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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggaaaattacctccaattatatcaggaatccaatacaataaaaaaattattagagacccaaaataaaaaatgatcatttatgagggatccaaaacatattttagccaattcaaaaatttggattgcatccatgactgaacttcaaatctaacaagacattcatttttgtttgtaccagATGCCTAGAAGAGGGAGCTGATGAATTCTTTCTGAAACCAGTTCAACAGTCAGATGTAAACAAGCTGAGGCCACATTTGATGAAATCAAAAGTTAAGGAT

Basic information

species Glycine max
transcript GLYMA11G21650.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G21650.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv13s0067g03490.t01 (Vitis vinifera), 3'ss of exon 5
gtgaggaaaattacctccaattatatcaggaatccaatacaataaaaaaattattagagacccaaaataaaaaatgatcatttatgagggatccaaaacatattttagccaattcaaa-aatttggattgcatccatgactgaacttcaaatctaacaagacattcatttttgtttgt-accagATGCCTAGAAGAGGGAGCTGATGAATTCTTTCTGAAACCAGTTCAACAGTCAGATGTAAACAAGCTGAGGCCACATTTGATGAAATCAAAAGTTAAGGAT
                                                                   | | |||  |  | |||  |||  ||   ||   | |||   ||    ||| ||  || | |  |    ||| | || |||  || | | ||   ||   |  | | |  | | ||||||  | ||||| ||||| || || |||||||||||||| |||||    |||||||| |||||||| ||||||||| |  |   ||| | |         
------------------------------------------------------------------gtgagaaa--actactta--aggattctggaattgaattttctcatccaaaagaaaatgaaatttagt--tgaatcaatttctgatgtgagaatgtatgtttaatgggtattgatcagATGTTTGGAAGAAGGAGCAGAAGATTTCTTTCTGAAACCTGTTCAGTTATCAGATGTGAACAAGCTTAGGCCACATCTACTCGGATCCAGAACCCTTTTG
















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|58018386|gb|CX705128.1|CX705128
EST:     ATACCAGTGGTGATTATGTCCTCAGAGAATGTCCCAGCAAGGATTAACAG                         ATGCCTAGAAGAGGGAGCTGATGAATTCTTTCTGAAACCAGTTCAACAGTC
genomic: ATACCAGTGGTGATTATGTCCTCAGAGAATGTCCCAGCAAGGATTAACAGgtgaggaaaa ... tttgtaccagATGCCTAGAAGAGGGAGCTGATGAATTCTTTCTGAAACCAGTTCAACAGTC
EST: gi|192334799|gb|FK025948.1|FK025948
EST:     ATACCAGTGGTGATTATGTCCTCAGAGAATGTCCCAGCAAGGATTAACAG                         ATGCCTAGAAGAGGGAGCTGATGAATTCTTTCTGAAACCAGTTCAACAGTC
genomic: ATACCAGTGGTGATTATGTCCTCAGAGAATGTCCCAGCAAGGATTAACAGgtgaggaaaa ... tttgtaccagATGCCTAGAAGAGGGAGCTGATGAATTCTTTCTGAAACCAGTTCAACAGTC
EST: gi|7283519|gb|AW596125.1|AW596125
EST:     ATACCAGTGGTGATTATGTCCTCAGAGAATGTCCCAGCAAGGATTAACAG                         ATGCCTAGAAGAGGGAGCTGATGAATTCTTTCTGANACCAGTTCAACAGTC
genomic: ATACCAGTGGTGATTATGTCCTCAGAGAATGTCCCAGCAAGGATTAACAGgtgaggaaaa ... tttgtaccagATGCCTAGAAGAGGGAGCTGATGAATTCTTTCTGAAACCAGTTCAACAGTC
EST: gi|7795492|gb|AW780889.1|AW780889
EST:     ATACCAGTGGTGATTATGTCCTCATAGAATGTCCCAGCAAGGATTAACAT                         ATGCCTAGAAGAGGGAGCTGATGAATTCTTTCTGAAACCAATTCAACAGTC
genomic: ATACCAGTGGTGATTATGTCCTCAGAGAATGTCCCAGCAAGGATTAACAGgtgaggaaaa ... tttgtaccagATGCCTAGAAGAGGGAGCTGATGAATTCTTTCTGAAACCAGTTCAACAGTC
EST: gi|6725940|gb|AW310339.1|AW310339
EST:     ATACCAGTGGTGATTATGTCCTCAGAGAATGTCCAAGCAAGGATTAACAG                         ATGCCTAGAAGAGGGAGCTGATGAATTCTTTCTGAAACCAGTTCAACAGTC
genomic: ATACCAGTGGTGATTATGTCCTCAGAGAATGTCCCAGCAAGGATTAACAGgtgaggaaaa ... tttgtaccagATGCCTAGAAGAGGGAGCTGATGAATTCTTTCTGAAACCAGTTCAACAGTC
EST: gi|192334800|gb|FK025949.1|FK025949
EST:     ATACCAGTGGTGATTATGTCCTCAGAGAATGTCCCAGCAAGGATTAACAG                         ATGCCTAGAAGAGGGAGCTGATGAATTCTTTCTGAAACCAGTTCAACAGTC
genomic: ATACCAGTGGTGATTATGTCCTCAGAGAATGTCCCAGCAAGGATTAACAGgtgaggaaaa ... tttgtaccagATGCCTAGAAGAGGGAGCTGATGAATTCTTTCTGAAACCAGTTCAACAGTC
EST: gi|6725905|gb|AW310304.1|AW310304
EST:     ATACCAGTGGTGATTATGTCCTCAGAGAATGTCCCAGCAAGGATTAACAG                         ATGCCTAGAAGAGGGAGCTGATGAATTCTTTCTGAAACCAGTTCAACAGTC
genomic: ATACCAGTGGTGATTATGTCCTCAGAGAATGTCCCAGCAAGGATTAACAGgtgaggaaaa ... tttgtaccagATGCCTAGAAGAGGGAGCTGATGAATTCTTTCTGAAACCAGTTCAACAGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatccatgactgaacttcaaatctaacaagacattcatttttgtttgtaccagATGCCTAGAAGAGGGAGCTGATGAATTCTTTCTGAAACCAGTTCAACAGTCAGATGTAAACAAGCTGAGGCCACATTTGATGAAATCAAAAGTTAAGGAT
                      atctaac  putative branch site (score: 2)
                                       tttttgttt  putative PPT
                                  attcatttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggaaaattacctccaattatatcaggaatccaatacaataaaaaaattattagagacccaaaataaaaaatgatcatttatgagggatccaaaacatattttagccaattcaaaaatttggattgcatccatgactgaacttcaaatctaacaagacattcatttttgtttgtaccagATGCCTAGAAGAGGGAGCTGATGAATTCTTTCTGAAACCAGTTCAACAGTCAGATGTAAACAAGCTGAGGCCACATTTGATGAAATCAAAAGTTAAGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA