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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtagaaggcacaaattgatattgtgagtgagaatttataggcccaatattcaaaattttcattattttgtgcagATATGCATTTCCTATAAAGTGCACTGAAGTTATTCTAGCTGATGATAATGAGACTATTCTTGAGATTCGAGCAGAGTATGATCCTTCAAAGAAGACCAAG

Basic information

species Glycine max
transcript GLYMA10G41920.2
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G41920.1 (Glycine max), 3'ss of exon 19
lower sequence: Vv15s0021g01230.t01 (Vitis vinifera), 3'ss of exon 19
----------gttagtagaaggcacaaattgatattgtgagtgagaatttataggcccaatattcaaaattttcattattttgtgcagATATGCATTTCCTATAAAGTGCACTGAAGTTATTCTAGCTGATGATAATGAGACTATTCTTGAGATTCGAGCAGAGTATGATCCTTCAAAGAAGACCAAG
            |  ||||||    |  ||  |  |     ||   |  |||      || ||| | ||| ||  | ||    ||||| |||||||| |||||||||||||| ||||| || ||   ||||||||| |||||  |  ||||| | || |||||||||||| |||| |||||||| |||
gtacttgtaaaattatagaagttgtattttttttattcacttgttcagatatcccattaaaattgagaatctttttcatgc-atgcagGTATGCATTCCCTATAAAGTGCACAGAAGTGATCCTTAGTGATGATAAGGAGACCGTGGTTGAGGTCCGGGCAGAGTATGATTCTTCGAAGAAGACAAAG

upper sequence: GLYMA10G41920.1 (Glycine max), 3'ss of exon 19
lower sequence: Vv01s0011g03740.t01 (Vitis vinifera), 3'ss of exon 19
--gttagtaga--aggcacaaattgatattgtgagtgagaatttataggcccaatattcaaaattttcattattttgtgcagATATGCATTTCCTATAAAGTGCACTGAAGTTATTCTAGCTGATGATAATGAGACTATTCTTGAGATTCGAGCAGAGTATGATCCTTCAAAGAAGACCAAG
   |   |||   |       |||   | | |   |||| ||    | ||  || ||| | ||||||| | ||     |||||||||| || |||||||||||||| |||||||| ||   ||||||||| || ||| || ||||| |  | || || | |||||||||||||||||| |||
gtatctatagtttaaatttgtatttccaatctacttgagtataagaaagcagaagattgagaattttcttcatgc-acgcagATATGCTTTCCCTATAAAGTGCACAGAAGTTATCCTCAGTGATGATAAAGAAACTGTTGTTGAGGTCTGGGCTGAATTTGATCCTTCAAAGAAGACAAAG
















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|17401220|gb|BM178002.1|BM178002
EST:     GATTCAAAAGATTATTATGGCCTTGCTCCTGGGAAATCTGTGATACTCAG                         ATATGCATTTCCTATAAAGTGCACTGAAGTTATTCTAGCTGATGATAATGA
genomic: GATTCAAAAGATTATTATGGCCTTGCTCCTGGGAAATCTGTGATACTCAGgttagtagaa ... ttttgtgcagATATGCATTTCCTATAAAGTGCACTGAAGTTATTCTAGCTGATGATAATGA
EST: gi|19346023|gb|BM890903.1|BM890903
EST:     GATTCAAAAGATTATTATGGCCTTGCTCCTGGGAAATCTGTGATACTCAG                         ATATGCATTTCCTATAAAGTGCACTGAAGTTATTCTAGCTGATGATAATGA
genomic: GATTCAAAAGATTATTATGGCCTTGCTCCTGGGAAATCTGTGATACTCAGgttagtagaa ... ttttgtgcagATATGCATTTCCTATAAAGTGCACTGAAGTTATTCTAGCTGATGATAATGA
EST: gi|16995857|gb|BM085229.1|BM085229
EST:     GATTCAAAAGATTATTATGGCCTTGCTCCTGGGAAATCTGTGATACTCAG                         ATATGCATTTCCTATAAAGTGCACTGAAGTTATT
genomic: GATTCAAAAGATTATTATGGCCTTGCTCCTGGGAAATCTGTGATACTCAGgttagtagaa ... ttttgtgcagATATGCATTTCCTATAAAGTGCACTGAAGTTATT
EST: gi|298164021|gb|HO013666.1|HO013666
EST:     GATTCAAAAGATTATTATGGCCTTGCTCCTGGGAAATCTGTGATACTCAG                         ATATGCATTTCCTATAAAGTGCACTGAAGTTATTCTAGCTGGTGATAATGA
genomic: GATTCAAAAGATTATTATGGCCTTGCTCCTGGGAAATCTGTGATACTCAGgttagtagaa ... ttttgtgcagATATGCATTTCCTATAAAGTGCACTGAAGTTATTCTAGCTGATGATAATGA
EST: gi|17401215|gb|BM177997.1|BM177997
EST:     GATTCAAAAGATTATTATGGCCTTGCTCCTGGGAAATCTGTGATACTCAG                         ATATGCATTTCCTATAAAGTGCACTGAAGTTATTCTAGCTGATGATAATGA
genomic: GATTCAAAAGATTATTATGGCCTTGCTCCTGGGAAATCTGTGATACTCAGgttagtagaa ... ttttgtgcagATATGCATTTCCTATAAAGTGCACTGAAGTTATTCTAGCTGATGATAATGA
EST: gi|20812918|gb|BQ297396.1|BQ297396
EST:     GATTCAAAAGATTATTATGGCCTTGCTCCTGGGAAATCTGTGATACTCAG                         ATATGCATTTCCTATAAAGTGCACTGAAGTTATTCTAGCTGATGATAATGA
genomic: GATTCAAAAGATTATTATGGCCTTGCTCCTGGGAAATCTGTGATACTCAGgttagtagaa ... ttttgtgcagATATGCATTTCCTATAAAGTGCACTGAAGTTATTCTAGCTGATGATAATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtgagtgagaatttataggcccaatattcaaaattttcattattttgtgcagATATGCATTTCCTATAAAGTGCACTGAAGTTATTCTAGCTGATGATAATGAGACTATTCTTGAGATTCGAGCAGAGTATGATCCTTCAAAGAAGACCAAG
                                          ttatttt  CT-rich tract
                         aatattcaaaattttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtagaaggcacaaattgatattgtgagtgagaatttataggcccaatattcaaaattttcattattttgtgcagATATGCATTTCCTATAAAGTGCACTGAAGTTATTCTAGCTGATGATAATGAGACTATTCTTGAGATTCGAGCAGAGTATGATCCTTCAAAGAAGACCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG