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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGCTGCATATGGTAATCTTGTGCAAATTCTTGATCCTCCAAGGGATGGCTTTAATCTCACATTAAAAATAAATCTGTCTAAGCTTCCAGCAAATCAAGgtacagagagcttctgtataaaatgccatcttaactttccattccccttctagcagaagtttttcctctttaagttgaatttagaagctgctatattttc...

Basic information

species Glycine max
transcript GLYMA08G32790.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G32790.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os01g46580.1 (Oryza sativa), 5'ss of exon 3
AAAGCTGCATATGGTAATCTTGTGCAAATTCTTGATCCTCCAAGGGATGGCTTTAATCTCACATTAAAAATAAATCTGTCTAAGCTTCCAGCAAATCAAGgtac-agagagcttctgtataaaatgccatcttaactttccattcccc--ttctagcagaagtttttcctctttaagttgaatttagaagctgctatattttc
|| || || |||||     | || ||||||||||||||||||| |||||||||| |||||||| | || |||||  || | ||||||||  || || ||||| | ||||  |   |    |   | ||||  |    ||    | |    ||  |  ||| | |  | || | ||  ||||  |   |  |    |||     
AAGGCAGCTTATGGACCAGTCGTTCAAATTCTTGATCCTCCAAAGGATGGCTTTGATCTCACAATGAAGATAAACTTGACAAAGCTTCCGCCAGATGAAGgttctagagttccctttccaaggttaccattgtcttgttgtgctacatgattgaattagatgatggttctatgtaccttgagatgtcatccattgataga---

upper sequence: GLYMA08G32790.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv01s0011g05400.t01 (Vitis vinifera), 5'ss of exon 4
AAAGCTGCATATGGTAATCTTGTGCAAATTCTTGATCCTCCAAGGGATGGCTTTAATCTCACATTAAAAATAAATCTGTCTAAGCTTCCAGCAAATCAAGgtacagagagcttctgtataaaatgccatcttaactttccattccccttctagcagaagtttttcctctttaagttgaatttagaagctgctatattttc
|||||| ||||||||   || || |||||||||||||||||||  || ||||| ||||||||||| ||| | ||| |||| || |||||  || || ||||| ||   || |||| |   ||   |  | | | ||| ||||  |  | ||   | |  |     |  |||       ||||  |      ||  |  ||
AAAGCTTCATATGGTGTACTCGTACAAATTCTTGATCCTCCAAAAGACGGCTTCAATCTCACATTGAAACTGAATTTGTCAAAACTTCCTCCAGATGAAGgttcaacaagtttcttttctaaggtcattatgagcttgccatggctatgctgaaacatataggaacagtttgtcacacattttcatctacataactactc
















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|254345502|gb|GR851664.1|GR851664
EST:     CTTTAATCTCACATTAAAAATAAATCTGTCTAAGCTTCCAGCAAATCAAG                         AGCAAAAACATGCTTTTTTGGTAAAAGTTGCATCAATAAGGGAGGTTGTCC
genomic: CTTTAATCTCACATTAAAAATAAATCTGTCTAAGCTTCCAGCAAATCAAGgtacagagag ... acttgtgcagAGCAAAAACATGCTTTTTTGGTAAAAGTTGCATCAATAAGGGAGGTTGTCC
EST: gi|209701869|gb|BW670510.1|BW670510
EST:     CTTTAATCTCACATTAAAAATAAATCTGTCTAAGCTTCCAGCAAATCAAG                         AGCAAAAACATGCTTTTTTGGTAAAAGTTGCATCAATAAGGGAGGTTGTCC
genomic: CTTTAATCTCACATTAAAAATAAATCTGTCTAAGCTTCCAGCAAATCAAGgtacagagag ... acttgtgcagAGCAAAAACATGCTTTTTTGGTAAAAGTTGCATCAATAAGGGAGGTTGTCC
EST: gi|16105999|gb|BI893739.1|BI893739
EST:     CTTTAATCTCACATTAAAAATAAATCTGTCTAAGCTTCCAGCAAATCAAG                         AGCAAAAACATGCTTTTTTGG
genomic: CTTTAATCTCACATTAAAAATAAATCTGTCTAAGCTTCCAGCAAATCAAGgtacagagag ... acttgtgcagAGCAAAAACATGCTTTTTTGG
EST: gi|19934903|gb|BQ079933.1|BQ079933
EST:     CTTTAATCTCACATTAAAAATAAATCTGTCTAAGCTTCCAGCAAATCAAG                         AGCAAAAACATGCTTTTTTGGTAAAAGTTGCATCAATAAGGGAGGTTGTCC
genomic: CTTTAATCTCACATTAAAAATAAATCTGTCTAAGCTTCCAGCAAATCAAGgtacagagag ... acttgtgcagAGCAAAAACATGCTTTTTTGGTAAAAGTTGCATCAATAAGGGAGGTTGTCC
EST: gi|11413514|gb|BF425525.1|BF425525
EST:     CTTTAATCTCACATTAAAAATAAATCTGTCTAAGCTTCCAGCAAATCAAG                         AGCAAAAACATGCTTTTTTGGTAAAAGTTGCATCAATAAGGGAGGTTGTCC
genomic: CTTTAATCTCACATTAAAAATAAATCTGTCTAAGCTTCCAGCAAATCAAGgtacagagag ... acttgtgcagAGCAAAAACATGCTTTTTTGGTAAAAGTTGCATCAATAAGGGAGGTTGTCC
EST: gi|27426707|gb|CA938227.1|CA938227
EST:     CTTTAATCTCACATTAAAAATAAATCTGTCTAAGCTTCCAGCAAATCAAG                         AGCAAAAACATGCTTTTTTGGTAAAAGTTGCATCAATAAGGGAGGTTGTCC
genomic: CTTTAATCTCACATTAAAAATAAATCTGTCTAAGCTTCCAGCAAATCAAGgtacagagag ... acttgtgcagAGCAAAAACATGCTTTTTTGGTAAAAGTTGCATCAATAAGGGAGGTTGTCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGCTGCATATGGTAATCTTGTGCAAATTCTTGATCCTCCAAGGGATGGCTTTAATCTCACATTAAAAATAAATCTGTCTAAGCTTCCAGCAAATCAAGgtacagagagcttctgtataaaatgccatcttaactttccattccccttctagcagaagtttttcctctttaagttgaatttagaagctgctatattttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcccct