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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACAATTACAATGGTGGTCCTTGCTATCGGTGCCTCTTTCCAACTCCACCACCTAGAACAGCATGCCAAAGTTGTGCTGAGGGTGGAGTTCTAGGAGTAGgtaatttctactgtttttgtgaactgcatcagttttacttctcaatgagaagttctcattgctagtttgggcgacatttacttgaacaatgccaaccata...

Basic information

species Glycine max
transcript GLYMA02G46300.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G46300.1 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G160842_T02 (Zea mays), 5'ss of exon 8
TACAATTACAATGGTGGTCCTTGCTATCGGTGCCTCTTTCCAACTCCACCACCTAGAACAGCATGCCAAAGTTGTGCTGAGGGTGGAGTTCTAGGAGTAGgtaatttctactgtttttgtgaactgcatcagttttacttctcaatgagaagttct--cattgctagtttgggcgacatttacttgaacaatgccaaccata-----
||  || | |||||  | || |||||||||||||||||||||||||||||||||    |||| ||||| || ||  | ||  |||| || || || || ||||  |   |||||      |||   | ||| |  |||   |  |  | || || |    |||  |   ||    | |||   |  | |  ||   |    |     
TATCATCATAATGGAAGCCCATGCTATCGGTGCCTCTTTCCAACTCCACCACCTGTGGCAGCCTGCCAGAGATGCTCAGACAGTGGTGTCCTTGGGGTTGgtaggtgacactgta-----gaagctcgtcattagtacgg-tggacaaaaacttatatttttgtcaacctgtttaaaattcg-tcaatctttgtttatatgatgtgt

upper sequence: GLYMA02G46300.1 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G157836_T03 (Zea mays), 5'ss of exon 9
TACAATTACAATGGTGGTCCTTGCTATCGGTGCCTCTTTCCAACTCCACCACCTAGAACAGCATGCCAAAGTTGTGCTGAGGGTGGAGTTCTAGGAGTAGgtaatttctactgtttttgtgaactgcatcagttttac--ttctcaatgagaagttctcattgctagtttgggcgacatttacttgaacaatgccaaccata----
||  || | |||||  | || |||||||||||||||||||||||||||||||||    |||| ||||| || ||  | ||  |||| || || || || ||||  |   |||||      |||   | ||| |  |||  |   |||  |    |  |  |||  |   ||    | ||| | |  | |  ||   |    |    
TATCATCATAATGGAAGCCCATGCTATCGGTGCCTCTTTCCAACTCCACCACCTGTGGCAGCCTGCCAGAGATGCTCAGACAGTGGTGTCCTTGGGGTTGgtaggtgacactgta-----gaagctcgtcattagtacggtggacaaaaacttatattttttgtcaacctgtttaaaattca-tcaatctttgtttatatgatgtg

upper sequence: GLYMA02G46300.1 (Glycine max), 5'ss of exon 8
lower sequence: Vv19s0090g01020.t01 (Vitis vinifera), 5'ss of exon 8
TACAATTACAATGGTGGTCCTTGCTATCGGTGCCTCTTTCCAACTCCACCACCTAGAACAGCATGCCAAAGTTGTGCTGAGGGTGGAGTTCTAGGAGTAGgtaatttctactgtttttgtgaactgcatcagttttacttctcaatgagaagttctcattgctag--tttgggcgacatttacttgaacaatgccaaccata
||||||||||| || ||||| |||||||||||||| ||||| ||||||||||| | ||||||||| ||||| ||| | ||  |||||||| |||||||||||||   || | |||||  | |  ||    |  || | ||   | |  |      |   | | |    |||    | ||   |||||       |       
TACAATTACAAAGGAGGTCCATGCTATCGGTGCCTTTTTCCTACTCCACCACCAACAACAGCATGTCAAAGATGTTCAGATAGTGGAGTTTTAGGAGTAGgtaa--gctgcagttttgctaacatgtccaatattaaattactagtctgctaacttgcctaccaaaccttgtaaaatatgatcttgagagggatcttttcct

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|26059118|gb|CA802032.1|CA802032
EST:     ACCTAGAACAGCATGCCAAAGTTGTGCTGAGGGTGGAGTTCTAGGAGTAG                         TTCCTGGCATAATTGGCTGTCTCCAAGCTCTTGAGGCTATTAAGATTGCAG
genomic: ACCTAGAACAGCATGCCAAAGTTGTGCTGAGGGTGGAGTTCTAGGAGTAGgtaatttcta ... tcattttcagTTCCTGGCATAATTGGCTGTCTCCAAGCTCTTGAGGCTATTAAGATTGCAG
EST: gi|208145588|gb|GD942709.1|GD942709
EST:     ACCTAGAACAGCATGCCAAAGTTGTGCTGAGGGTGGAGTTCTAGGAGTAG                         TTCCTGGCATAATTGGCTGTCTCCAAGCTCTTGAGGCTATTAAGATTGCAG
genomic: ACCTAGAACAGCATGCCAAAGTTGTGCTGAGGGTGGAGTTCTAGGAGTAGgtaatttcta ... tcattttcagTTCCTGGCATAATTGGCTGTCTCCAAGCTCTTGAGGCTATTAAGATTGCAG
EST: gi|208232144|gb|GE033955.1|GE033955
EST:     ACCTAGAACAGCATGCCAAAGTTGTGCTGAGGGTGGAGTTCTAGGAGTAG                         TTCCTGGCATAATTGGCTGTCTCCAAGCTCTTGAGGCTATTAAGATTGCAG
genomic: ACCTAGAACAGCATGCCAAAGTTGTGCTGAGGGTGGAGTTCTAGGAGTAGgtaatttcta ... tcattttcagTTCCTGGCATAATTGGCTGTCTCCAAGCTCTTGAGGCTATTAAGATTGCAG
EST: gi|208266973|gb|GE062340.1|GE062340
EST:     ACCTAGAACAGCATGCCAAAGTTGTGCTGAGGGTGGAGTTCTAGGAGTAG                         TTCCTGGCATAATTGGCTGTCTCCAAGCTCTTGAGGCTATTAAGATTGCAG
genomic: ACCTAGAACAGCATGCCAAAGTTGTGCTGAGGGTGGAGTTCTAGGAGTAGgtaatttcta ... tcattttcagTTCCTGGCATAATTGGCTGTCTCCAAGCTCTTGAGGCTATTAAGATTGCAG
EST: gi|208250717|gb|GE043764.1|GE043764
EST:     CCTTAGAACAGCATGCCAAAGTTGTGCTGAGGGTGGAGTTCTAGGAGTAG                         TTCCTGGCATAATTGGCTGTCTCCAAGCTCTTGAGGCTATTAAGATTGCAG
genomic: CC-TAGAACAGCATGCCAAAGTTGTGCTGAGGGTGGAGTTCTAGGAGTAGgtaatttcta ... tcattttcagTTCCTGGCATAATTGGCTGTCTCCAAGCTCTTGAGGCTATTAAGATTGCAG
EST: gi|193310286|gb|FK273692.1|FK273692
EST:     ACCTAGAACAGCATGCCAAAGTTGTGCTGAGGGTGGAGTTCTAGGAGTAG                         TTCCTGGCATAATTGGCTGTCTCCAAGCTCTTGAGGCTATTAAGATTGCAG
genomic: ACCTAGAACAGCATGCCAAAGTTGTGCTGAGGGTGGAGTTCTAGGAGTAGgtaatttcta ... tcattttcagTTCCTGGCATAATTGGCTGTCTCCAAGCTCTTGAGGCTATTAAGATTGCAG
EST: gi|9899477|gb|BE608445.1|BE608445
EST:     ACCTAGAACAGCATGCCAAAGTTGTGCTGAGGGTGGAGTTCTAGGAGTAG                         TTCCTGGCATAATTGGCTGTCTCCAAGCTCTTGAGGCTATTAAGATTGCAG
genomic: ACCTAGAACAGCATGCCAAAGTTGTGCTGAGGGTGGAGTTCTAGGAGTAGgtaatttcta ... tcattttcagTTCCTGGCATAATTGGCTGTCTCCAAGCTCTTGAGGCTATTAAGATTGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACAATTACAATGGTGGTCCTTGCTATCGGTGCCTCTTTCCAACTCCACCACCTAGAACAGCATGCCAAAGTTGTGCTGAGGGTGGAGTTCTAGGAGTAGgtaatttctactgtttttgtgaactgcatcagttttacttctcaatgagaagttctcattgctagtttgggcgacatttacttgaacaatgccaaccata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG