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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGCTGATGGAGATAAGGTCACTAATGACATAATTTTTGCTCCAGGAAAGAAGAAATATAGATTCTGTAAGgtaaagaaatctctattgagatattcattttctcacataatgtatatatagaggaacattatgatcatttttctataaaaaaaaagagcatttacttcaa...

Basic information

species Glycine max
transcript GLYMA03G40000.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G40000.2 (Glycine max), 5'ss of exon 3
lower sequence: AT5G27410.2 (Arabidopsis thaliana), 5'ss of exon 13
GAAGCTGATGGAGATAAGGTCACTAATGACATAATTTTTGCTCCAGGAAAGAAGAAATATAGATTCTGTAAGgtaaag---aaatctct-------attgagatattcattttctcacataatgta---tatatagaggaacattatgatcat---ttttctataaaaaaaaagagcatttacttcaa
||   ||||||||| |||||    || || || |||| || ||||||||||||||||||||| || |||||||| |     |  |||||       || ||||  |  ||||| |   |||    |   | | | |   ||  || || |  |    ||||| |  | |                   
GAGTGTGATGGAGAAAAGGTGGTGAAGGATATCATTTATGGTCCAGGAAAGAAGAAATATAGGTTTTGTAAGgttatactcacttctctttctgatatagagacttcaattttgttctataccacactgtgtttgggataaatttgtgtttctggcctttctctgcacag------------------
















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|298180727|gb|HO022166.1|HO022166
EST:     CTAATGACATAATTTTTGCTCCAGGAAAGAAGAAATATAGATTCTGTAAG                         CATATATCAAAGCAACGGTTACAAGGTTTGACAGATGATCTGATGAAGAAA
genomic: CTAATGACATAATTTTTGCTCCAGGAAAGAAGAAATATAGATTCTGTAAGgtaaagaaat ... ctgtttacagCATATATCAAAGCAACGGTTACAAGGTTTGACAGATGATCTGATGAAGAAA
EST: gi|213615160|gb|DB964968.1|DB964968
EST:     CTAATGACATAATTTTTGCTCCAGGAAAGAAGAAATATAGATTCTGTAAG                         CATATATCAAAGCAACGGTTACAAGGTTTGACAGATGATCTGATGAAGAAA
genomic: CTAATGACATAATTTTTGCTCCAGGAAAGAAGAAATATAGATTCTGTAAGgtaaagaaat ... ctgtttacagCATATATCAAAGCAACGGTTACAAGGTTTGACAGATGATCTGATGAAGAAA
EST: gi|192301788|gb|FG997674.1|FG997674
EST:     CTAATGACATAATTTTTGCTCCAGGAAAGAAGAAATATAGATTCTGTAAG                         CATATATCAAAGCAACGGTTACAAGGTTTGACAGATGATCTGATGAAGAAA
genomic: CTAATGACATAATTTTTGCTCCAGGAAAGAAGAAATATAGATTCTGTAAGgtaaagaaat ... ctgtttacagCATATATCAAAGCAACGGTTACAAGGTTTGACAGATGATCTGATGAAGAAA
EST: gi|213614510|gb|DB969115.1|DB969115
EST:     CTAATGACATAATTTTTGCTCCAGGAAAGAAGAAATATAGATTCTGTAAG                         CATATATCANAGCAACGGTTACAAGGTTTGACAGATGATCTGATGAAGAAA
genomic: CTAATGACATAATTTTTGCTCCAGGAAAGAAGAAATATAGATTCTGTAAGgtaaagaaat ... ctgtttacagCATATATCAAAGCAACGGTTACAAGGTTTGACAGATGATCTGATGAAGAAA
EST: gi|46492660|gb|CN472216.1|CN472216
EST:     CTAATGACATAATTTTTGCTCCAGGAAAGAAGAAATATAGATTCTGTAAG                         CATATATCAAAGCAACGGTTACAAGGTTTGACAGATGATCTGATGAAGAAA
genomic: CTAATGACATAATTTTTGCTCCAGGAAAGAAGAAATATAGATTCTGTAAGgtaaagaaat ... ctgtttacagCATATATCAAAGCAACGGTTACAAGGTTTGACAGATGATCTGATGAAGAAA
EST: gi|298170197|gb|HO018821.1|HO018821
EST:     CTAATGACATAATTTTTGCTCCAGGAAAGAAGAAATATAGATTCTGTAAG                         CATATATCAAAGCAACGGTTACAAGGTTTGACAGATGATCTGATGAAGAAA
genomic: CTAATGACATAATTTTTGCTCCAGGAAAGAAGAAATATAGATTCTGTAAGgtaaagaaat ... ctgtttacagCATATATCAAAGCAACGGTTACAAGGTTTGACAGATGATCTGATGAAGAAA
EST: gi|151396136|gb|EV266013.1|EV266013
EST:     CTAATGACATAATTTTTGCTCCAGGAAAGAAGAAATATAGATTCTGTAAG                         CATATATCAAAGCAACGGTTACAAGGTTTGACAGATGATCTGATGAAGAAA
genomic: CTAATGACATAATTTTTGCTCCAGGAAAGAAGAAATATAGATTCTGTAAGgtaaagaaat ... ctgtttacagCATATATCAAAGCAACGGTTACAAGGTTTGACAGATGATCTGATGAAGAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGCTGATGGAGATAAGGTCACTAATGACATAATTTTTGCTCCAGGAAAGAAGAAATATAGATTCTGTAAGgtaaagaaatctctattgagatattcattttctcacataatgtatatatagaggaacattatgatcatttttctataaaaaaaaagagcatttacttcaa

- - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA