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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaaaaaatgtagtatagaggactggtatttagatgttgtttgtgggagaattttatttatttataatgagttttggtgtttggtttaatggtttttcagGTCGAGTAGATTTGCAAGGCTCCAAGGTATTCAGTGTGCTATGGCTGGGAAGAATGCTTATTTGAGATTCACTTGTAGCACGGGTGATGCCATGGGGATG

Basic information

species Glycine max
transcript GLYMA02G44070.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G44070.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0122g00610.t01 (Vitis vinifera), 3'ss of exon 1
-agaaaaaatgtagtatagaggactggtatttagatgtt-gtttgtgggagaattttatttatttataatgagttttggtgtttggtttaatggtttttcagGTCGAGTAGATTTGCAAGGCTCCAAGGTATTCAGTGTGCTATGGCTGGGAAGAATGCTTATTTGAGATTCACTTGTAGCACGGGTGATGCCATGGGGATG
    ||| |   |  ||   | | | | ||||||  |   |   |||    | |||||  | |    | |      || | ||   |||  | | |||| || |||||||||||||||||||| ||| ||||||| ||||||||||| |||||||||  |||  | ||||| |  || ||||| |||||||| ||||| |||
actcaaacactgataatcctgaagttg-atttagcagccagaaagtgtcctagttttaactgtgctcattttacaatgatattccattttcttgatttt-agATCGAGTAGATTTGCAAGGCTGCAAAGTATTCAATGTGCTATGGCGGGGAAGAATCTTTACATAAGATTTAGCTGCAGCACTGGTGATGCAATGGGCATG
















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|13563483|gb|BG551703.1|BG551703
EST:     TCAATTTTGATACCTTGTCACTTGTTTTCAACAG                         GTCGAGTAGATTTGCAAGGCTCCAAGGTATTCAGTGTGCTATGGCTGGGAA
genomic: TCAATTTTGATACCTTGTCACTTGTTTTCAACAGgtttgatttt ... ggtttttcagGTCGAGTAGATTTGCAAGGCTCCAAGGTATTCAGTGTGCTATGGCTGGGAA
EST: gi|207800299|gb|GD773680.1|GD773680
EST:     TTCCTTGAGGATCCTCTCAATTTTGATACCTTGTCACTTGTTTTCAACAG                         GTCGAGTAGATTTGCAAGGCTCCAAGGTATTCAGTGTGCTATGGCT
genomic: TTCCTTGAGGATCCTCTCAATTTTGATACCTTGTCACTTGTTTTCAACAGgtttgatttt ... ggtttttcagGTCGAGTAGATTTGCAAGGCTCCAAGGTATTCAGTGTGCTATGGCT
EST: gi|192301149|gb|FG990159.1|FG990159
EST:     TTCCTTGAGGATCCTCTCAATTTTGATACCTTGTCACTTGTTTTCAACAG                         GTCGAGTAGATTTGCAAGGCTCCAAGGTATTCAGTGTGCTATGGCTGGGAA
genomic: TTCCTTGAGGATCCTCTCAATTTTGATACCTTGTCACTTGTTTTCAACAGgtttgatttt ... ggtttttcagGTCGAGTAGATTTGCAAGGCTCCAAGGTATTCAGTGTGCTATGGCTGGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggagaattttatttatttataatgagttttggtgtttggtttaatggtttttcagGTCGAGTAGATTTGCAAGGCTCCAAGGTATTCAGTGTGCTATGGCTGGGAAGAATGCTTATTTGAGATTCACTTGTAGCACGGGTGATGCCATGGGGATG
                                      gtttaat  putative branch site (score: 4)
                                               tttttc  putative PPT
     attttatttatttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaaaaaatgtagtatagaggactggtatttagatgttgtttgtgggagaattttatttatttataatgagttttggtgtttggtttaatggtttttcagGTCGAGTAGATTTGCAAGGCTCCAAGGTATTCAGTGTGCTATGGCTGGGAAGAATGCTTATTTGAGATTCACTTGTAGCACGGGTGATGCCATGGGGATG

- aaaaaat
- - - - - - - - - - - - - - - - gatgttg
- - - - - - - - - - - - - - - - - - - - ttgtggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtttg