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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGGTAACAGGTATCCATTACCTAACAAATCAGCACCTGTTTACATAACAGTCGGAGATGGTGGAAATCAAGAAGGTCTTGCTTCAAGgtaaattaaacaaaccatatctaaaatccttcttgaatatgattatgtcaaagatgtcttgtcatataggttttaattctatccttggtcatgcag

Basic information

species Glycine max
transcript GLYMA17G11790.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G11790.2 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os06g43640.2 (Oryza sativa), 5'ss of exon 8
------------GCGGTAACAGGTATCCATTACCTAACAAATCAGCACCTGTTTACATAACAGTCGGAGATGGTGGAAATCAAGAAGGTCTTGCTTCAAGgtaaat-taaacaaacc-atatctaaaatccttct-tgaatatgattat-gtcaaagatgtcttgtcatataggttttaattctatccttggtcatgcag
              |||||  | |||||| | ||  ||||||| || ||||| ||||||||||| || ||||| || || || ||||| ||||||||||||||||   |||  ||   ||| |  ||| | | || |   ||  ||| | ||  | |   || |    |  |    ||  |   |  |  |||  |||||
ACAACATAACATCGGGTAATCGATATCCAGTGCCAGACAAATCTGCTCCTGTGTACATAACAGTTGGTGATGGAGGCAACCAGGAAGGGCTTGCTTCAAGgtaaaggcaaatgaatttatagcggaaaacatactatttgtaatattgttgtttacgcactcctacggttcactcattgttcaaaatcacggtgttgcag

upper sequence: GLYMA17G11790.2 (Glycine max), 5'ss of exon 8
lower sequence: AC211394.4_FGT004 (Zea mays), 5'ss of exon 8
------------GCGGTAACAGGTATCCATTACCTAACAAATCAGCACCTGTTTACATAACAGTCGGAGATGGTGGAAATCAAGAAGGTCTTGCTTCAAGgtaaattaaacaaaccatatctaaaatccttcttgaatatgattatgtcaaagatgtcttgtcatataggttttaattctatccttggtcatgcag-----
              || ||  |||||||| | ||  ||||||| || || ||||||||||| ||||| ||||| || || || ||||| ||||||||||||| |    ||| ||        |||||  ||      |   |||||||  |           |  |||   |    |    | || |  ||   |      
ACAACATAACGTCGGGAAATCGGTATCCAGTGCCGGACAAATCTGCTCCCGTTTACATAACGGTCGGTGATGGAGGCAACCAGGAAGGACTTGCTTCAAGgtgagaggaactaatagccagcaaaatgttttactggtgctattatgtttactgaactcatactcatacactcacgtggcctactaga-cagaaacttatg

upper sequence: GLYMA17G11790.2 (Glycine max), 5'ss of exon 8
lower sequence: AT5G34850.1 (Arabidopsis thaliana), 5'ss of exon 7
------------GCGGTAACAGGTATCCATTACCTAACAAATCAGCACCTGTTTACATAACAGTCGGAGATGGTGGAAATCAAGAAGGTCTTGCTTCAAGgtaaattaaacaaaccatatctaaaatccttcttgaatatgatta-tgtcaaagatgtcttgtcata--taggttttaattctatccttggtcatgcag-
            ||||  |  | || ||| | ||  | || ||||| |||||||| || ||||| ||||| || ||||||||||||||||| |||  ||||| | | | |  | |    || |  |   | || ||| |  |  |  || |    ||   ||| |||  || | | | ||   |    |  |||| |   
ATAACGTGTCAAGCGGAGATCGTTACCCAGTTCCAGATAAGTCAGCGCCTGTTTATATCACAGTTGGAGACGGAGGAAATCAAGAAGGTCTGGCTGGAAGgttagtaacatgatcagattcaattagattactggaacacaaaaagcgtgagccttggaatgttataagtacgatgttataaaactgcttctcattccaa

upper sequence: GLYMA17G11790.2 (Glycine max), 5'ss of exon 8
lower sequence: Vv04s0008g06520.t01 (Vitis vinifera), 5'ss of exon 8
------------GCGGTAACAGGTATCCATTACCTAACAAATCAGCACCTGTTTACATAACAGTCGGAGATGGTGGAAATCAAGAAGGTCTTGCTTCAAGgta-----aattaaacaaacc-atatctaa---aatccttcttgaatatgattatgtcaaagatgtcttgtcatataggttttaattctatccttggtcatgcag---------------------------------------------------------
              ||  |  |||||||  ||||| |||||||||| || || |||||||| || |||||||| || ||||| ||||||||||||  ||||||     ||||  ||||    | |||| |     | ||| ||   |   | |  ||    ||   ||  |  ||    |||        |  ||   ||   |                                                          
ATAATATAACAAATGGCGATCGGTATCCTATACCTGACAAATCAGCTCCAGTGTACATAACTGTTGGAGATGGAGGGAATCAGGAAGGTCTTGCTGGAAGgtatgaaaaattttacaatttgaaatctcaccggttacttgttattttctaatgagttggggaaagctctttgtactcatttagtccactttattttccagaaaatttatggttccctcctgaagcattccttacattactgattttggcaattgattgtag

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|209714893|gb|BW682058.1|BW682058
EST:     GTTTACATAACAGTCGGAGATGGTGGAAATCAAGAAGGTCTTGCTTCAAG                         GTTTTTGGATCCACAGCCAGAATATTCTGCTTTTCGAGAAGCAAGCTACGG
genomic: GTTTACATAACAGTCGGAGATGGTGGAAATCAAGAAGGTCTTGCTTCAAGgtaaattaaa ... ggtcatgcagGTTTTTGGATCCACAGCCAGAATATTCTGCTTTTCGAGAAGCAAGCTACGG
EST: gi|209728181|gb|BW651616.1|BW651616
EST:     GTTTACATAACAGTCGGAGATGGTGGAAATCAAGAAGGTCTTGCTTCAAG                         GTTTTTGGATCCACAGCCAGAATATTCTGCTTTTCGAGAAGCAAGCTACGG
genomic: GTTTACATAACAGTCGGAGATGGTGGAAATCAAGAAGGTCTTGCTTCAAGgtaaattaaa ... ggtcatgcagGTTTTTGGATCCACAGCCAGAATATTCTGCTTTTCGAGAAGCAAGCTACGG
EST: gi|193681333|gb|FK624469.1|FK624469
EST:     AAGAAGGTCTTGCTTCAAG                         GTTTTTGGATCCACAGCCAGAATATTCTGCTTTTCGAGAAGCAAGCTACGG
genomic: AAGAAGGTCTTGCTTCAAGgtaaattaaa ... ggtcatgcagGTTTTTGGATCCACAGCCAGAATATTCTGCTTTTCGAGAAGCAAGCTACGG
EST: gi|193392304|gb|FK360129.1|FK360129
EST:     GTTTACATAACAGTCGGAGATGGTGGAAATCAAGAAGGTCTTGCTTCAAG                         GTTTTTGGATCCACAGCCAGAATATTCTGCTTTTCGAGAAGCAAGCTACGG
genomic: GTTTACATAACAGTCGGAGATGGTGGAAATCAAGAAGGTCTTGCTTCAAGgtaaattaaa ... ggtcatgcagGTTTTTGGATCCACAGCCAGAATATTCTGCTTTTCGAGAAGCAAGCTACGG
EST: gi|151399107|gb|EV268978.1|EV268978
EST:     GTTTACATAACAGTCGGAGATGGTGGAAATCAAGAAGGTCTTGCTTCAAG                         GTTTTTGGATCCACAGCCAGAATATTCTGCTTTTCGAGAAGCAAGCTACGG
genomic: GTTTACATAACAGTCGGAGATGGTGGAAATCAAGAAGGTCTTGCTTCAAGgtaaattaaa ... ggtcatgcagGTTTTTGGATCCACAGCCAGAATATTCTGCTTTTCGAGAAGCAAGCTACGG
EST: gi|208316365|gb|GE114049.1|GE114049
EST:     AGAAGGCCTTGCTTCAAG                         GTTTTTGGATCCACAGCCAGAATATTCTGCTTTTCGAGAAGCAAGCTACGG
genomic: AGAAGGTCTTGCTTCAAGgtaaattaaa ... ggtcatgcagGTTTTTGGATCCACAGCCAGAATATTCTGCTTTTCGAGAAGCAAGCTACGG
EST: gi|193463690|gb|FK426522.1|FK426522
EST:     GTTTACATAACAGTCGGAGATGGTGGAAATCAAGAAGGTCTTGCTTCAAG                         GTTTTTGGATCCACAGCCAGAATATTCTGCTTTTCGAGAAGCAAGCTACGG
genomic: GTTTACATAACAGTCGGAGATGGTGGAAATCAAGAAGGTCTTGCTTCAAGgtaaattaaa ... ggtcatgcagGTTTTTGGATCCACAGCCAGAATATTCTGCTTTTCGAGAAGCAAGCTACGG
EST: gi|193332504|gb|FK301622.1|FK301622
EST:     ATGGTGGAAATCAAGAAGGTCTTGCTTCAAG                         GTTTTTGGATCCACAGCCAGAATATTCTGCTTTTCGAGAAGCAAGCTACGG
genomic: ATGGTGGAAATCAAGAAGGTCTTGCTTCAAGgtaaattaaa ... ggtcatgcagGTTTTTGGATCCACAGCCAGAATATTCTGCTTTTCGAGAAGCAAGCTACGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGGTAACAGGTATCCATTACCTAACAAATCAGCACCTGTTTACATAACAGTCGGAGATGGTGGAAATCAAGAAGGTCTTGCTTCAAGgtaaattaaacaaaccatatctaaaatccttcttgaatatgattatgtcaaagatgtcttgtcatataggttttaattctatccttggtcatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG