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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAATTATGTGTGGTGGTGAGCCAAGGGCTATGCTTAGAAAATATCGAGGCAAAGCTGATGCCCCAATATATTCCATTCAGATATGCATTCCTAAGCATGgtaatttggtactcttgtttcttaatatattttgttcacaaaatgattcagtgtttttcttgctaacgtctcttttttgtgcag

Basic information

species Glycine max
transcript GLYMA08G22740.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G22740.1 (Glycine max), 5'ss of exon 5
lower sequence: AT3G15840.1 (Arabidopsis thaliana), 5'ss of exon 5
CCAATTATGTGTGGTGGTGAGCCAAGGGCTATGCTTAGAAAATATCGAGGCAAAGCTGATGCCCCAATATATTCCATTCAGATATGCATTCCTAAGCATGgtaa------tttggtactcttgtttcttaatatattttgttcacaaaatgattcagtgtttttcttgctaacgtctcttttttgtgcag-----------
||||| ||||||||||| |||||||| || |||||||  ||| ||||||||||||| ||| | || |||||  | || ||||| ||||||||||||||||||        |||  || ||     ||  |  ||  |||||  || ||||  ||   ||| ||  ||    || | | | |||  |               
CCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTAAGAAAGATCGAGGCAAAGCCGATTCTCCGATATACACTATGCAGATTTGCATTCCTAAGCATGgttcgttttcttttataatcaaaaatcaaatcatggtttgtg-accaaatagttatttgtattaatttgacacttttatctttcctatgaatcattatcag

upper sequence: GLYMA08G22740.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv09s0002g06980.t01 (Vitis vinifera), 5'ss of exon 5
CCAATTATGTGTGGTGGTGAGCCAAGGGCTATGCTTAGAAAATATCGAGGCAAAGCTGATGCCCCAATATATTCCATTCAGATATGCATTCCTAAGCATGgtaatttggtactcttgtttcttaatatattttgttcacaaaatgattcagtgtttttcttgctaacgtctcttttttgtgcag
|| || |||||||||||||| |||||||| ||||||| ||||   ||||| |||||||||   || |||||| | || ||||||||||||||||||||||||   |    | ||     || |  |   |||| |||  |||   ||      || | ||  | ||| ||   ||||       
CCCATCATGTGTGGTGGTGAACCAAGGGCAATGCTTAAAAAAGCCCGAGGAAAAGCTGATCGTCCCATATATACTATCCAGATATGCATTCCTAAGCATGgttgataataaatcagaactcatcttgcctttt-ttcttaaatacataattccttctcctgacaaacatccacttttcacag--
















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|9984428|gb|BE658536.1|BE658536
EST:     CAAAGCTGATGCCCCAATATATTCCATTCAGATATGCATTCCTAAGCATG                         CTTTGAACTTGATCTTTTCATTTACAAATGGAGTAGACTGGGATGGTCCAT
genomic: CAAAGCTGATGCCCCAATATATTCCATTCAGATATGCATTCCTAAGCATGgtaatttggt ... ttttgtgcagCTTTGAACTTGATCTTTTCATTTACAAATGGAGTAGACTGGGATGGTCCAT
EST: gi|192314804|gb|FK006016.1|FK006016
EST:     CAAAGCTGATGCCCCAATATATTCCATTCAGATATGCATTCCTAAGCATG                         CTTTGAACTTGATCTTTTCATTTACAAATGGAGTAGACTGGGATGGTCCAT
genomic: CAAAGCTGATGCCCCAATATATTCCATTCAGATATGCATTCCTAAGCATGgtaatttggt ... ttttgtgcagCTTTGAACTTGATCTTTTCATTTACAAATGGAGTAGACTGGGATGGTCCAT
EST: gi|209725498|gb|BW677795.1|BW677795
EST:     CAAAGCTGATGCCCCAATATATTCCATTCAGATATGCATTCCTAAGCATG                         CTTTGAACTTGATCTTTTCATTTACAAATGGAGTAGACTGGGATGGTCCAT
genomic: CAAAGCTGATGCCCCAATATATTCCATTCAGATATGCATTCCTAAGCATGgtaatttggt ... ttttgtgcagCTTTGAACTTGATCTTTTCATTTACAAATGGAGTAGACTGGGATGGTCCAT
EST: gi|17519754|gb|BM188796.1|BM188796
EST:     CAAAGCTGATGCCCCAATATATTCCATTCAGATATGCATTCCTAAGCATG                         CTTTGAACTTGATCTTTTCATTTACAAATGGAGTAGACTGGGATGGTCCAT
genomic: CAAAGCTGATGCCCCAATATATTCCATTCAGATATGCATTCCTAAGCATGgtaatttggt ... ttttgtgcagCTTTGAACTTGATCTTTTCATTTACAAATGGAGTAGACTGGGATGGTCCAT
EST: gi|20448322|gb|BQ252446.1|BQ252446
EST:     CAAAGCTGATGCCCCAATATATTCCATTCAGATATGCATTCCTAAGCATG                         CTTTGAACTTGATCTTTTCATTTACAAATGGAG
genomic: CAAAGCTGATGCCCCAATATATTCCATTCAGATATGCATTCCTAAGCATGgtaatttggt ... ttttgtgcagCTTTGAACTTGATCTTTTCATTTACAAATGGAG
EST: gi|151400172|gb|EV269986.1|EV269986
EST:     CAAAGCTGATGCCCCAATATATTCCATTCAGATATGCATTCCTAAGCATG                         CCTTGAACTTGATCTTTTCATTTACAAATGGAGTAGACTGGGATGGTCCAT
genomic: CAAAGCTGATGCCCCAATATATTCCATTCAGATATGCATTCCTAAGCATGgtaatttggt ... ttttgtgcagCTTTGAACTTGATCTTTTCATTTACAAATGGAGTAGACTGGGATGGTCCAT
EST: gi|213596677|gb|DB977993.1|DB977993
EST:     CAAAGCTGATGCCCCAATATATTCCATTCAGATATGCATTCCTAAGCATG                         CTTTGAACTTGATCTTTTCATTTACAAATGGAGTAGACTGGGATGGTCCAT
genomic: CAAAGCTGATGCCCCAATATATTCCATTCAGATATGCATTCCTAAGCATGgtaatttggt ... ttttgtgcagCTTTGAACTTGATCTTTTCATTTACAAATGGAGTAGACTGGGATGGTCCAT
EST: gi|213608233|gb|DB970830.1|DB970830
EST:     CAAAGCTGATGCCCCAATATATTCCATTCAGATATGCATTCCTAAGCATG                         CTTTGAACTTGATCTTTTCATTTACAAATGGAGTAGACTGGGATGG-CCAT
genomic: CAAAGCTGATGCCCCAATATATTCCATTCAGATATGCATTCCTAAGCATGgtaatttggt ... ttttgtgcagCTTTGAACTTGATCTTTTCATTTACAAATGGAGTAGACTGGGATGGTCCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAATTATGTGTGGTGGTGAGCCAAGGGCTATGCTTAGAAAATATCGAGGCAAAGCTGATGCCCCAATATATTCCATTCAGATATGCATTCCTAAGCATGgtaatttggtactcttgtttcttaatatattttgttcacaaaatgattcagtgtttttcttgctaacgtctcttttttgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT