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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtgttttcttttcaatttaatttcgggaaagtggggaagggggttaaatgcatcagtcattgtggttctttgtaattttttggttgttggtggtgaaatatagtcgtgtgtgtatttcctttgtattatggcagAGAATGCAACTTGCGGCAAAACTACTTATGTTCACTGTAAAGCTGGGCGGGGGAGGAGTACAACAATTGTGCTTTGTTATATG

Basic information

species Glycine max
transcript GLYMA08G03600.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G03600.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0016g02890.t01 (Vitis vinifera), 3'ss of exon 4
gtgggtgttttcttttcaatttaatttcgggaaagtggggaagggggttaaatgcatcagtcattgtggttctttg-taattttttggttgttggtggtgaaatatagtcgtgtgtgtatttcctttgtattatgg--cagAGAATGCAACTTGCGGCAAAACTACTTATGTTCACTGTAAAGCTGGGCGGGGGAGGAGTACAACAATTGTGCTTTGTTATATG
                            | | || |       |   ||| ||    ||||   |||| ||||| | |    |  ||  |  | | | |||||  |  |  | | | |   |  |   |  |  ||  ||||||||||| ||| ||| | ||||||||||||||| ||||||||||| || || ||||| ||||| ||||||||||| ||| ||
--------------------------gtgagcaattcttctttgactttacatctgccagtt-ctgtgattcttagatgccatggtgtgtagttgagatgaaagtttcttttctttttgggttttcccttctggggaacagAGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTG
















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|193582765|gb|FK537419.1|FK537419
EST:     CCGGGCTGTGCAGTTCATTCATC                         AGAATGCAACTTGCGGC-AAACTACTTATGTTCACTGTAAAGCTGGGCGGG
genomic: CCGGGCTGTGCAGTTCATTCATCgtgggtgttt ... attatggcagAGAATGCAACTTGCGGCAAAACTACTTATGTTCACTGTAAAGCTGGGCGGG
EST: gi|192295656|gb|FG990510.1|FG990510
EST:     GTTCATTCATC                         AGAATGCAACTTGCGGCAAAACTACTTATGTTCACTGTAAAGCTGGGCGGG
genomic: GTTCATTCATCgtgggtgttt ... attatggcagAGAATGCAACTTGCGGCAAAACTACTTATGTTCACTGTAAAGCTGGGCGGG
EST: gi|207832678|gb|GD803494.1|GD803494
EST:     AGTTCATTCATC                         AGAATGCAACTTGCGGCAAAACTACTTATGTTCACTGTAAAGCTGGGC-GG
genomic: AGTTCATTCATCgtgggtgttt ... attatggcagAGAATGCAACTTGCGGCAAAACTACTTATGTTCACTGTAAAGCTGGGCGGG
EST: gi|207819140|gb|GD793274.1|GD793274
EST:     CCGGGCTGTGTCAGTTCATTTCATC                         AGAATGCAACTTGCGGCAAAACTACTTATGTTCACTGTAAAGCTGGGCGG
genomic: CCGGGCTGTG-CAGTTCA-TTCATCgtgggtgttt ... attatggcagAGAATGCAACTTGCGGCAAAACTACTTATGTTCACTGTAAAGCTGGGCGG
EST: gi|19453452|gb|BM954862.1|BM954862
EST:     CTTTGCCCCCTCATTCGTGGATATTAACCGGGCTGTGCAGTTCATTCATC                         AGAATGCAACTTGCGGCAAAACTACTTATGTTCACTGTAAAGCTGGGCGGG
genomic: CTTTGCCCCCTCATTCGTGGATATTAACCGGGCTGTGCAGTTCATTCATCgtgggtgttt ... attatggcagAGAATGCAACTTGCGGCAAAACTACTTATGTTCACTGTAAAGCTGGGCGGG
EST: gi|213598064|gb|DB972252.1|DB972252
EST:     CTTTGCCCCCTCATTCGTGGATATTAACCGGGCTGTGCAGTTCATTCATC                         AGAATGCAACTTGCGGCAAAACTACTTATGTTCACTGTAAAGCTGGGCGGG
genomic: CTTTGCCCCCTCATTCGTGGATATTAACCGGGCTGTGCAGTTCATTCATCgtgggtgttt ... attatggcagAGAATGCAACTTGCGGCAAAACTACTTATGTTCACTGTAAAGCTGGGCGGG
EST: gi|10254074|gb|BE821840.1|BE821840
EST:     GCAGTTCATTCATC                         AGAATGCAACTTGCNNCAAAACTACTTATGTTCACTGTAAAGCTGGGCGGG
genomic: GCAGTTCATTCATCgtgggtgttt ... attatggcagAGAATGCAACTTGCGGCAAAACTACTTATGTTCACTGTAAAGCTGGGCGGG
EST: gi|193425492|gb|FK388639.1|FK388639
EST:     CTGTGCAGTCCATTCATC                         AGAATGCAACTTGCGGCAAAACTACTTATGTTCACTGTAAAGCTGGGCGGG
genomic: CTGTGCAGTTCATTCATCgtgggtgttt ... attatggcagAGAATGCAACTTGCGGCAAAACTACTTATGTTCACTGTAAAGCTGGGCGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggttgttggtggtgaaatatagtcgtgtgtgtatttcctttgtattatggcagAGAATGCAACTTGCGGCAAAACTACTTATGTTCACTGTAAAGCTGGGCGGGGGAGGAGTACAACAATTGTGCTTTGTTATATG
                                        tttgtattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtgttttcttttcaatttaatttcgggaaagtggggaagggggttaaatgcatcagtcattgtggttctttgtaattttttggttgttggtggtgaaatatagtcgtgtgtgtatttcctttgtattatggcagAGAATGCAACTTGCGGCAAAACTACTTATGTTCACTGTAAAGCTGGGCGGGGGAGGAGTACAACAATTGTGCTTTGTTATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG