTC                         ATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
genomic: CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTCgtgagtatta ... ttgtgtgcagATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
EST: gi|17023513|gb|BM094547.1|BM094547
EST:     CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTC                         ATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
genomic: CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTCgtgagtatta ... ttgtgtgcagATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
EST: gi|254339962|gb|GR858087.1|GR858087
EST:     CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTC                         ATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG
genomic: CACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTCgtgagtatta ... ttgtgtgcagATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatctctccgtaccttggtgcacatgtaatgtgactgcacttttttgtgtgcagATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAA
                                      cactttttt  CT-rich tract
                                       actttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttttcttcgtcttggcttgaagatcttgtttttattctttaatggcatctctccgtaccttggtgcacatgtaatgtgactgcacttttttgtgtgcagATGAGAAGGTACCAACTGAACTTAAGAAGGCCATAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - -tggcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcactt