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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACATGTGGTTCTTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCTTCTCTCCGAAgtaagtagtaacactctttctccacaatttttgtgcttcgtgcgtgattgataagtgtttgtgatttttttgttttttgaattaaaaactcgttttatgc...

Basic information

species Glycine max
transcript GLYMA12G08760.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G08760.1 (Glycine max), 5'ss of exon 3
lower sequence: AT2G27960.1 (Arabidopsis thaliana), 5'ss of exon 2
ACATGTGGTTCTTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCTTCTCTCCGAAgtaagtagtaacactctttctccac-aatttttg-tgcttcgtgcgt-gatt-gat-----aagtgtttgtgatttttttgttttttgaattaaaaactcgttttatgc
 || || |||||||||||||||||||| ||||| ||||| |||||||||||||||||||||||||||  |    | | || | | |  |||| || | ||   | | | |||| |||     |||  | ||  | ||| ||| | ||   |    ||  |          
GCACGTCGTTCTTCCTCCTGAAGTCGCTAAACTTCTTCCAAAGAATCGTCTTCTCTCCGAAgtaagtttttttccgcattgttctctgatttctgattctaaatccttcgattagatcatcgaagactatgaaaatttgttgctcttaagaaattaagttt---------

upper sequence: GLYMA12G08760.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv06s0061g00810.t01 (Vitis vinifera), 5'ss of exon 3
ACATGTGGTTCTTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCTTCTCTCCGAAgtaagtagtaacactctttctccacaatttttgtgcttcgtgcgtgattgataagtgtttgtgatttttttgttttttgaattaaaaactcgttttatgc----------
 ||||||||||||||||||||||| || |||||||| |  |||||||| |||||||| ||||| |||        || ||       |  |||  | ||||    |   |  | ||| ||  |  | | |||| ||  ||||  || |    ||||||             
GCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAAgtgagtg-------tcgttggatctgaaatttagggttcgaagatttctt-ttagttttgattctgtgtttggttgctgaaacaata--cagttttagaaaaaaaaaaaa
















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|57574369|gb|CX547344.1|CX547344
EST:     TTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCTTCTCTCCGAA                         AATGAGTGGCGAGCTATTGGGGTTCAGCAGAGCCGTGGCTGGGTTCACTAT
genomic: TTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCTTCTCTCCGAAgtaagtagta ... tatgttacagAATGAGTGGCGAGCTATTGGGGTTCAGCAGAGCCGTGGCTGGGTTCACTAT
EST: gi|192324097|gb|FK019388.1|FK019388
EST:     TTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCTTCTCTCCGAA                         AATGAGCGGCGAGCTATTGGGGTTCAGCAGAGCCGTGGCTGGGTTCACTAT
genomic: TTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCTTCTCTCCGAAgtaagtagta ... tatgttacagAATGAGTGGCGAGCTATTGGGGTTCAGCAGAGCCGTGGCTGGGTTCACTAT
EST: gi|302141347|gb|HO212223.1|HO212223
EST:     TTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGGATCGTCTTCTCTCCGAA                         AATGAGTGGCGAGCTATTGGGGTTCAGCAGAGCCGTGGTTGGGTTCACTAT
genomic: TTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCTTCTCTCCGAAgtaagtagta ... tatgttacagAATGAGTGGCGAGCTATTGGGGTTCAGCAGAGCCGTGGCTGGGTTCACTAT
EST: gi|192301123|gb|FG988948.1|FG988948
EST:     TTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCTTCTCTCCGAA                         AATGAGTGGCGAGCTATTGGGGTTCAGCAGAGCCGTGGCTGGGTTCACTAT
genomic: TTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCTTCTCTCCGAAgtaagtagta ... tatgttacagAATGAGTGGCGAGCTATTGGGGTTCAGCAGAGCCGTGGCTGGGTTCACTAT
EST: gi|192317957|gb|FK010235.1|FK010235
EST:     TTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCTTCTCTCCGAA                         AATGAGTGGCGAGCTATTGGGGTTCAGCAGAGCCGTGGCTGGGTTCACTAT
genomic: TTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCTTCTCTCCGAAgtaagtagta ... tatgttacagAATGAGTGGCGAGCTATTGGGGTTCAGCAGAGCCGTGGCTGGGTTCACTAT
EST: gi|151412005|gb|EV281816.1|EV281816
EST:     TTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCTTCTCTCCGAA                         AATGAGTGGCGAGCTATTGGGGTTCAGCAGAGCCGTGGCTGGGTTCACTAT
genomic: TTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCTTCTCTCCGAAgtaagtagta ... tatgttacagAATGAGTGGCGAGCTATTGGGGTTCAGCAGAGCCGTGGCTGGGTTCACTAT
EST: gi|57574181|gb|CX547156.1|CX547156
EST:     TTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCTTCTCTCCGAA                         AATGAGTGGCGAGCTATTGGGGTTCAGCAGAGCCGTGGCTGGGTTCACTAT
genomic: TTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCTTCTCTCCGAAgtaagtagta ... tatgttacagAATGAGTGGCGAGCTATTGGGGTTCAGCAGAGCCGTGGCTGGGTTCACTAT
EST: gi|31469530|gb|CD411558.1|CD411558
EST:     TTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCTTCTCTCCGAA                         AATGAGTGGCGAGCTATTGGGGTTCAGCAGAGCCGTGGCTGGGTTCACTAT
genomic: TTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCTTCTCTCCGAAgtaagtagta ... tatgttacagAATGAGTGGCGAGCTATTGGGGTTCAGCAGAGCCGTGGCTGGGTTCACTAT
EST: gi|151399098|gb|EV268969.1|EV268969
EST:     TTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCTTCTCTCCGAA                         AATGAGTGGCGAGCTATTGGGGTTCAGCAGAGCCGTGGCTGGGTTCACTAT
genomic: TTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCTTCTCTCCGAAgtaagtagta ... tatgttacagAATGAGTGGCGAGCTATTGGGGTTCAGCAGAGCCGTGGCTGGGTTCACTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACATGTGGTTCTTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCTTCTCTCCGAAgtaagtagtaacactctttctccacaatttttgtgcttcgtgcgtgattgataagtgtttgtgatttttttgttttttgaattaaaaactcgttttatgc

- - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctttctcc