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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGACACGGTGATCTTCTTAACAAATATCTTTACTTGAGTGGTCGAGTTGACATGAAACAAATTGAAAAGACAATTCAGTACCTTATTGGGTCTGGAATGgtaagatcctatacaactgtagtctattttggtcttccgcaatggtagttttattaatgaatcacacaatcatgcaatgtcaaagaaactcttgctaccc...

Basic information

species Glycine max
transcript GLYMA02G15600.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G15600.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv05s0094g00550.t01 (Vitis vinifera), 5'ss of exon 1
CAGACACGGTGATCTTCTTAACAAATATCTTTACTTGAGTGGTCGAGTTGACATGAAACAAATTGAAAAGACAATTCAGTACCTTATTGGGTCTGGAATGgtaagatccta--tacaactgtagtctattttggtcttccgcaat--ggtagttttattaatgaatcacacaatcatgcaatgtcaaagaaactcttgctaccc
|||  ||||||| |||||||| || ||||| ||  ||  |||  |||| |||||||||||||| || ||||| ||||||||  | |||||| |||||||||| |||| ||   ||||       | | ||||  | ||| | | |  |  |   |  | | |   ||    | ||| |   |        | || ||  ||   
CAGGGACGGTGACCTTCTTAATAAGTATCTCTATCTGTCTGGAAGAGTAGACATGAAACAAATCGAGAAGACGATTCAGTATTTGATTGGGGCTGGAATGgtgagattcttgctacatgcccttttttttttttttttctgtagtcagtcacaatcttcactagttcttgaactcaagttcttcttctccatcttttcatag--

upper sequence: GLYMA02G15600.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv05s0094g00580.t01 (Vitis vinifera), 5'ss of exon 2
CAGACACGGTGATCTTCTTAACAAATATCTTTACTTGAGTGGTCGAGTTGACATGAAACAAATTGAAAAGACAATTCAGTACCTTATTGGGTCTGGAATGgtaagatcctatacaactgtagtctattttggtcttccgcaatggtagttttattaatgaatcacacaatcatgcaatgtcaaagaaactcttgctaccc--------
||| |||||||| |||||||| || ||||| ||  ||  |||  |||| |||||||||||||| || ||||| ||||||||  | |||||| |||||||||| |||| || | | ||     | | ||||  | ||        |||||   | | |  |    ||| |       |  ||||        |  | | |         
CAGGCACGGTGACCTTCTTAATAAGTATCTCTATCTGTCTGGAAGAGTAGACATGAAACAAATCGAGAAGACGATTCAGTATTTGATTGGGGCTGGAATGgtgagattct-tgctacatgctttttttttttttttttttttctgtagtc--aatcacaatcttcactagttcttgaactcaagttcttcttctccatcttttcatag

upper sequence: GLYMA02G15600.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S157_50V6.1 (Physcomitrella patens), 5'ss of exon 3
CAGACACGGTGATCTTCTTAACAAATATCTTTACTTGAGTGGTCGAGTTGACATGAAACAAATTGAAAAGACAATTCAGTACCTTATTGGGTCTGGAATGgtaagatcctataca---actgtagtctattttggtcttccgcaatggtagtttt--attaatgaatc-acacaa-tcatgcaatgtcaaagaaactcttgctaccc
| | ||||| || || || ||||| ||  | |||||||  || ||||| ||||||| |||||| || ||||||||||||||| | ||||| ||||| |||||||||  | ||      ||  ||    ||| || |  ||    |  ||   |      || || ||| || ||| | |      || |  |||  ||         
CCGTCACGGAGACCTGCTGAACAAGTACTTGTACTTGACAGGGCGAGTGGACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATGgtaagaagccatgttttcaccctaaaaaattatgatgctcgctgaatgtgtctgccagctactgtatctacgcaaattaaattgcgt-acggaagttcgaa------

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|15287505|gb|BI471396.1|BI471396
EST:     ACATGAAACAAATTGAAAAGACAATTCAGTACCTTATTGGGTCTGGAATG                         GATCCTCGAACCGAGAACAGCCCCTACCTTGGTTTCATTTACACTTCATTT
genomic: ACATGAAACAAATTGAAAAGACAATTCAGTACCTTATTGGGTCTGGAATGgtaagatcct ... tgatggatagGATCCTCGAACCGAGAACAGCCCCTACCTTGGTTTCATTTACACTTCATTT
EST: gi|9901530|gb|BE610498.1|BE610498
EST:     ACATGAAACAAATTGAAAAGACAATTCAGTACCTTATTGGGTCTGGAATG                         GATCCTCGAACCGAGAACAGCCCCTACCTTGGTTTCATTTACACTTCATTT
genomic: ACATGAAACAAATTGAAAAGACAATTCAGTACCTTATTGGGTCTGGAATGgtaagatcct ... tgatggatagGATCCTCGAACCGAGAACAGCCCCTACCTTGGTTTCATTTACACTTCATTT
EST: gi|27426453|gb|CA937973.1|CA937973
EST:     ACATGAAACAAATTGAAAAGACAATTCAGTACCTTATTGGGTCTGGAATG                         GATCCTCGAACCGAGAACAGCCCCTACCTTGGTTTCATTTACACTTCATTT
genomic: ACATGAAACAAATTGAAAAGACAATTCAGTACCTTATTGGGTCTGGAATGgtaagatcct ... tgatggatagGATCCTCGAACCGAGAACAGCCCCTACCTTGGTTTCATTTACACTTCATTT
EST: gi|120533729|gb|EH261862.1|EH261862
EST:     ACATGAAACAAATTGAAAAGACAATTCAGTACCTTATTGGGTCTGGAATG                         GATCCTCGAACCGAGAACAGCCCCTACCTTGGTTTCATTTACACTTCATTT
genomic: ACATGAAACAAATTGAAAAGACAATTCAGTACCTTATTGGGTCTGGAATGgtaagatcct ... tgatggatagGATCCTCGAACCGAGAACAGCCCCTACCTTGGTTTCATTTACACTTCATTT
EST: gi|298179192|gb|HO027663.1|HO027663
EST:     ACATGAAACAAATTGAAAAGACAATTCAGTACCTTATTGGGTCTGGAATG                         GATCCTCGAACCGAGAACAGCCCCTACCTTGGTTCCATTTACACTTCATTT
genomic: ACATGAAACAAATTGAAAAGACAATTCAGTACCTTATTGGGTCTGGAATGgtaagatcct ... tgatggatagGATCCTCGAACCGAGAACAGCCCCTACCTTGGTTTCATTTACACTTCATTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGACACGGTGATCTTCTTAACAAATATCTTTACTTGAGTGGTCGAGTTGACATGAAACAAATTGAAAAGACAATTCAGTACCTTATTGGGTCTGGAATGgtaagatcctatacaactgtagtctattttggtcttccgcaatggtagttttattaatgaatcacacaatcatgcaatgtcaaagaaactcttgctaccc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaagaaa