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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTCTCTATGCGTGAAACGGCTAGTGTACACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGTgtaaggatgagtagttttagattttacataatgtaggctggaagaaatttagttatatcgtttttggttgatttactttgttatactaaatggtacatacccttcttttaccatttatttatattcctctttattcag

Basic information

species Glycine max
transcript GLYMA16G23710.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G23710.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv04s0023g03510.t01 (Vitis vinifera), 5'ss of exon 4
GTTTCTCTATGCGTGAAACGGCTAGTGTACACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGTgtaaggatgagtag----ttttagattttacat-aatgtaggctg------gaagaaatttagttatatcg----tttttggttgatttactttgttatactaaatggtacatacccttcttttaccattta--tttatattcctctttattcag
|||||||| || ||||||||||| || ||||| ||||| ||||| ||| | || ||||||||||||||||||||||||||||||  ||   |     || |  |||  | |  |||  || |        ||    |   |||| ||| |    |   |   |   | |     |||  ||||  | | | | |  ||  | |||  || |  | || ||  ||     |||||
GTTTCTCTTTGTGTGAAACGGCTTGTCTACACCAATGAGAATGGGGAACTAGTTAAGGGAGTCTGCTCAAATTTCTTGTgtaagtctgctcaaaattttcttaattgcataggaatccagcccaccttctgatttcaaacagttgtatgggaaatcaatctctcggtgaagacattagtctaagagatgc-ttctgttaatgtacttttgagctctaaatctcttccatttcag
















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|19452467|gb|BM953877.1|BM953877
EST:     CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGT                         GTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAG
genomic: CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGTgtaaggatga ... ctttattcagGTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAG
EST: gi|16281497|gb|BI944518.1|BI944518
EST:     TGCTCAAATTTCTTGT                         GTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAG
genomic: TGCTCAAATTTCTTGTgtaaggatga ... ctttattcagGTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAG
EST: gi|213610723|gb|DB961198.1|DB961198
EST:     CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGT                         GTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTG
genomic: CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGTgtaaggatga ... ctttattcagGTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTG
EST: gi|120532662|gb|EH260795.1|EH260795
EST:     CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGT                         GTGACCTTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAA
genomic: CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGTgtaaggatga ... ctttattcagGTGACCT-GAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAA
EST: gi|213611575|gb|DB960855.1|DB960855
EST:     CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGT                         GTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTG
genomic: CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGTgtaaggatga ... ctttattcagGTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTG
EST: gi|213592264|gb|DB965999.1|DB965999
EST:     CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGT                         GTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAA
genomic: CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGTgtaaggatga ... ctttattcagGTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAA
EST: gi|192296690|gb|FG991258.1|FG991258
EST:     CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGT                         GTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAG
genomic: CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGTgtaaggatga ... ctttattcagGTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAG
EST: gi|13480735|gb|BG510078.1|BG510078
EST:     CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGT                         GTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGGTGGGAAAG
genomic: CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGTgtaaggatga ... ctttattcagGTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTCTCTATGCGTGAAACGGCTAGTGTACACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGTgtaaggatgagtagttttagattttacataatgtaggctggaagaaatttagttatatcgtttttggttgatttactttgttatactaaatggtacatacccttcttttaccatttatttatattcctctttattcag

- - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - GGAGAA