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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAAGATCCAGTTCCCTCTCCAACACGCTTTCGGCGACTCCGATTTCTCCGACGCCGGCAACTTCTCCGCTCGCCTCAAGACTTGGAGCCACGGCGCCCAggttcccttcctcctctctctgtttatgttataatttaggagctgatatgcgatttatgaattgaatttgtgtcgattcgaatctacttctgttcgattc...

Basic information

species Glycine max
transcript GLYMA18G47920.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G47920.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv04s0023g00820.t01 (Vitis vinifera), 5'ss of exon 2
CCAAGATCCAGTTCCCTCTCCAACACGCTTTCGGCGACTCCGATTTCTCCGACGCCGGCAACTTCTCCGCTCGCCTCAAGACTTGGAGCCACGGCGCCCAggttcccttcctcctctctctgtttatgttataatttaggagctgatatgcgatttatgaattgaatttgtgtc-gattcgaatctacttctg-----ttcgattc
 ||||||||||||| | ||| ||||||| ||||| |||||||||||||||  ||| |||   ||||| |||||||||||||| | |||||| ||||| ||||| |||| |      |||  | ||   |||   ||  |    |  | ||   ||  |||||||  || ||||  | || || | |    |||     |  |||| 
-CAAGATCCAGTTCTCCCTCGAACACGCCTTCGGAGACTCCGATTTCTCCCCCGCTGGCGCGTTCTCTGCTCGCCTCAAGACCTCGAGCCATGGCGCTCAGgtgccctactg---ttctgcgcttgatttagtgttgggttttttttttggttttggtgaattg--ttagtgttaggtttgagtttggggctgaagtttgggattt
















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|298193158|gb|HO033592.1|HO033592
EST:     GACGCCGGCAACTTCTCCGCTCGCCTCAAGACTTGGAGCCACGGCGCCCA                         GACGCTGACGAAGCTGCGGTTTAAGCGTGATCTTTTGACTGACGTTGAGCA
genomic: GACGCCGGCAACTTCTCCGCTCGCCTCAAGACTTGGAGCCACGGCGCCCAggttcccttc ... tgttgtgataGACGCTGACGAAGCTGCGGTTTAAGCGTGATCTTTTGACTGACGTTGAGCA
EST: gi|192325685|gb|FK015042.1|FK015042
EST:     GACGCCGGCAACTTCTCCGCTCGCCTCAAGACTTGGAGCCACGGCGCCCA                         GACGCTGACGAAGCTGCGGTTTAAGCGTGATCTTTTGACTGACGTTGAGCA
genomic: GACGCCGGCAACTTCTCCGCTCGCCTCAAGACTTGGAGCCACGGCGCCCAggttcccttc ... tgttgtgataGACGCTGACGAAGCTGCGGTTTAAGCGTGATCTTTTGACTGACGTTGAGCA
EST: gi|298173457|gb|HO016793.1|HO016793
EST:     GACGCCGGCAACTTCTCCGCTCGCCTCAAGACTTGGAGCCACGGCGCCCA                         GACGCTGACGAAGCTGCGGTTTAAGCGTGATCTTTTGACTGACGTTGAGCA
genomic: GACGCCGGCAACTTCTCCGCTCGCCTCAAGACTTGGAGCCACGGCGCCCAggttcccttc ... tgttgtgataGACGCTGACGAAGCTGCGGTTTAAGCGTGATCTTTTGACTGACGTTGAGCA
EST: gi|254331914|gb|GR843657.1|GR843657
EST:     GACGCCGGCAACTTCTCCGCTCGCCTCAAGACTTGGAGCCACGGCGCCCA                         GACGCTGACGAAGCTGCGGTTTAAGCGTGATCTTTTGACTGACGTTGAGCA
genomic: GACGCCGGCAACTTCTCCGCTCGCCTCAAGACTTGGAGCCACGGCGCCCAggttcccttc ... tgttgtgataGACGCTGACGAAGCTGCGGTTTAAGCGTGATCTTTTGACTGACGTTGAGCA
EST: gi|208336506|gb|GE136786.1|GE136786
EST:     GACGCCGGCAACTTCTCCGCTCGCCTCAAGACTTGGAGCCACGGCGCCCA                         GACGCTGACGAAGCTGCGGTTTAAGCGTGATCTTTTGACTGACGTTGAGCA
genomic: GACGCCGGCAACTTCTCCGCTCGCCTCAAGACTTGGAGCCACGGCGCCCAggttcccttc ... tgttgtgataGACGCTGACGAAGCTGCGGTTTAAGCGTGATCTTTTGACTGACGTTGAGCA
EST: gi|254345762|gb|GR859409.1|GR859409
EST:     GACGCCGGCAACTTCTCCGCTCGCCTCAAGACTTGGAGCCACGGCGCCCA                         GACGCTGACGAAGCTGCGGTTTAAGCGTGATCTTTTGACTGACGTTGAGCA
genomic: GACGCCGGCAACTTCTCCGCTCGCCTCAAGACTTGGAGCCACGGCGCCCAggttcccttc ... tgttgtgataGACGCTGACGAAGCTGCGGTTTAAGCGTGATCTTTTGACTGACGTTGAGCA
EST: gi|298193094|gb|HO033528.1|HO033528
EST:     GACGCCGGCAACTTCTCCGCTCGCCTCAAGACTTGGAGCCACGGCGCCCA                         GACGCTGACGAAGCTGCGGTTTAAGCGTGATCTTTTGACTGACGTTGAGCA
genomic: GACGCCGGCAACTTCTCCGCTCGCCTCAAGACTTGGAGCCACGGCGCCCAggttcccttc ... tgttgtgataGACGCTGACGAAGCTGCGGTTTAAGCGTGATCTTTTGACTGACGTTGAGCA
EST: gi|192299870|gb|FG987828.1|FG987828
EST:     GACGCCGGCAACTTCTCCGCTCGCCTCAAGACTTGGAGCCACGGCGCCCA                         GACGCTGACGAAGCTGCGGTTTAAGCGTGATCTTTTGACTGACGTTGAGCA
genomic: GACGCCGGCAACTTCTCCGCTCGCCTCAAGACTTGGAGCCACGGCGCCCAggttcccttc ... tgttgtgataGACGCTGACGAAGCTGCGGTTTAAGCGTGATCTTTTGACTGACGTTGAGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAAGATCCAGTTCCCTCTCCAACACGCTTTCGGCGACTCCGATTTCTCCGACGCCGGCAACTTCTCCGCTCGCCTCAAGACTTGGAGCCACGGCGCCCAggttcccttcctcctctctctgtttatgttataatttaggagctgatatgcgatttatgaattgaatttgtgtcgattcgaatctacttctgttcgattc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttcctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctctc