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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcagaattactatctgtgtgcttatgcatttgtataataatggtttatcttgagtcgggctaacttttggtttgtttttgtgtgttgctatatatcttcagGAGGATGCAAAGAAGCTTGACAGAGGTGCTAAAAATAAATACGTTGTATGAAGTTTATAGCGTTCTTAACTGGAAGCAAATGAAGGAATGCAGTACATTC

Basic information

species Glycine max
transcript GLYMA15G09630.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G09630.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv10s0003g02250.t01 (Vitis vinifera), 3'ss of exon 4
gtgagcagaattactatctgtgtgcttatgcatttgtataataatggtttatcttgagtcgggctaacttttggtttgtttttgtgtgttgctatatatctt-----cagGAGGATGCAAAGAAGCTTGACAGAGGTGCTAAAAATAAATACGTTGTATGAAGTT-TATAGCGTTCT-TAACTGGAAGCAAATGAAGGAATGCAGTACATTC
|| ||  || ||  | | ||  ||| || | |   | ||  |    |    |  ||  ||    | |      |   |    |   |  || | ||| | |      |||||||||||||||||||||||||||| ||| || |||  ||||    ||||| | | || ||  || | |   |||| | | |  ||   || ||  || |  
gtaag--gattttgtgtttg-atgcata-gtagaagcatc-tgcctgccctttctggttccaattcatcaaaagcaagggcctacataatgttctatttttctgttacagGAGGATGCAAAGAAGCTTGACAGAGCTGCCAAGAATCGATACACGATATGAGGCTGTACAGAATTGTGTCTGTGGAGGGACACCAAATGATTCAAGACGT--
















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|31457012|gb|CD399040.1|CD399040
EST:     AGTGGAAGGAGTTTCTTGATTACAATGACACTATTGGCTTTATATTTCAT                         GAGGATGCAAAGAAGCTTGACAGAGGTGCTAAAAATAAATACGTTGTATGA
genomic: AGTGGAAGGAGTTTCTTGATTACAATGACACAATTGGCTTTATATTTCATgtgagcagaa ... atatcttcagGAGGATGCAAAGAAGCTTGACAGAGGTGCTAAAAATAAATACGTTGTATGA
EST: gi|192308366|gb|FK002794.1|FK002794
EST:     AGTGGAAGGAGTTTCTTGATTACAATGACACAATTGGCTTTATATTTCAT                         GAGGATGCAAAGAAGCTTGACAGAGGTGCTAAAAATAAATACGTTGTATGA
genomic: AGTGGAAGGAGTTTCTTGATTACAATGACACAATTGGCTTTATATTTCATgtgagcagaa ... atatcttcagGAGGATGCAAAGAAGCTTGACAGAGGTGCTAAAAATAAATACGTTGTATGA
EST: gi|208251693|gb|GE044236.1|GE044236
EST:     GTGGAAGGAGTTTCTTGATTACAATGACACAATTGGCTTTATATTTCTAT                         GAGGATGCAAAGAAAGACTTGACAGAGGT
genomic: GTGGAAGGAGTTTCTTGATTACAATGACACAATTGGCTTTATATTTC-ATgtgagcagaa ... atatcttcagGAGGATGCAAAGAA-G-CTTGACAGAGGT
EST: gi|208147586|gb|GD951539.1|GD951539
EST:     TTTATATTTCAT                         GAGGATGCAAAGAAGCTTGACAGAGGTGCTAAAAATAAATACGTTGTATGA
genomic: TTTATATTTCATgtgagcagaa ... atatcttcagGAGGATGCAAAGAAGCTTGACAGAGGTGCTAAAAATAAATACGTTGTATGA
EST: gi|213616888|gb|DB978878.1|DB978878
EST:     AGTGGAAGGAGTTTCTTGATTACAATGACACAATTGGCTTTATATTTCAT                         GAGGATGCAAAGAAGCTTGACAGAGGTGCTAAAAATAAATACGTTGTATGA
genomic: AGTGGAAGGAGTTTCTTGATTACAATGACACAATTGGCTTTATATTTCATgtgagcagaa ... atatcttcagGAGGATGCAAAGAAGCTTGACAGAGGTGCTAAAAATAAATACGTTGTATGA
EST: gi|6846595|gb|AW348885.1|AW348885
EST:     AGTGGAAGGAGTTTCTTGATTACAATGACACAATTGGCTTTATATTTCAT                         GAGGATGCAAAGAAGCTTGACAGAGGTGCTAAAAATAAATACGTTGTATGA
genomic: AGTGGAAGGAGTTTCTTGATTACAATGACACAATTGGCTTTATATTTCATgtgagcagaa ... atatcttcagGAGGATGCAAAGAAGCTTGACAGAGGTGCTAAAAATAAATACGTTGTATGA
EST: gi|31470645|gb|CD412673.1|CD412673
EST:     AGTGGAAGGAGTTTCTTGATTACAATGACACAATTGGCTTTATATTTCAT                         GAGGATGCAAAGAAGCTTGACAGAGGTGCTAAAAATAAATACGTTGTATGA
genomic: AGTGGAAGGAGTTTCTTGATTACAATGACACAATTGGCTTTATATTTCATgtgagcagaa ... atatcttcagGAGGATGCAAAGAAGCTTGACAGAGGTGCTAAAAATAAATACGTTGTATGA
EST: gi|209698256|gb|BW678027.1|BW678027
EST:     AGTGGAAGGAGTTTCTTGATTACAATGACACAATTGGCTTTATATTTCAT                         GAGGATGCAAAGAAGCTTGACAGAGGTGCTAAAAATAAATACGTTGTATGA
genomic: AGTGGAAGGAGTTTCTTGATTACAATGACACAATTGGCTTTATATTTCATgtgagcagaa ... atatcttcagGAGGATGCAAAGAAGCTTGACAGAGGTGCTAAAAATAAATACGTTGTATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttgagtcgggctaacttttggtttgtttttgtgtgttgctatatatcttcagGAGGATGCAAAGAAGCTTGACAGAGGTGCTAAAAATAAATACGTTGTATGAAGTTTATAGCGTTCTTAACTGGAAGCAAATGAAGGAATGCAGTACATTC
           ggctaac  putative branch site (score: 2)
                                              tatcttc  putative PPT
                                          tatatatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcagaattactatctgtgtgcttatgcatttgtataataatggtttatcttgagtcgggctaacttttggtttgtttttgtgtgttgctatatatcttcagGAGGATGCAAAGAAGCTTGACAGAGGTGCTAAAAATAAATACGTTGTATGAAGTTTATAGCGTTCTTAACTGGAAGCAAATGAAGGAATGCAGTACATTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA