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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGATACCAAACATGATGGGAAGATTGACAAGGAAGAATGGCGAAACCTTGTCTTACAGCATCCATCCCTTCTGAAAAATATGACTCTTCAGTATCTCAAgtgagtttctttccgttaataaccacaatttggattttgaaattgtctggtaagtgagggaaatgttaccaagcttatttggatgtgttaaaatgagtca...

Basic information

species Glycine max
transcript GLYMA07G39940.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G39940.1 (Glycine max), 5'ss of exon 8
lower sequence: AT4G26570.2 (Arabidopsis thaliana), 5'ss of exon 8
CTGATACCAAACATGATGGGAAGATTGACAAGGAAGAATGGCGAAACCTTGTCTTACAGCATCCATCCCTTCTGAAAAATATGACTCTTCAGTATCTCAAgtgagtttctttccgttaa--taaccacaatttggattttgaaattgtctggtaagtgagggaaatgttaccaagcttatttggatgtgttaaaatgagtca
||||||| |||||||| |||| ||| || |||||||| ||| ||| ||||||  |   |||||| |||||||| || ||||||||||| |||||||| ||||||||| ||   |    |  || ||    ||| |    || || |  |   |   |  | |   | |||  ||      |      | ||      ||   
CTGATACAAAACATGACGGGAGGATCGATAAGGAAGAGTGGAGAACCCTTGTTCTCAGGCATCCTTCCCTTCTAAAGAATATGACTCTCCAGTATCTTAAgtgagttcctaaaccaagacttatccgaggtttaggcaatgcaacttccaattttttctgtg--ttattattaacaccgatctctgatattgtgtgcag---

upper sequence: GLYMA07G39940.1 (Glycine max), 5'ss of exon 8
lower sequence: AT5G55990.1 (Arabidopsis thaliana), 5'ss of exon 9
CTGATACCAAACATGATGGGAAGATTGACAAGGAAGAATGGCGAAACCTTGTCTTACAGCATCCATCCCTTCTGAAAAATATGACTCTTCAGTATCTCAAgtgagtt-----tctttccgttaata--accacaatttggattttgaaattgtctggtaagtgagggaaatgttaccaagcttatttg-gatgtgttaaaatgagtca---------------------------
| || || ||||| ||||| ||||| || |||||||| ||| ||| ||||||  |    |||||   ||||||||| || ||||||||||| |||||||||||||||     ||||||  || |||  ||||  |||     | |  ||     |      |  ||    | || |     || |    ||| ||| | ||   |||                            
CAGACACAAAACACGATGGAAAGATCGATAAGGAAGAGTGGAGAAGCCTTGTTCTTAGACATCCCAGCCTTCTGAAGAACATGACTCTTCAATATCTCAAgtgagttccaaatctttctatttatataaccaggattgaatctattcaaccaaattccttctctggtttctctttcttctattctccatgatatgtaataa-aggtcgtgatcctgttgtgtgcttgctctgcag

upper sequence: GLYMA07G39940.1 (Glycine max), 5'ss of exon 8
lower sequence: Vv00s1569g00020.t01 (Vitis vinifera), 5'ss of exon 7
CTGATACCAAACATGATGGGAAGATTGACAAGGAAGAATGGCGAAACCTTGTCTTACAGCATCCATCCCTTCTGAAAAATATGACTCTTCAGTATCTCAAgtgagtttctttccgttaataaccacaattt-ggattttgaaattgtctggtaagtgagggaaatgttaccaagcttatttggatgtgttaaaatgagtca
||||||| ||||||||||||||||| ||||||||||||||||||| |||||| || |  |||||||| ||| |||| |||||||| ||||| || || |||| ||||    |||   |          ||    ||  || |     |||| |   |   |     || |         |    |    |  | |||    
CTGATACTAAACATGATGGGAAGATAGACAAGGAAGAATGGCGAAGCCTTGTTTTGCGACATCCATCTCTTTTGAAGAATATGACCCTTCAATACCTAAAgtaagttctcctcctccaccctttttttttccaaatgatggatggaactggcatccgtctggctatttgctgctggagatcctttaccctttagtgaact-

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|151398163|gb|EV268041.1|EV268041
EST:     GTCTTACAGCATCCATCCCTTCTGAAAAATATGACTCTTCAGTATCTCAA                         AGATATCACTACTACATTTCCCAGTTTTGTTTTTCACTCACAAGTTGATGA
genomic: GTCTTACAGCATCCATCCCTTCTGAAAAATATGACTCTTCAGTATCTCAAgtgagtttct ... tccttggcagAGATATCACTACTACATTTCCCAGTTTTGTTTTTCACTCACAAGTTGATGA
EST: gi|151404635|gb|EV274449.1|EV274449
EST:     GTCTTACAGCATCCATCCCTTCTGAAAAATATGACTCTTCAGTATCTCAA                         AGATATCACTACTACATTTCCCAGTTTTGCTTTTCACTCACAAGTTGATGA
genomic: GTCTTACAGCATCCATCCCTTCTGAAAAATATGACTCTTCAGTATCTCAAgtgagtttct ... tccttggcagAGATATCACTACTACATTTCCCAGTTTTGTTTTTCACTCACAAGTTGATGA
EST: gi|207844987|gb|GD815312.1|GD815312
EST:     GTCTTACAGCATCCATCCCTTCTGAAAAATATGACTCTTCAGTATCTCAA                         AGATATCACTACTACATTTCCCAGTTTTGTTTTTCACTCACAAGTTGATGA
genomic: GTCTTACAGCATCCATCCCTTCTGAAAAATATGACTCTTCAGTATCTCAAgtgagtttct ... tccttggcagAGATATCACTACTACATTTCCCAGTTTTGTTTTTCACTCACAAGTTGATGA
EST: gi|208087510|gb|GD888538.1|GD888538
EST:     CTTAACAAGCATCCATCCCTTCTGAAAAATATGACTCTTCAGTATCTCAA                         AGATATCACTACTACATTTCCCAGTTTTGTTTTTCACTCACAAGTTGATGA
genomic: CTTA-CA-GCATCCATCCCTTCTGAAAAATATGACTCTTCAGTATCTCAAgtgagtttct ... tccttggcagAGATATCACTACTACATTTCCCAGTTTTGTTTTTCACTCACAAGTTGATGA
EST: gi|192304196|gb|FG993508.1|FG993508
EST:     AAAATATGACTCTTCAGTATCTCAA                         AGATATCACTACTACATTTCCCAGTTTTGTTTTTCACTCACAAGTTGATGA
genomic: AAAATATGACTCTTCAGTATCTCAAgtgagtttct ... tccttggcagAGATATCACTACTACATTTCCCAGTTTTGTTTTTCACTCACAAGTTGATGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGATACCAAACATGATGGGAAGATTGACAAGGAAGAATGGCGAAACCTTGTCTTACAGCATCCATCCCTTCTGAAAAATATGACTCTTCAGTATCTCAAgtgagtttctttccgttaataaccacaatttggattttgaaattgtctggtaagtgagggaaatgttaccaagcttatttggatgtgttaaaatgagtca

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