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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTAATTGGCAAAGAGAGTGTACAATGGAAGACATTTTGATGCAATTGAAGAAAGAAATGATGTCTCCACAAAATCGGAAGCTAGCTCAGCCACCTGAAGgtgtgtcaatcttatttctgattgttgttacttgatagtttatttataatgtaatctttattttagctattggataagtgattggatgtgaactttatgt...

Basic information

species Glycine max
transcript GLYMA08G04710.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G04710.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv01s0011g05630.t01 (Vitis vinifera), 5'ss of exon 4
GCTAATTGGCAAAGAGAGTGTACAATGGAAGACATTTTGATGCAATTGAAGAAAGAAATGATGTCTCCACAAAATCGGAAGCTAGCTCAGCCACCTGAAGgtgtgtcaatcttatttctgattgttgttacttgatagtttatttataatgtaatctttattttagctattggataagtgattggatgtgaactttatgt--
|||| |||||| || |||  ||||||||| ||||| ||||  |||||||||||||||||||||||||| || ||||| ||||| |||||||| ||||||||| ||| ||| || |||||| |  |||  |    ||||| | ||  |  | |  |||| |   | | ||    | || | |  ||        | | |||  
GCTACTTGGCAGAGGGAGCATACAATGGAGGACATATTGACTCAATTGAAGAAAGAAATGATGTCTCCCCAGAATCGAAAGCTGGCTCAGCCTCCTGAAGgtttgttaattttgtttctggtgattgacaga-aatagtgttttctttctatc-tcttcaagattgttaaaaaaaaaataaaagggaagattgtctttgtag
















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|9985928|gb|BE659934.1|BE659934
EST:     GAAAGAAATGATGTCTCCACAAAATCGGAAGCTAGCTCAGCCACCTGAAG                         GCAATGAAGATGGCAGGATTGATCAAAAGGGGCTGGTGCTGAGATGTTGTA
genomic: GAAAGAAATGATGTCTCCACAAAATCGGAAGCTAGCTCAGCCACCTGAAGgtgtgtcaat ... tgacttttagGCAATGAAGATGGCAGGATTGATCAAAAGGGGCTGGTGCTGAGATGTTGTA
EST: gi|18041432|gb|BM309726.1|BM309726
EST:     GAAAGAAATGATGTCTCCACAAAATCGGAAGCTAGCTCAGCCACCTGAAG                         GCAATGAAGATGGCAGGATTGATCAAAAGGGGCTGGTGCTGAGATGTTGTA
genomic: GAAAGAAATGATGTCTCCACAAAATCGGAAGCTAGCTCAGCCACCTGAAGgtgtgtcaat ... tgacttttagGCAATGAAGATGGCAGGATTGATCAAAAGGGGCTGGTGCTGAGATGTTGTA
EST: gi|192319053|gb|FK010617.1|FK010617
EST:     GAAAGAAATGATGTCTCCACAAAATCGGAAGCTAGCTCAGCCACCTGAAG                         GCAATGAAGATGGCAGGATTGATCAAAAGGGGCTGGTGCTGAGATGCTGTA
genomic: GAAAGAAATGATGTCTCCACAAAATCGGAAGCTAGCTCAGCCACCTGAAGgtgtgtcaat ... tgacttttagGCAATGAAGATGGCAGGATTGATCAAAAGGGGCTGGTGCTGAGATGTTGTA
EST: gi|7029314|gb|AW459097.1|AW459097
EST:     ATGATGTCTCCACAAAATCGGAAGCTAGCTCAGCCACCTGAAG                         GCAATGAAGATGGCAGGATTGATCAAAAGGGGCTGGTGCTGAGATGTTGTA
genomic: ATGATGTCTCCACAAAATCGGAAGCTAGCTCAGCCACCTGAAGgtgtgtcaat ... tgacttttagGCAATGAAGATGGCAGGATTGATCAAAAGGGGCTGGTGCTGAGATGTTGTA
EST: gi|18716865|gb|BM522906.1|BM522906
EST:     GAAAGAAATGATGTCTCCACAAAATCGGAAGCTAGCTCAGCCACCTGAAG                         GCAATGAAGATGGCAGGATTGATCAAAAGGGGCTGGTGCTGAGATGTTGTA
genomic: GAAAGAAATGATGTCTCCACAAAATCGGAAGCTAGCTCAGCCACCTGAAGgtgtgtcaat ... tgacttttagGCAATGAAGATGGCAGGATTGATCAAAAGGGGCTGGTGCTGAGATGTTGTA
EST: gi|10252728|gb|BE820494.1|BE820494
EST:     ATGATGTCTCCACAAAATCGGAAGCTAGCTCAGCCACCTGAAG                         GCAATGAAGATGGCAGGATTGATCAAAAGGGGCTGGTGCTGAGATGTTGTA
genomic: ATGATGTCTCCACAAAATCGGAAGCTAGCTCAGCCACCTGAAGgtgtgtcaat ... tgacttttagGCAATGAAGATGGCAGGATTGATCAAAAGGGGCTGGTGCTGAGATGTTGTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTAATTGGCAAAGAGAGTGTACAATGGAAGACATTTTGATGCAATTGAAGAAAGAAATGATGTCTCCACAAAATCGGAAGCTAGCTCAGCCACCTGAAGgtgtgtcaatcttatttctgattgttgttacttgatagtttatttataatgtaatctttattttagctattggataagtgattggatgtgaactttatgt

- - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG