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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAAATTCAAGCCCGTGATCAAGAAAGCAATGGTGGAGCTTGAAGgtaaacatatatattcatgaaaacctcattgttttgggctccatagtccactaacgtagcaagtgaactacactttttacccatattgagccacaaaaat...

Basic information

species Glycine max
transcript GLYMA09G01050.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G01050.1 (Glycine max), 5'ss of exon 14
lower sequence: AT4G04040.1 (Arabidopsis thaliana), 5'ss of exon 14
GTAAATTCAAGCCCGTGATCAAGAAAGCAATGGTGGAGCTTGAAGgtaaacatatatattcatgaaaacctcattgtt-ttgggctccatagtccactaacgtagcaagtgaactacactttttacccatattgagccacaaaaat
||||||||||||| || ||||||||||| ||||| || |||||||||||  |    |   |   |||     ||| || || || | | |      |||||        | || | ||                            
GTAAATTCAAGCCTGTTATCAAGAAAGCTATGGTTGAACTTGAAGgtaattagtctttagctcaaaacatatattattcttcggtttcttttcttgctaacacta----taaatttcag---------------------------

upper sequence: GLYMA09G01050.1 (Glycine max), 5'ss of exon 14
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 5'ss of exon 14
GTAAATTCAAGCCCGTGATCAAGAAAGCAATGGTGGAGCTTGAAGgtaaacatatatattcatgaaaacctcattgttttgggctccatagtccactaacgtagcaagtgaactacactttttacccatattgagccacaaaaat
|||| |||||||| ||||||||||||||||||||||| ||||||||| | | | |   | | |       |||| ||||| |  |     | |   ||   |  |  |   |||    |||| | |  |   |            
GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAGgtgaccctttgattcccttcccttttcatagttttcgatt-----ggcggttagattgtcttgctgactgtctttttgagctctgcag------------
















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|4313688|gb|AI460807.1|AI460807
EST:     GTAAATTCAAGCCCGTGATCAAGAAAGCAATGGTGGAGCTTGAAG                         GG-CACCCTTCAAAA
genomic: GTAAATTCAAGCCCGTGATCAAGAAAGCAATGGTGGAGCTTGAAGgtaaacatat ... gatcattcagGGGCACCCTTCAAAA
EST: gi|213598262|gb|DB979705.1|DB979705
EST:     GTAAATTCAAGCCCGTGATCAAGAAAGCAATGGTGGAGCTTGAAG                         GGGCACCCTTCAAAAAGTTTGCCTCCTTGCGTGATGAATGGGCCCTGAAGA
genomic: GTAAATTCAAGCCCGTGATCAAGAAAGCAATGGTGGAGCTTGAAGgtaaacatat ... gatcattcagGGGCACCCTTCAAAAAGTTTGCCTCCTTGCGTGATGAATGGGCCCTGAAGA
EST: gi|15813400|gb|BI785675.1|BI785675
EST:     GTAAATTCAAGCCCGTGATCAAGAAAGCAATGGTGGAGCTTGAAG                         GGGCACCCTTCAAAAAGTTTGCCTCCTTGCGTGATGAATGGGCCCTGAAGA
genomic: GTAAATTCAAGCCCGTGATCAAGAAAGCAATGGTGGAGCTTGAAGgtaaacatat ... gatcattcagGGGCACCCTTCAAAAAGTTTGCCTCCTTGCGTGATGAATGGGCCCTGAAGA
EST: gi|7284788|gb|AW597213.1|AW597213
EST:     GTAAATTCAAGCCCGTGATCAAGAAAGCAATGGTGGAGCTTGAAG                         GGGCACCCTTCAAAAAGTTTGCCTCCTTGCGTGATGAATGGGCCCTGAAGA
genomic: GTAAATTCAAGCCCGTGATCAAGAAAGCAATGGTGGAGCTTGAAGgtaaacatat ... gatcattcagGGGCACCCTTCAAAAAGTTTGCCTCCTTGCGTGATGAATGGGCCCTGAAGA
EST: gi|4313349|gb|AI460468.1|AI460468
EST:     GTAAATTCAAGCCCGTGATCAAGAAAGCAATGGTGGAGCTTGAAG                         GGGCACCCTTCANAAAGTTTGCCTCCTTGCGTGATGAATGGGCCCTGAAGA
genomic: GTAAATTCAAGCCCGTGATCAAGAAAGCAATGGTGGAGCTTGAAGgtaaacatat ... gatcattcagGGGCACCCTTCAAAAAGTTTGCCTCCTTGCGTGATGAATGGGCCCTGAAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAAATTCAAGCCCGTGATCAAGAAAGCAATGGTGGAGCTTGAAGgtaaacatatatattcatgaaaacctcattgttttgggctccatagtccactaacgtagcaagtgaactacactttttacccatattgagccacaaaaat

- - - - - - - - - - AAGAAA
- - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - -  TTGAAG