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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACTCGTGTGCAGTTCCATTTAGACCAAATCCGGTTACTGGTGGCCCATGAGACTCAGTTGGCAATATATGATGCCTCTAAGATGGATCGCATTAGGCAGgtaagaggatttttctatctagtattggtattattgcttgttgctgtcaaaaattaaaattgagacatccttataaatcaacttgctgcag

Basic information

species Glycine max
transcript GLYMA03G39290.1
intron # 24
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G39290.1 (Glycine max), 5'ss of exon 24
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 5'ss of exon 23
CACTCGTGTGCAGTTCCATTTAGACCAAATCCGGTTACTGGTGGCCCATGAGACTCAGTTGGCAATATATGATGCCTCTAAGATGGATCGCATTAGGCAGgtaagaggatttttctatctagtattggtattattgcttgttgctgtcaaaaattaaaattgagacatccttataaatcaacttgctgcag
|||||| || ||||| || |  || ||||||||||| |||||   |||||| || |||||||||| |||||||||||| || ||||| || ||| | ||||||  | | ||  ||  |   |  |  |  |  ||   ||||       | ||||    |    |  | |||||   |  |||||| |   
CACTCGAGTACAGTTTCACTCTGATCAAATCCGGTTGCTGGTATTCCATGAAACACAGTTGGCAACATATGATGCCTCAAAAATGGAGCGGATTCGTCAGgtagaaagtttagtcagt---gactcagcttacttcaatgtttgacatcagaatttttgtaataagtttcttatgtgt--acttgcag---
















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|163917881|gb|EH039022.1|EH039022
EST:     AGACTCAGTTGGCAATATATGATGCCTCTAAGATGGATCGCATTAGGCAG                         TGGGTTCCACAAGATGTTCTGGCTGCTCCCATATCATATGCAGCTTATTCC
genomic: AGACTCAGTTGGCAATATATGATGCCTCTAAGATGGATCGCATTAGGCAGgtaagaggat ... cttgctgcagTGGGTTCCACAAGATGTTCTGGCTGCTCCCATATCATATGCAGCTTATTCC
EST: gi|11413763|gb|BF425774.1|BF425774
EST:     AGACTCAGTTGGCAATATATGATGCCTCTAAGATGGATCGCATTAGGCAG                         TGGGTTCCACAAGATGTTCTGGCTGCTCCCATATCATATGCAGCTTATTCC
genomic: AGACTCAGTTGGCAATATATGATGCCTCTAAGATGGATCGCATTAGGCAGgtaagaggat ... cttgctgcagTGGGTTCCACAAGATGTTCTGGCTGCTCCCATATCATATGCAGCTTATTCC
EST: gi|254343985|gb|GR857741.1|GR857741
EST:     AGACTCAGTTGGCAATATATGATGCCTCTAAGATGGATCGCATTAGGCAG                         TGGGTTCCACAAGATGTTCTGGCTGCTCCCATATCATATGCAGCTTATTCC
genomic: AGACTCAGTTGGCAATATATGATGCCTCTAAGATGGATCGCATTAGGCAGgtaagaggat ... cttgctgcagTGGGTTCCACAAGATGTTCTGGCTGCTCCCATATCATATGCAGCTTATTCC
EST: gi|193346467|gb|FK313389.1|FK313389
EST:     AGACTCAGTTGGCAATATATGATGCCTCTAAGATGGATCGCATTAGGCAG                         TGGGTTCCACAAGATGTTCCGGCTGCTCCCATATCATATGCAGCTTATTCC
genomic: AGACTCAGTTGGCAATATATGATGCCTCTAAGATGGATCGCATTAGGCAGgtaagaggat ... cttgctgcagTGGGTTCCACAAGATGTTCTGGCTGCTCCCATATCATATGCAGCTTATTCC
EST: gi|254318653|gb|GR828597.1|GR828597
EST:     GATCGCATTAGGCAG                         TGGGTTCCACAAGATGTTCTGGCTGCTCCCATATCATATGCAGCTTATTCC
genomic: GATCGCATTAGGCAGgtaagaggat ... cttgctgcagTGGGTTCCACAAGATGTTCTGGCTGCTCCCATATCATATGCAGCTTATTCC
EST: gi|27446247|gb|CA953370.1|CA953370
EST:     TGGCAATATATGATGCCTCTAAGATGGATCGCATTAGGCAG                         TGGGTTCCACAAGATGTTCTGGCTGCTCCCATATCATATGCAGCTTATTCC
genomic: TGGCAATATATGATGCCTCTAAGATGGATCGCATTAGGCAGgtaagaggat ... cttgctgcagTGGGTTCCACAAGATGTTCTGGCTGCTCCCATATCATATGCAGCTTATTCC
EST: gi|19453486|gb|BM954896.1|BM954896
EST:     AGACTCAGTTGGCAATATATGATGCCTCTAAGATGGATCGCATTAGGCAG                         TGGGTTCCACAAGATGTTCTGGCTGCTCCCATATCATATGCAGCTTATTCC
genomic: AGACTCAGTTGGCAATATATGATGCCTCTAAGATGGATCGCATTAGGCAGgtaagaggat ... cttgctgcagTGGGTTCCACAAGATGTTCTGGCTGCTCCCATATCATATGCAGCTTATTCC
EST: gi|19453554|gb|BM954964.1|BM954964
EST:     AGACTCAGTTGGCAATATATGATGCCTCTAAGATGGATCGCATTAGGCAG                         TGGGTTCCACAAGATGTTCTGGCTGCTCCCATATCATATGCAGCTTATTCC
genomic: AGACTCAGTTGGCAATATATGATGCCTCTAAGATGGATCGCATTAGGCAGgtaagaggat ... cttgctgcagTGGGTTCCACAAGATGTTCTGGCTGCTCCCATATCATATGCAGCTTATTCC
EST: gi|14011684|gb|BG726606.1|BG726606
EST:     AGACTCAGTTGGCAATATATGATGCCTCTAAGATGGATCGCATTAGGCAG                         TGGGTTCCACAAGATGTTCTGGCTGCTCCCATATCATATGCAGCTTATTCC
genomic: AGACTCAGTTGGCAATATATGATGCCTCTAAGATGGATCGCATTAGGCAGgtaagaggat ... cttgctgcagTGGGTTCCACAAGATGTTCTGGCTGCTCCCATATCATATGCAGCTTATTCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACTCGTGTGCAGTTCCATTTAGACCAAATCCGGTTACTGGTGGCCCATGAGACTCAGTTGGCAATATATGATGCCTCTAAGATGGATCGCATTAGGCAGgtaagaggatttttctatctagtattggtattattgcttgttgctgtcaaaaattaaaattgagacatccttataaatcaacttgctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA