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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGGAAGAACGGGGGAGCTGTGGAGAAGGTGATTGAGAGGAGGCAGAGAAGGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAGgtgatgttttgttctattatcctaaagttagcaatcgttcttttctagcatttgcttattcaaatgaacacttacttggatggaagaatacaaatttaac...

Basic information

species Glycine max
transcript GLYMA04G04170.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G04170.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ33090 (Selaginella moellendorffii), 5'ss of exon 1
AAGGAAGAACGGGGGAGCTGTGGAGAAGGTGATTGAGAGGAGGCAGAGAAGGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAGgtgatgttttgttctattatcctaaagttagcaatcgttcttttctagcatttgcttattcaaatgaacacttacttggatggaagaatacaaatttaac
 |||      |  ||| | || |||  |||  | ||| |||||||| || ||||||| |||||| | ||||| ||||| ||||| || ||||||||||||||    | |  ||||      ||    ||   | |     ||    |  || |      | | |  || | ||  ||   |       | |||       
GAGGGGACTGGACGGACCGGTTGAGGTGGTTTTGGAGCGGAGGCAGCGACGGATGATCAAGAATCGCGAGTCGGCTGCGAGGTCTCGAGCTCGCAAACAGgttggttctctttcttcctgtctgcttttgatatttagcattg---atgatgtcaaagctgagacaaagatttgttt---tatgtttttccaag------

upper sequence: GLYMA04G04170.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ27417 (Selaginella moellendorffii), 5'ss of exon 1
AAGGAAGAACGGGGGAGCTGTGGAGAAGGTGATTGAGAGGAGGCAGAGAAGGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAGgtgatgttttgttctattatcctaaagttagcaatcgttcttttctagcatttgcttattcaaatgaacacttacttggatggaagaatacaaatttaac
 |||      |  ||| | || |||  |||  | ||| |||||||| || ||||||| |||||| | ||||| ||||| ||||| || ||||||||||||||    | |  ||||      |||   ||   | |     ||    |  || |      | | |  || | ||  ||   |       | |||       
GAGGGGACTGGACGGACCGGTTGAGGTGGTTTTGGAGCGGAGGCAGCGACGGATGATCAAGAATCGCGAGTCGGCTGCGAGGTCTCGAGCTCGCAAACAGgttggttctctttcttcctgtctactcttgatatttagcattg---atgatgtcaaagctgagacaaagatttgttt---tatgtttttccaag------
















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|193466718|gb|FK433455.1|FK433455
EST:     GGATGNTAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAG                         GCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAGTTAAAAGAGGAGAAC
genomic: GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAGgtgatgtttt ... tttattccagGCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAGTTAAAAGAGGAGAAC
EST: gi|207830846|gb|GD803742.1|GD803742
EST:     GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAG                         GCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAGTTAAAAGNGGAGAAC
genomic: GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAGgtgatgtttt ... tttattccagGCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAGTTAAAAGAGGAGAAC
EST: gi|208027955|gb|GD822153.1|GD822153
EST:     GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAG                         GCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAGTTAAAAGAGGAGAAC
genomic: GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAGgtgatgtttt ... tttattccagGCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAGTTAAAAGAGGAGAAC
EST: gi|193334350|gb|FK300114.1|FK300114
EST:     GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAG                         GCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAAGTTAAAA
genomic: GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAGgtgatgtttt ... tttattccagGCTTATACCATGGAATTAGAAGCAGAAGTTGCTAA-GTTAAAA
EST: gi|193548975|gb|FK505382.1|FK505382
EST:     GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAG                         GCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAGTTAAAAGAGGAGAAC
genomic: GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAGgtgatgtttt ... tttattccagGCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAGTTAAAAGAGGAGAAC
EST: gi|207750222|gb|GD723390.1|GD723390
EST:     GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAG                         GCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAGTTAAAAGAGGAGAAC
genomic: GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAGgtgatgtttt ... tttattccagGCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAGTTAAAAGAGGAGAAC
EST: gi|193415667|gb|FK376273.1|FK376273
EST:     GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAG                         GCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAGTTAAAAGAGGAGAAC
genomic: GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAGgtgatgtttt ... tttattccagGCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAGTTAAAAGAGGAGAAC
EST: gi|193334383|gb|FK297585.1|FK297585
EST:     GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAG                         GCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAGTTAAAAGAGGAGAAC
genomic: GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAGgtgatgtttt ... tttattccagGCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAGTTAAAAGAGGAGAAC
EST: gi|208104141|gb|GD902704.1|GD902704
EST:     GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAG                         GCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAGTTAAAAGAGGAGAAC
genomic: GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAGgtgatgtttt ... tttattccagGCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAGTTAAAAGAGGAGAAC
EST: gi|193346057|gb|FK310501.1|FK310501
EST:     GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAG                         GCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAGTTAAAAGAGGAGAAC
genomic: GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAGgtgatgtttt ... tttattccagGCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAGTTAAAAGAGGAGAAC
EST: gi|208241024|gb|GE039574.1|GE039574
EST:     GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAG                         GCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAGTTAAAAGAGGAGAAC
genomic: GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAGgtgatgtttt ... tttattccagGCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAGTTAAAAGAGGAGAAC
EST: gi|193409385|gb|FK370407.1|FK370407
EST:     GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAG                         GCTTATACCATGGAATTAGAAGCAGAAGTTGCAAAGTTAAAAGAGGAGAAC
genomic: GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAGgtgatgtttt ... tttattccagGCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAGTTAAAAGAGGAGAAC
EST: gi|193499684|gb|FK461311.1|FK461311
EST:     GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAG                         GCTTATACCATGGAATTAGAAGCAGAAGTTGC
genomic: GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAGgtgatgtttt ... tttattccagGCTTATACCATGGAATTAGAAGCAGAAGTTGC
EST: gi|207740274|gb|GD714212.1|GD714212
EST:     GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAG                         GCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAG
genomic: GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAGgtgatgtttt ... tttattccagGCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAG
EST: gi|193313919|gb|FK281652.1|FK281652
EST:     GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAG                         GCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAGTTAAAAGAGGAGAAC
genomic: GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAGgtgatgtttt ... tttattccagGCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAGTTAAAAGAGGAGAAC
EST: gi|208156795|gb|GD955075.1|GD955075
EST:     GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAG                         GCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAGTTAAAAGAGGAGAAC
genomic: GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAGgtgatgtttt ... tttattccagGCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAGTTAAAAGAGGAGAAC
EST: gi|193680024|gb|FK625260.1|FK625260
EST:     GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAG                         GCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAGTTAA--GAGGAGAAC
genomic: GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAGgtgatgtttt ... tttattccagGCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAGTTAAAAGAGGAGAAC
EST: gi|10237462|gb|BE806350.1|BE806350
EST:     GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAG                         GCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAGTTAAAAGAGGAGAAC
genomic: GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAGgtgatgtttt ... tttattccagGCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAGTTAAAAGAGGAGAAC
EST: gi|207835788|gb|GD806513.1|GD806513
EST:     GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAG                         GCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAGTTAAAAGAGGAGAAC
genomic: GGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAGgtgatgtttt ... tttattccagGCTTATACCATGGAATTAGAAGCAGAAGTTGCTAAGTTAAAAGAGGAGAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGGAAGAACGGGGGAGCTGTGGAGAAGGTGATTGAGAGGAGGCAGAGAAGGATGATAAAGAATAGAGAGTCAGCTGCCAGGTCGCGGGCTCGCAAACAGgtgatgttttgttctattatcctaaagttagcaatcgttcttttctagcatttgcttattcaaatgaacacttacttggatggaagaatacaaatttaac

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC