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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTATGCGGATGGCAGTATATGCTTGGACATTTTACAGAATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtgattcacttaatatttcagaattgcattaagaccatacttatgctaaaaatgatttgattgtatcctgtacataatttatttaaaatactat...

Basic information

species Glycine max
transcript GLYMA18G16160.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G16160.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G110983_T03 (Zea mays), 5'ss of exon 3
TTTATGCGGATGGCAGTATATGCTTGGACATTTTACAGAATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtgattcacttaatatttcagaattgcattaagaccatacttatgctaaaaatgatt-tgattgtatcctgtacataatttatttaaaatactat
||||||| ||||| || |||||||| || ||  | |||||||||||||| || || ||||| |||||||| || || || ||||||||||||      || ||   ||| ||| |    |      |||  ||  || | | || | |  |     |||  |  | ||||  |    |  |   | |  |
TTTATGCTGATGGAAGCATATGCTTAGATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAGgta-caaccatacaagaaatcttttatttcttacaagagattattgtttttccaacatttgtaacttttgcttgttatacagtaacattcaactttgcagt

upper sequence: GLYMA18G16160.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G110983_T02 (Zea mays), 5'ss of exon 4
TTTATGCGGATGGCAGTATATGCTTGGACATTTTACAGAATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtgattcacttaatatttcagaattgcattaagaccatacttatgctaaaaatgatt-tgattgtatcctgtacataatttatttaaaatactat
                           | ||  | |||||||||||||| || || ||||| |||||||| || || || ||||||||||||      || ||   ||| ||| |    |      |||  ||  || | | || | |  |     |||  |  | ||||  |    |  |   | |  |
---------------------------ATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAGgta-caaccatacaagaaatcttttatttcttacaagagattattgtttttccaacatttgtaacttttgcttgttatacagtaacattcaactttgcagt

upper sequence: GLYMA18G16160.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv01s0026g01770.t01 (Vitis vinifera), 5'ss of exon 6
TTTATGCGGATGGCAGTATATGCTTGGACATTTTACAGAATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAGgtaat---tgtgattcacttaatatttcagaattgcattaagaccatacttatgctaaaaatgatttgattgtatcctgtacataatttatttaaaatactat
||||||||||||| || || ||||| |||||| |||| ||||||||||| || |||||||| |||||||| || ||||| || ||||||||| |   | || |    ||| | |||     |||||| ||  |       ||| ||   |  |  |||  | || ||| |  | |  ||| |      || |
TTTATGCGGATGGAAGCATTTGCTTAGACATTCTACAAAATCAGTGGAGTCCAATTTATGATGTAGCTGCCATACTTACATCCATCCAGgtattggatatgttcatattattgtttggatgttgcatcaa--ctgagaacatgatatttaaaacatgaaagaatgctg-atttgacctatgtttttgccttt

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|209728174|gb|BW651609.1|BW651609
EST:     ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAG                         TCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
genomic: ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
EST: gi|9986725|gb|BE660833.1|BE660833
EST:     ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAG                         TCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
genomic: ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
EST: gi|22926835|gb|BU543974.1|BU543974
EST:     ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAG                         TCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
genomic: ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
EST: gi|254320792|gb|GR827241.1|GR827241
EST:     ATTTATGACGTAGCTGCAATTCTTACCTCAATCCAG                         TCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
genomic: ATTTATGACGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
EST: gi|16105946|gb|BI893686.1|BI893686
EST:     CGTAGCTGCAATTCTTACCTCAATCCAG                         TCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
genomic: CGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
EST: gi|13311395|gb|BG405046.1|BG405046
EST:     ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAG                         TCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
genomic: ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
EST: gi|16342610|gb|BI968205.1|BI968205
EST:     ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAG                         TCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
genomic: ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
EST: gi|14125836|gb|BG790274.1|BG790274
EST:     ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAG                         TCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
genomic: ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
EST: gi|16105927|gb|BI893667.1|BI893667
EST:     GACGTAGCTGCAATTCTTACCTCAATCCAG                         TCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
genomic: GACGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
EST: gi|21255605|gb|BQ452493.1|BQ452493
EST:     ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAG                         TCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
genomic: ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
EST: gi|13480716|gb|BG510059.1|BG510059
EST:     ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAG                         TCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
genomic: ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
EST: gi|254333697|gb|GR848615.1|GR848615
EST:     ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAG                         TCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
genomic: ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
EST: gi|17518903|gb|BM187945.1|BM187945
EST:     ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAG                         TCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
genomic: ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
EST: gi|192294426|gb|FG987355.1|FG987355
EST:     ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAG                         TCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
genomic: ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
EST: gi|4292045|gb|AI437706.1|AI437706
EST:     ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAG                         TCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGGC
genomic: ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTG-C
EST: gi|11274154|gb|BF324522.1|BF324522
EST:     ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAG                         TCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
genomic: ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
EST: gi|254333698|gb|GR848616.1|GR848616
EST:     ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAG                         TCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
genomic: ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
EST: gi|31311823|gb|CD397026.1|CD397026
EST:     ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAG                         TCATTGCTGTGTGATCCAAACCCAAATTCACCAGCGAATTCTGAAGCTGCT
genomic: ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
EST: gi|192305566|gb|FG998322.1|FG998322
EST:     ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAG                         TCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
genomic: ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
EST: gi|26269575|gb|CA820638.1|CA820638
EST:     ATCAGTGGAGCCCTATTTATGACGTAACTGCAATTCTTACCTCAATCCAG                         TCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
genomic: ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
EST: gi|254320629|gb|GR827078.1|GR827078
EST:     ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAG                         TCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
genomic: ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
EST: gi|15812366|gb|BI784641.1|BI784641
EST:     ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAG                         TCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
genomic: ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
EST: gi|22926846|gb|BU543985.1|BU543985
EST:     ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAG                         TCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
genomic: ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
EST: gi|4295885|gb|AI442396.1|AI442396
EST:     ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAG                         TCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
genomic: ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
EST: gi|192296666|gb|FG991234.1|FG991234
EST:     ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAG                         TCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
genomic: ATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTATGCGGATGGCAGTATATGCTTGGACATTTTACAGAATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtgattcacttaatatttcagaattgcattaagaccatacttatgctaaaaatgatttgattgtatcctgtacataatttatttaaaatactat

- - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC