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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTCACTGAGAAGTCCGATGTGTATAGCTATGGTATCGTATTGCTTGAGCTTCTAACTGGGAGGAAAGCTGTTGACAACGAATCAAACCTCCATCATCTGgtgagtcttctagtgtgtgtctggtttgtaggtgtcacaaatttcatagcaccccattggaaaagtatgtgacttgttggattggctcaaacgaatgttt...

Basic information

species Glycine max
transcript GLYMA06G05900.1
intron # 27
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G05900.1 (Glycine max), 5'ss of exon 27
lower sequence: Vv04s0008g01970.t01 (Vitis vinifera), 5'ss of exon 26
CCTCACTGAGAAGTCCGATGTGTATAGCTATGGTATCGTATTGCTTGAGCTTCTAACTGGGAGGAAAGCTGTTGACAACGAATCAAACCTCCATCATCTGgtgagtcttctagtgtgtgtctggtttgtaggtgtcacaaatttcatagcaccccattggaaaagtatgtgacttgttggattggct--caaacgaatgttt---
 ||||| || ||||| ||||| || |||||||| || ||  | |||||||| || ||||| |||||||| || ||||| ||||| || |||||||||||||| | ||      | |  || |    |  |    ||      |  || | |  |||||   |   |  |  | || ||    | |    |||| ||  |||    
TCTCACGGAAAAGTCTGATGTCTACAGCTATGGAATTGTTCTACTTGAGCTGCTGACTGGAAGGAAAGCAGTAGACAATGAATCCAATCTCCATCATCTGgtaaatcaatcgcttttggtttctacttgaaccttcgtg---tctattgaattccattt--agcatgagaaattttttatgctagacgacaaatgatagttaatc
















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|208196246|gb|GD991769.1|GD991769
EST:     TAACTGGGAGGAAAGCTTGTTTGACAACGAATCAAACCTCCATCATCTG                         ATTTTGTCCAAGACAGCTAATGATGGCGTAATGGAAACCGTTGATCCAGAT
genomic: TAACTGGGAGGAAAGC-TG-TTGACAACGAATCAAACCTCCATCATCTGgtgagtcttc ... acttgcgtagATTTTGTCCAAGACAGCTAATGATGGCGTAATGGAAACCGTTGATCCAGAT
EST: gi|193668501|gb|FK608931.1|FK608931
EST:     CAACGAATCAAACCTTCCATCATCTG                         ATTTTGTCCAAGACAGCTAATGATGGCGTAATGGAAACCGTTGATCCAGAT
genomic: CAACGAATCAAACC-TCCATCATCTGgtgagtcttc ... acttgcgtagATTTTGTCCAAGACAGCTAATGATGGCGTAATGGAAACCGTTGATCCAGAT
EST: gi|193497998|gb|FK458738.1|FK458738
EST:     CAACGAATCAAACCTCCATCATCTG                         ATTTTGTCCAAGACAGCTAATGATGGCGTAATGGAAACCGTTGATCCAGAT
genomic: CAACGAATCAAACCTCCATCATCTGgtgagtcttc ... acttgcgtagATTTTGTCCAAGACAGCTAATGATGGCGTAATGGAAACCGTTGATCCAGAT
EST: gi|208174059|gb|GD968538.1|GD968538
EST:     TTCTAACTGGGAGGAAAGCTGTTGACAACGAATCAAACCTCCATCATCTG                         ATTTTGTCCAAGACAG
genomic: TTCTAACTGGGAGGAAAGCTGTTGACAACGAATCAAACCTCCATCATCTGgtgagtcttc ... acttgcgtagATTTTGTCCAAGACAG
EST: gi|5677050|gb|AI938180.1|AI938180
EST:     AACGAATCAAACCTCCATCATCTG                         ATTTTGTCCAAGACAGCTAATGATGGCGTAATGGAAACCGTTGATCCAGAT
genomic: AACGAATCAAACCTCCATCATCTGgtgagtcttc ... acttgcgtagATTTTGTCCAAGACAGCTAATGATGGCGTAATGGAAACCGTTGATCCAGAT
EST: gi|193564229|gb|FK518378.1|FK518378
EST:     CAACGAATCAAACCTCCATCATCTG                         ATTTTGTCCAAGACAGCTAATGATGGCGTAATGGAAACCGTTGATCCAGAT
genomic: CAACGAATCAAACCTCCATCATCTGgtgagtcttc ... acttgcgtagATTTTGTCCAAGACAGCTAATGATGGCGTAATGGAAACCGTTGATCCAGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTCACTGAGAAGTCCGATGTGTATAGCTATGGTATCGTATTGCTTGAGCTTCTAACTGGGAGGAAAGCTGTTGACAACGAATCAAACCTCCATCATCTGgtgagtcttctagtgtgtgtctggtttgtaggtgtcacaaatttcatagcaccccattggaaaagtatgtgacttgttggattggctcaaacgaatgttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT