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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGCCTCCACGATACAGAGATTCTGTTCGGGCCATTACTCCGGGGTTGCCCCTTTTCCTTTACAACTATTCCACTCACCAACTCCATGGAATCTTTGAGgtgtgttaagtgttaacaattcaacatcttctttctcaattaatttagtttaatttaatgaggctgcttgttctggagtccaatttgcattataaattatttatggattgggccattagattaattaacctttagcagcttcatgttttgaatacttttttggaattaactcataatatgtggtggggtttgttcag

Basic information

species Glycine max
transcript GLYMA08G02840.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G02840.2 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM5G860590_T02 (Zea mays), 5'ss of exon 2
TCTGCCTCCACGATACAGAGATTCTGTTCGGGCCATTACTCCGGGGTTGCCCCTTTTCCTTTACAACTATTCCACTCACCAACTCCATGGAATCTTTGAGgtgtgttaagtgttaacaattcaacatcttctttctcaattaatttagtttaatttaatgaggctgcttgttctgg-agtccaatttgcattataa-attatttatggattgggccattagattaattaacctttagcagcttcatgttttgaatacttttttggaattaactcataatatgtggtggggtttgttcag
    | |||| | ||||| ||||||||  ||||||| |  || ||  ||||||| ||||| |||||||| ||||| ||||| ||||| || ||||||||||||    | ||   ||| ||   || |  |||     | |   ||  |||||   | || |   |  ||  ||    ||||  ||    || ||   || ||||  | ||       ||  | | ||   | | | |   ||  || |    || |       |||| |  |||||  | | |||   |       |||
----CGTCCA-GGTACAGGGATTCTGTGAGGGCCATCAGGCCCGGCCTGCCCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTTGAGGTG----AGgtccaaactat---acctactctactctactcttttgtgtttatcatcatcatcattattactcgatcagtcgtatgcatatgattccatcatttcagcatctttatctttcaatcat--gcttgtggttactaaatata--aaaaaagaagggggaaatttctcatcgtctatgggacga---acgcag

upper sequence: GLYMA08G02840.2 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM5G860590_T01 (Zea mays), 5'ss of exon 2
TCTGCCTCCACGATACAGAGATTCTGTTCGGGCCATTACTCCGGGGTTGCCCCTTTTCCTTTACAACTATTCCACTCACCAACTCCATGGAATCTTTGAGgtgtgttaagtgttaacaattcaacatcttctttctcaattaatttagtttaatttaatgaggctgcttgttctgg-agtccaatttgcattataa-attatttatggattgggccattagattaattaacctttagcagcttcatgttttgaatacttttttggaattaactcataatatgtggtggggtttgttcag
 |||||  |  | ||||| ||||||||  ||||||| |  || ||  ||||||| ||||| |||||||| ||||| ||||| ||||| || ||||||||||||    | ||   ||| ||   || |  |||     | |   ||  |||||   | || |   |  ||  ||    ||||  ||    || ||   || ||||  | ||       ||  | | ||   | | | |   ||  || |    || |       |||| |  |||||  | | |||   |       |||
GCTGCCGTCCAGGTACAGGGATTCTGTGAGGGCCATCAGGCCCGGCCTGCCCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTTGAGgtg----aggtccaaactat---acctactctactctactcttttgtgtttatcatcatcatcattattactcgatcagtcgtatgcatatgattccatcatttcagcatctttatctttcaatcat--gcttgtggttactaaatata--aaaaaagaagggggaaatttctcatcgtctatgggacga---acgcag
















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|193522381|gb|FK479916.1|FK479916
EST:     CCCTTTTCCTTTACAACTATTCCACTCACCAACTCCATGGAATCTTTGAG                         GCTGCAAGTTTTGGAGGGT
genomic: CCCTTTTCCTTTACAACTATTCCACTCACCAACTCCATGGAATCTTTGAGgtgtgttaag ... gtttgttcagGCTGCAAGTTTTGGAGGGT
EST: gi|207749632|gb|GD721890.1|GD721890
EST:     ACCAACTCCATGGAATCTTTGAG                         GCTGCAAGTTTTGGAGGGTCAAATATTG
genomic: ACCAACTCCATGGAATCTTTGAGgtgtgttaag ... gtttgttcagGCTGCAAGTTTTGGAGGGTCAAATATTG
EST: gi|208240854|gb|GE036856.1|GE036856
EST:     CCCTTTTCCTTTACAACTATTCCACTCACCAACTCCATGGAATCTTTGAG                         GCTGCAAGTTTTGGAGGGTCAAATATTGATCCATCAGCTTGGGAGGATAAG
genomic: CCCTTTTCCTTTACAACTATTCCACTCACCAACTCCATGGAATCTTTGAGgtgtgttaag ... gtttgttcagGCTGCAAGTTTTGGAGGGTCAAATATTGATCCATCAGCTTGGGAGGATAAG
EST: gi|193447072|gb|FK416277.1|FK416277
EST:     CCCTTTTCCTTTACAACTATTCCACTCACCAACTCCATGGAATCTTTGAG                         GCTGCAAGTTTTGGAGGGTCAAATATTGATCCATCAGCTTGGGAGGATAAG
genomic: CCCTTTTCCTTTACAACTATTCCACTCACCAACTCCATGGAATCTTTGAGgtgtgttaag ... gtttgttcagGCTGCAAGTTTTGGAGGGTCAAATATTGATCCATCAGCTTGGGAGGATAAG
EST: gi|208028223|gb|GD826286.1|GD826286
EST:     CCCTTTTCCTTTACAACTATTCTACTCACCAACTTCATGGAATCTTTCAG                         GCTGCAAGTTTTGGAGGGTCAAATATTGATCCATCAGCTTGGGAGGATAAG
genomic: CCCTTTTCCTTTACAACTATTCCACTCACCAACTCCATGGAATCTTTGAGgtgtgttaag ... gtttgttcagGCTGCAAGTTTTGGAGGGTCAAATATTGATCCATCAGCTTGGGAGGATAAG
EST: gi|193718263|gb|FK653071.1|FK653071
EST:     CCCTTTTCCTTTACAACTATTCCACTCACCAACTCCATGGAATCTTTGAG                         GCTGCAAGTTTTGGAGGGTC
genomic: CCCTTTTCCTTTACAACTATTCCACTCACCAACTCCATGGAATCTTTGAGgtgtgttaag ... gtttgttcagGCTGCAAGTTTTGGAGGGTC
EST: gi|207695662|gb|GD677185.1|GD677185
EST:     CCCTTTTCCTTTACAACTATTCCACTCACCAACTCCATGGAATCTTTGAG                         GCTGCAAGTTTTGGAGGGTCAAATATTGATCCATCAGCTTGGGAGGATAAG
genomic: CCCTTTTCCTTTACAACTATTCCACTCACCAACTCCATGGAATCTTTGAGgtgtgttaag ... gtttgttcagGCTGCAAGTTTTGGAGGGTCAAATATTGATCCATCAGCTTGGGAGGATAAG
EST: gi|208270862|gb|GE069898.1|GE069898
EST:     CCCTTTTCCTTTACAACTATTCCACTCACCAACTCCATGGAATCTTTGAG                         GCTGCAAGTTTTGGAGGGTCAAATATTGATCCATCAGCTTGGGAGGATAAG
genomic: CCCTTTTCCTTTACAACTATTCCACTCACCAACTCCATGGAATCTTTGAGgtgtgttaag ... gtttgttcagGCTGCAAGTTTTGGAGGGTCAAATATTGATCCATCAGCTTGGGAGGATAAG
EST: gi|193371017|gb|FK335354.1|FK335354
EST:     CCCTTTTCCTTTACAACTATTCCACTCACCAACTCCATGGAATCTTTGAG                         GCTGCAAGTTTTGGAGGGTCAAATATTGATCCATCAGCTTGGGAGGATAAG
genomic: CCCTTTTCCTTTACAACTATTCCACTCACCAACTCCATGGAATCTTTGAGgtgtgttaag ... gtttgttcagGCTGCAAGTTTTGGAGGGTCAAATATTGATCCATCAGCTTGGGAGGATAAG
EST: gi|254313599|gb|GR831228.1|GR831228
EST:     CCCTTTTCCTTTACA-CTATTCCACTCACCAACTCCATGGAATCTTTGAG                         -CTGCAAGTTTTGGAGGGTCAAATATTGAT
genomic: CCCTTTTCCTTTACAACTATTCCACTCACCAACTCCATGGAATCTTTGAGgtgtgttaag ... gtttgttcagGCTGCAAGTTTTGGAGGGTCAAATATTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTGCCTCCACGATACAGAGATTCTGTTCGGGCCATTACTCCGGGGTTGCCCCTTTTCCTTTACAACTATTCCACTCACCAACTCCATGGAATCTTTGAGgtgtgttaagtgttaacaattcaacatcttctttctcaattaatttagtttaatttaatgaggctgcttgttctggagtccaatttgcattataaattatttatggattgggccattagattaattaacctttagcagcttcatgttttgaatacttttttggaattaactcataatatgtggtggggtttgttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA