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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataggactgtaggtagtattttgatgaggcctgctttttcgtaaatcaccattgattccttatcctgtcaatttgttcatcttgcatttattttttgcagACAAACTTAATTAAGGAAAGCATTAGAATGGGATACAATGATTTTGGAGAGTTTTACTATGCTCATGGTCAATTGGGGGACGCTTTTAAAAGTTATGTCC

Basic information

species Glycine max
transcript GLYMA03G01880.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G01880.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G61140.1 (Arabidopsis thaliana), 3'ss of exon 1
ataggactgtaggtagtattttgatga----ggcctgcttt-ttcgtaaat--caccattgattccttatcctgtcaatttgttcatcttgcatttattttttgcagACAAACTTAATTAAGGAAAGCATTAGAATGGGATACAATGATTTTGGAGAGTTTTACTATGCTCATGGTCAATTGGGGGACGCTTTTAAAAGTTATGTCC
   | | | |   |||   ||| |||      || |||||  ||| |||||  ||  | || |   |  || | |  || |||  || |   || | | |    |||||||| || || ||||||||||| |||||||| |||||||| |||||||| || || || ||   ||||    | || || ||||| || |  ||| |||
---gcattatgcatagctctttcatggtaatagcttgcttgattcttaaattgcattaatgttgattcttcttcttgatatgtgtat-tgatatgtgtat---acagACAAATTTGATCAAGGAAAGCATCAGAATGGGTTACAATGACTTTGGAGATTTCTATTACGCATGTGGTATGCTCGGAGATGCTTTCAAGAACTATATCC

upper sequence: GLYMA03G01880.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0048g01980.t01 (Vitis vinifera), 3'ss of exon 1
ataggactgtaggtagtattttgatgaggcctgctttttcgtaaatcacc-----attgattccttatcctgtcaatttgttcatcttgcatttat--tttttgcagACAAACTTAATTAAGGAAAGCATTAGAATGGGATACAATGATTTTGGAGAGTTTTACTATGCTCATGGTCAATTGGGGGACGCTTTTAAAAGTTATGTCC
       | | |||||  | | |  |   | | | |||  |  |||  |      |   ||||   ||    | | ||   || |  ||   | ||  ||| |||||||||| ||||| || |||||||| ||||||||||||||||| || ||||| ||||||||||| || |||  | | | ||| |||||||| | |||||| |
-------ttttggtaggttataggggtaacgtacctttgtgcgaatggctgaagtacccattctgaatttcataatttgcctccttatggtgtgatcctttctgcagACAAATTTAATCAAAGAAAGCATAAGAATGGGATACAATGACTTCGGAGATTTTTACTATGCCCACGGTTTACTTGCGGATGCTTTTAAGAATTATGTTC
















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|6566989|gb|AW234616.1|AW234616
EST:     GAGCGGAGCAGAAGAAGGAGAAGCTCGAGAACGAACTCAATGCGTATAGG                         ACAAACTTAATTAAGGAAAGCATTAGAATGGGATACAATGATTTTGGAGAG
genomic: GAGCGGAGCAGAAGAAGGAGAAGCTCGAGAACGAACTCAATGCGTATAGGgtgagttttt ... ttttttgcagACAAACTTAATTAAGGAAAGCATTAGAATGGGATACAATGATTTTGGAGAG
EST: gi|27427398|gb|CA938918.1|CA938918
EST:     AGAAGCTCGAGAACGAACTCAATGCGTATAGG                         ACAAACTTAATTAAGGAAAGCATTAGAATGGGATACAATGATTTTGGAGAG
genomic: AGAAGCTCGAGAACGAACTCAATGCGTATAGGgtgagttttt ... ttttttgcagACAAACTTAATTAAGGAAAGCATTAGAATGGGATACAATGATTTTGGAGAG
EST: gi|37997756|gb|CF809345.1|CF809345
EST:     GAACTCAATGCGTATAGG                         ACAAACTTAATTAAGGAAAGCATTAGAATGGGATACAATGATTTTGGAGAG
genomic: GAACTCAATGCGTATAGGgtgagttttt ... ttttttgcagACAAACTTAATTAAGGAAAGCATTAGAATGGGATACAATGATTTTGGAGAG
EST: gi|11688928|gb|BF596666.1|BF596666
EST:     GAGCGGAGCAGAAGAAGGAGAAGCTCGAGAACGAACTCAATGCGTATAGG                         ACAAACTTAATTAAGGAAAGCATTAGAATGGGATACAATGATTTTGGAGAG
genomic: GAGCGGAGCAGAAGAAGGAGAAGCTCGAGAACGAACTCAATGCGTATAGGgtgagttttt ... ttttttgcagACAAACTTAATTAAGGAAAGCATTAGAATGGGATACAATGATTTTGGAGAG
EST: gi|13562787|gb|BG551007.1|BG551007
EST:     GAGCGGAGCAGAAGAAGGAGAAGCTCGAGAACGAACTCAATGCGTATAGG                         ACAAACTTAATTAAGGAAAGCATTAGAATGGGATACAATGATTTTGGAGAG
genomic: GAGCGGAGCAGAAGAAGGAGAAGCTCGAGAACGAACTCAATGCGTATAGGgtgagttttt ... ttttttgcagACAAACTTAATTAAGGAAAGCATTAGAATGGGATACAATGATTTTGGAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaccattgattccttatcctgtcaatttgttcatcttgcatttattttttgcagACAAACTTAATTAAGGAAAGCATTAGAATGGGATACAATGATTTTGGAGAGTTTTACTATGCTCATGGTCAATTGGGGGACGCTTTTAAAAGTTATGTCC
    cattgat  putative branch site (score: 4)
                                         tttatttttt  putative PPT
                                    ttgcatttatttttt  TA-rich tract