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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccaagcttccttagtgcttataaccaacctctgatcgttataattgccttttcttatgtttctatgttgtaatctgcagATTCGTGATGCATACATGCTTAGGATTTTTGAGGATAACCAAACACGTCTACCAAGATGGTGCAACAATGAGAACGATCGGCATCCATTCTGCCAGATTC

Basic information

species Glycine max
transcript GLYMA02G03160.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G03160.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv01s0026g00920.t01 (Vitis vinifera), 3'ss of exon 6
gtaagc-caagcttccttagtgcttata-----accaacctctgatcgttataattgccttttcttatgtttctatgttgtaatctgcagATTCGTGATGCATACATGCTTAGGATTTTTGAGGATAACCAAACACGTCTACCAAGATGGTGCAACAATGAGAACGATCGGCATCCATTCTGCCAGATTC
|||||    | || ||||  ||  ||        |     ||   || ||| ||||||    | | |  |  || |  |        ||||||||||||||||| |||||||  || |||||| | |||||| ||||||| ||||| ||||||  | ||||  | | |||||  |  ||||||||||| |
gtaagtatcaactgccttgctgtatacgtggatgcatctttcctctccttacaattgc----tgtaacatggctttactactgctcacagATTCGTGATGCATATATGCTTAAAATCTTTGAGAACAACCAATCACGTCTGCCAAGTTGGTGCGGCGATGAAGATGGTCGGCTCCAGTTCTGCCAGATCC
















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|9900785|gb|BE609753.1|BE609753
EST:     CTGGAATATTCGGCCCTATTTCTAGCTCCATTCAAGTAACTGAATTCACA                         ATTCGTGATGCATACATGCTTAGGATTTTTGAGGATAACCAAACACGTCTA
genomic: CTGGAATATTCGGCCCTATTTCTAGCTCCATTCAAGTAACTGAATTCACAgtaagccaag ... taatctgcagATTCGTGATGCATACATGCTTAGGATTTTTGAGGATAACCAAACACGTCTA
EST: gi|10253715|gb|BE821481.1|BE821481
EST:     CTGGAATATTCGGCCCTATTTCTAGCTCCATTCAAGTAACTGAATTCACA                         ATTCGTGATGCATACATGCTTAGGATTTTTGAGGATAACCAAACACGTCTA
genomic: CTGGAATATTCGGCCCTATTTCTAGCTCCATTCAAGTAACTGAATTCACAgtaagccaag ... taatctgcagATTCGTGATGCATACATGCTTAGGATTTTTGAGGATAACCAAACACGTCTA
EST: gi|192309026|gb|FK001802.1|FK001802
EST:     CTGGAATATTCGGCCCTATTTCTAGCTCCATTCAAGTAACTGAATTCACA                         ATTCGTGATGCATACATGCTTAGGATTTTTGAGGATAACCAAACACGTCTA
genomic: CTGGAATATTCGGCCCTATTTCTAGCTCCATTCAAGTAACTGAATTCACAgtaagccaag ... taatctgcagATTCGTGATGCATACATGCTTAGGATTTTTGAGGATAACCAAACACGTCTA
EST: gi|7030112|gb|AW459895.1|AW459895
EST:     CTGGAATATTCGGCCCTATTTCTAGCTCCATTCAAGTAACTGAATTCACA                         ATTCGTGATGCATACATGCTTAGGATTTTTGAGGATAACCAAACACGTCTA
genomic: CTGGAATATTCGGCCCTATTTCTAGCTCCATTCAAGTAACTGAATTCACAgtaagccaag ... taatctgcagATTCGTGATGCATACATGCTTAGGATTTTTGAGGATAACCAAACACGTCTA
EST: gi|192309025|gb|FK001801.1|FK001801
EST:     CTGGAATATTCGGCCCTATTTCTAGCTCCATTCAAGTAACTGAATTCACA                         ATTCGTGATGCATACATGCTTAGGATTTTTGAGGATAACCAAACACGTCTA
genomic: CTGGAATATTCGGCCCTATTTCTAGCTCCATTCAAGTAACTGAATTCACAgtaagccaag ... taatctgcagATTCGTGATGCATACATGCTTAGGATTTTTGAGGATAACCAAACACGTCTA
EST: gi|298187517|gb|HO034666.1|HO034666
EST:     CTGGAATATTCGGCCCTATTTCTAGCTCCATTCAAGTAACTGAATTCACA                         ATTCGCGATGCATACATGCTTAGGATTTTTGAGGATAACCAAACACGTCTA
genomic: CTGGAATATTCGGCCCTATTTCTAGCTCCATTCAAGTAACTGAATTCACAgtaagccaag ... taatctgcagATTCGTGATGCATACATGCTTAGGATTTTTGAGGATAACCAAACACGTCTA
EST: gi|13252536|gb|BG363439.1|BG363439
EST:     CTGAATTCACA                         ATTCGTGATGCATACATGCTTAGGATTTTTGAGGATAACCAAACACGTCTA
genomic: CTGAATTCACAgtaagccaag ... taatctgcagATTCGTGATGCATACATGCTTAGGATTTTTGAGGATAACCAAACACGTCTA
EST: gi|6912952|gb|AW394540.1|AW394540
EST:     CTGGAATATTCGGCCCTATTTCTAGCTCCATTCAAGTAACTGAATTCACA                         ATTCGTGATGCATACATGCTTAGGATTTTTGAGGATAACCAAACACGTCTA
genomic: CTGGAATATTCGGCCCTATTTCTAGCTCCATTCAAGTAACTGAATTCACAgtaagccaag ... taatctgcagATTCGTGATGCATACATGCTTAGGATTTTTGAGGATAACCAAACACGTCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caacctctgatcgttataattgccttttcttatgtttctatgttgtaatctgcagATTCGTGATGCATACATGCTTAGGATTTTTGAGGATAACCAAACACGTCTACCAAGATGGTGCAACAATGAGAACGATCGGCATCCATTCTGCCAGATTC
    ctctgat  putative branch site (score: 4)
             ttataatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagccaagcttccttagtgcttataaccaacctctgatcgttataattgccttttcttatgtttctatgttgtaatctgcagATTCGTGATGCATACATGCTTAGGATTTTTGAGGATAACCAAACACGTCTACCAAGATGGTGCAACAATGAGAACGATCGGCATCCATTCTGCCAGATTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG