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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGATGACAAATTCAGCTGAAAAGGTCCGGTTAGCTGGAAATCCTAATGTGATGGTTTGTGAGAGAGGAACAATGTTTGGATACAgtgagttagtagcaactattttgaggttttctgttcgtgaatgatgtgaatcttgcaagaaccattcaataattgatatcagtaattgcttaatgcagag...

Basic information

species Glycine max
transcript GLYMA09G38010.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G38010.1 (Glycine max), 5'ss of exon 8
lower sequence: AT1G79500.2 (Arabidopsis thaliana), 5'ss of exon 8
GTGATGACAAATTCAGCTGAAAAGGTCCGGTTAGCTGGAAATCCTAATGTGATGGTTTGTGAGAGAGGAACAATGTTTGGATACAgtgagttagtagcaactattttgaggttttctgttcg----tgaatgatgtgaatcttgcaagaac-cattcaa--taattgatatcagtaattgcttaat-gcagag-------------------------------------------------------------------------------------
|| |||   ||||||||||| ||| || |  | ||||| ||||| ||||| ||||||||||| |||||||| ||||| ||||||||| |||||  | |  || ||   |  || | |   ||    | | |  |||  || ||   | | | ||| |||     |||  || |  ||    |  || || ||                                                                                      
GTCATGGAGAATTCAGCTGAGAAGATCAGACTGGCTGGGAATCCAAATGTTATGGTTTGTGAAAGAGGAACCATGTTCGGATACAgtaagttatcatctccttttcaaatattgtgtccacggaatttagtattgtagatattctcaaatctcatgcaaatctcttggaattaaaaaaaattggattgctgaagtatacattagagggtgctaaaacaattttttttctctgcctttacaattgactgactgatactctttttggttttgattatcag

upper sequence: GLYMA09G38010.1 (Glycine max), 5'ss of exon 8
lower sequence: AT1G16340.2 (Arabidopsis thaliana), 5'ss of exon 8
GTGATGACAAATTCAGCTGAAAAGGTCCGGTTAGCTGGAAATCCTAATGTGATGGTTTGTGAGAGAGGAACAATGTTTGGATACAgtgagttagtagcaactatttt-----gaggttttctgttcgtgaatgatgtgaatcttgcaagaaccattcaataattgatatcagtaattgcttaatgcagag------------------
|| |||| ||| || ||||| |||||  |  | || || ||||| ||||||||||||||||| |||||||| ||||||||||||||| |||||   |    |  | |     ||  |   |  ||  |     |   ||  ||   |   || |    | | | ||||| | |  |   |      | |                   
GTCATGAGAAACTCGGCTGAGAAGGTTAGACTCGCAGGGAATCCAAATGTGATGGTTTGTGAAAGAGGAACCATGTTTGGATACAgtaagttaactgttctttgtgtcaatagaattcaccaatttttttgcaaatagagactaaaatagactaaaagacactggatataactcctgagtgtccttacattttaattttgttcctcag

upper sequence: GLYMA09G38010.1 (Glycine max), 5'ss of exon 8
lower sequence: Vv19s0085g00720.t01 (Vitis vinifera), 5'ss of exon 7
GTGATGACAAATTCAGCTGAAAAGGTCCGGTTAGCTGGAAATCCTAATGTGATGGTTTGTGAGAGAGGAACAATGTTTGGATACAgtgagttagtagcaact-attttgaggttttctgttcgtgaatgatgtgaatcttgcaagaaccattcaataattgatatcagtaattgctta-atgcagag
|| |||  |||||| ||||||||| || | || ||||| |||   |||||||||||||||||||| ||||| |||||||| || ||| ||| |      | | |  || |  | |    |     |    | ||  |  ||         |    ||||  |||   ||  |  |  | ||| ||| 
GTCATGGTAAATTCTGCTGAAAAGATCAGATTGGCTGGGAATGAAAATGTGATGGTTTGTGAGAGGGGAACTATGTTTGGCTATAgtaagtcacccttgatttaagttcaaatgtctaatggcctaggcttttgggttgtgtttttttggtgttctaat--ataaaggtgttgacgcacatggagat

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|192326691|gb|FK018878.1|FK018878
EST:     TGGAAATCCTAATGTGATGGTTTGTGAGAGAGGAACAATGTTTGGATACA                         ATGATTTGATTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATT
genomic: TGGAAATCCTAATGTGATGGTTTGTGAGAGAGGAACAATGTTTGGATACAgtgagttagt ... tttcatacagATGATTTGATTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATT
EST: gi|208275338|gb|GE079372.1|GE079372
EST:     TGGAAATCCTAATGTGATGGTTTGTGAGAGAGGAACAATGTTTGGATACA                         ATGATTTGATTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATT
genomic: TGGAAATCCTAATGTGATGGTTTGTGAGAGAGGAACAATGTTTGGATACAgtgagttagt ... tttcatacagATGATTTGATTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATT
EST: gi|23063937|gb|BU578710.1|BU578710
EST:     TGGAAATCCTAATGTGATGGTTTGTGAGAGAGGAACAATGTTTGGATACA                         ATGATTTGATTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATT
genomic: TGGAAATCCTAATGTGATGGTTTGTGAGAGAGGAACAATGTTTGGATACAgtgagttagt ... tttcatacagATGATTTGATTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATT
EST: gi|58017972|gb|CX704714.1|CX704714
EST:     TGGAAATCCTAATGTGATGGTTTGTGAGAGAGGAACAATGTTTGGATACA                         ATGATTTGATTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATT
genomic: TGGAAATCCTAATGTGATGGTTTGTGAGAGAGGAACAATGTTTGGATACAgtgagttagt ... tttcatacagATGATTTGATTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATT
EST: gi|208262320|gb|GE059681.1|GE059681
EST:     TGGAAATCCTAATGTGATGGTTTGTGAGAGAGGAACAATGTTTGGATACA                         ATGATTTGATTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATT
genomic: TGGAAATCCTAATGTGATGGTTTGTGAGAGAGGAACAATGTTTGGATACAgtgagttagt ... tttcatacagATGATTTGATTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATT
EST: gi|207767250|gb|GD739662.1|GD739662
EST:     TGGAAATCCTAATGTGATGGTTTGTGAGAGAGGAACAATGTTTGGATACA                         ATGATTTGATTGTTGATCCACGTAACTTGGAGTGG
genomic: TGGAAATCCTAATGTGATGGTTTGTGAGAGAGGAACAATGTTTGGATACAgtgagttagt ... tttcatacagATGATTTGATTGTTGATCCACGTAACTTGGAGTGG
EST: gi|58021325|gb|CX708066.1|CX708066
EST:     TGGAAATCCTAATGTGATGGTTTGTGAGAGAGGAACAATGTTTGGATACA                         ATGATTTGATTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATT
genomic: TGGAAATCCTAATGTGATGGTTTGTGAGAGAGGAACAATGTTTGGATACAgtgagttagt ... tttcatacagATGATTTGATTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATT
EST: gi|57575913|gb|CX548884.1|CX548884
EST:     TGGAAATCCTAATGTGATGGTTTGTGAGAGAGGAACAATGTTTGGATACA                         ATGATTTGATTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATT
genomic: TGGAAATCCTAATGTGATGGTTTGTGAGAGAGGAACAATGTTTGGATACAgtgagttagt ... tttcatacagATGATTTGATTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATT
EST: gi|151406834|gb|EV276649.1|EV276649
EST:     TGGAAATCCTAATGTGATGGTTTGTGAGAGAGGAACAATGTTTGGATACA                         ATGATTTGATTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATT
genomic: TGGAAATCCTAATGTGATGGTTTGTGAGAGAGGAACAATGTTTGGATACAgtgagttagt ... tttcatacagATGATTTGATTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGATGACAAATTCAGCTGAAAAGGTCCGGTTAGCTGGAAATCCTAATGTGATGGTTTGTGAGAGAGGAACAATGTTTGGATACAgtgagttagtagcaactattttgaggttttctgttcgtgaatgatgtgaatcttgcaagaaccattcaataattgatatcagtaattgcttaatgcagag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA