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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATGGTGGTGGTATGAGTTCTGCAAAAGCTGCACTGGAGAGTGATACACGAgtaagcttcaactcctacccacaccaccaaaaaaaaactcaccagattacatactgacttagacgtgcttcatttttacttctctctcttttaaattacatcatatgtcatgccttttcag

Basic information

species Glycine max
transcript GLYMA12G03060.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G03060.1 (Glycine max), 5'ss of exon 11
lower sequence: GRMZM2G079256_T02 (Zea mays), 5'ss of exon 10
ATATGGTGGTGGTATGAGTTCTGCAAAAGCTGCACTGGAGAGTGATACACGAgtaagcttcaactcctacccacaccaccaaaaaaaaactcaccagattacatactgacttagacgtgcttcatttttacttctctctcttttaaattacatcatatgtcatgccttttcag
 || ||||||||||||||||| |||||||| || || |||||||||||| |||||         | |||      |   ||   |    || |  |  ||   |  ||  ||   | ||| | ||  ||||| |     |||||    ||  |||                  
CTACGGTGGTGGTATGAGTTCAGCAAAAGCAGCTCTTGAGAGTGATACAAGAgtacaaact--tttctatgagatctcacatgcattgccttatgatgttcagtggtg-tttccccatgcat-ataattactgccaagccttttttcctat-tcag-----------------

upper sequence: GLYMA12G03060.1 (Glycine max), 5'ss of exon 11
lower sequence: GRMZM2G125052_T01 (Zea mays), 5'ss of exon 8
ATATGGTGGTGGTATGAGTTCTGCAAAAGCTGCACTGGAGAGTGATACACGAgtaagcttcaactcctacccacaccaccaaaaaaaaactcaccagattacat--actgacttagacgtgcttcatttttacttctctctcttttaaattacatcatatgtcatgccttttcag
 ||||||||||| ||||||||||| ||||| || || |||||||||||||| ||| | |    |          ||||  ||    |   ||      ||||||  |   || ||    ||                                                      
GTATGGTGGTGGCATGAGTTCTGCTAAAGCAGCTCTCGAGAGTGATACACGGgtatggtcttgcgtaattgtgtaccatgaattttatgttcttttttttacatttataaacctatcgatgtag---------------------------------------------------

upper sequence: GLYMA12G03060.1 (Glycine max), 5'ss of exon 11
lower sequence: GRMZM2G070422_T01 (Zea mays), 5'ss of exon 10
ATATGGTGGTGGTATGAGTTCTGCAAAAGCTGCACTGGAGAGTGATACACGAgtaagcttcaactcctacccacaccaccaaaaaaaaactcaccagattacatactgacttagacgtgcttcatttttacttctctctcttttaaattacatcatatgtcatgccttttcag
 ||||||||||| ||||||||||| ||||| || || |||||||||||||| ||| | |    |   ||           |||      ||  ||  || |   | | | ||   | |  | | ||| ||   ||  |  | |                              
GTATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgttgca--taattgtgtgcttaaattcttcctttccccatga---attcattttctctt-ttacgtttataaacctgccgatatag----------------------------

upper sequence: GLYMA12G03060.1 (Glycine max), 5'ss of exon 11
lower sequence: AT2G05990.2 (Arabidopsis thaliana), 5'ss of exon 9
ATATGGTGGTGGTATGAGTTCTGCAAAAGCTGCACTGGAGAGTGATACACGAgtaagctt-caactcctacccacaccaccaaaaaaaaactcaccagattacatactgacttagacgtgcttcatttttacttctctctcttttaaattacatcatatgtcatgccttttcag
 |||||||| |||||||||||||| ||||||||||| |||||||| ||||| || || || ||| ||     |  |    |||| |   |      |||   |     | |  |   ||| ||      ||                                           
GTATGGTGGAGGTATGAGTTCTGCCAAAGCTGCACTAGAGAGTGACACACGGgtgagtttacaattctgtttcgtaaactcaaagatgtatcggttagaagtctcttagtccaaactgtgttttcaacatag------------------------------------------

upper sequence: GLYMA12G03060.1 (Glycine max), 5'ss of exon 11
lower sequence: PP1S99_59V6.3 (Physcomitrella patens), 5'ss of exon 9
ATATGGTGGTGGTATGAGTTCTGCAAAAGCTGCACTGGAGAGTGATACACGAgtaagcttcaactcctacccacaccaccaaaaaaaaactcaccagattacatactgacttagacgtgcttcatttttacttctctct--cttttaaattacatcatatgtcatgccttttcag
||||||||| || ||||| ||||| ||||||||||| |||||||| ||||| ||||| |      | || |  |          || ||        | || ||  | | ||     |    ||| | ||  |   ||   ||  |  ||||  |   | ||   |         
ATATGGTGGAGGGATGAGCTCTGCCAAAGCTGCACTTGAGAGTGACACACGTgtaagtt-----ccttatctgcgt--------aagaatctcttgtagta-atcgtcatttgcgaataacccatctctaggttattccgactacttgatta-gtagcaagtttggt--------

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|6915325|gb|AW396855.1|AW396855
EST:     ATGGTGGTGGTATGAGTTCTGCAAAAGCTGCACTGGAGAGTGATACACGA                         GTTCTTGCTTTTGAAGCAGGAAGAAAGCGCAAAATTAGAGTCAATACTATA
genomic: ATGGTGGTGGTATGAGTTCTGCAAAAGCTGCACTGGAGAGTGATACACGAgtaagcttca ... gccttttcagGTTCTTGCTTTTGAAGCAGGAAGAAAGCGCAAAATTAGAGTCAATACTATA
EST: gi|192301956|gb|FG995574.1|FG995574
EST:     ATGGTGGTGGTATGAGTTCTGCAAAAGCTGCACTGGAGAGTGTTACACGA                         GTTCTTGCTTTTGAAGCAGGAAGAAAGCGCAAAATTAGAGTCAATACTATA
genomic: ATGGTGGTGGTATGAGTTCTGCAAAAGCTGCACTGGAGAGTGATACACGAgtaagcttca ... gccttttcagGTTCTTGCTTTTGAAGCAGGAAGAAAGCGCAAAATTAGAGTCAATACTATA
EST: gi|16347093|gb|BI972688.1|BI972688
EST:     ATGGCGGTGGTATGAGTTCTGCACAAGCTGCACTGGAGAGTGATACACGA                         GTTCTTGCTTTTGAAGCGGGAAGAAAGCGCAAAATTAGAGGCAATACTATA
genomic: ATGGTGGTGGTATGAGTTCTGCAAAAGCTGCACTGGAGAGTGATACACGAgtaagcttca ... gccttttcagGTTCTTGCTTTTGAAGCAGGAAGAAAGCGCAAAATTAGAGTCAATACTATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATGGTGGTGGTATGAGTTCTGCAAAAGCTGCACTGGAGAGTGATACACGAgtaagcttcaactcctacccacaccaccaaaaaaaaactcaccagattacatactgacttagacgtgcttcatttttacttctctctcttttaaattacatcatatgtcatgccttttcag

-  TGGTGG
- - - TGGTGG
- - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - -  TGGAGA