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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGGCAAATGACCTTGTCAGGAACAAGATTCATCCTACCTCGATTATCAGTGGATATAGAgtaagtgtcttttaataatttcttaaacttaactaactgtttattgctatttttaaactttgtagctaccattatggagtttttgtgttctgctatttgaattgcgaatttgcatggtttaactaacttctctttttgttgattattctgtatag

Basic information

species Glycine max
transcript GLYMA08G12970.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G12970.1 (Glycine max), 5'ss of exon 5
lower sequence: AT3G20050.1 (Arabidopsis thaliana), 5'ss of exon 5
AGGGCAAATGACCTTGTCAGGAACAAGATTCATCCTACCTCGATTATCAGTGGATATAGAgtaagtgtcttttaataatttcttaaact-taactaactgtttattgctatttttaaactttgtagctaccattatggagtttttgtgttctgctatttgaattgcgaatttgcatggtttaactaacttctctttttgttgattattctgtatag
|||||||||||  | ||||||||||| || ||||| || || ||||||||||||||||| |||||   |   |  ||||||| ||   | ||||   |  |  |    | |||  |   | |  |    |  || |   |||                                                                          
AGGGCAAATGATTTGGTCAGGAACAAAATACATCCAACATCAATTATCAGTGGATATAGGgtaagctgcgactt-taatttcatatgttgtaacctgcactgcagaagtgtttccagtgtgttcattatcttttttactgttgacag---------------------------------------------------------------------
















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|33389970|gb|CA853177.1|CA853177
EST:     ACCTCGTCAGGAACAAGATTCATCCTACCTCGATTATCAGTGGATATAGA                         CTTGCTATGCGAGAGGCTTGTAAATATGTAGAAGAAAAACTAGCTGTCAAG
genomic: ACCTTGTCAGGAACAAGATTCATCCTACCTCGATTATCAGTGGATATAGAgtaagtgtct ... ttctgtatagCTTGCTATGCGAGAGGCTTGTAAATATGTAGAAGAAAAACTAGCTGTCAAG
EST: gi|208197847|gb|GE001197.1|GE001197
EST:     ACCTTGTCAGGAACAAGATTCATCCTACCTCGATTATCAGTGGATATAGA                         CTTGCTATGCGTGAGGCTTGTAAATATGTAGAAGAAAAACTAGCTGTCAAG
genomic: ACCTTGTCAGGAACAAGATTCATCCTACCTCGATTATCAGTGGATATAGAgtaagtgtct ... ttctgtatagCTTGCTATGCGAGAGGCTTGTAAATATGTAGAAGAAAAACTAGCTGTCAAG
EST: gi|24205364|gb|BU964617.1|BU964617
EST:     ACCTCGTCAGGAACAAGATTCATCCTACCTCGATTATCAGTGGATATAGA                         CTTGCTATGCGAGAGGCTTGTAAATATGTAGAAGAAAAACTAGCTGTCAAG
genomic: ACCTTGTCAGGAACAAGATTCATCCTACCTCGATTATCAGTGGATATAGAgtaagtgtct ... ttctgtatagCTTGCTATGCGAGAGGCTTGTAAATATGTAGAAGAAAAACTAGCTGTCAAG
EST: gi|6070782|gb|AW100169.1|AW100169
EST:     ACCTTGTCAGGAACAAGATTCATCCTACCTCGATTATCAGTGGATATAGA                         CTTGCTATGCGAGAGGCT
genomic: ACCTTGTCAGGAACAAGATTCATCCTACCTCGATTATCAGTGGATATAGAgtaagtgtct ... ttctgtatagCTTGCTATGCGAGAGGCT
EST: gi|207810478|gb|GD782484.1|GD782484
EST:     ACCTTGTCAGGAACAAGATTCATCCTACCTCGATTATCAGTGGATATAGA                         CTTGCTATGCGAGAGGCTTGTAAATATGTAGAAGAAAAACTAGCTGTCAAG
genomic: ACCTTGTCAGGAACAAGATTCATCCTACCTCGATTATCAGTGGATATAGAgtaagtgtct ... ttctgtatagCTTGCTATGCGAGAGGCTTGTAAATATGTAGAAGAAAAACTAGCTGTCAAG
EST: gi|33390479|gb|CA853674.1|CA853674
EST:     ACAAGATTCATCCTACCTCGATTATCAGTGGATATAGA                         CTTGCTATGCGAGAGGCTTGTAAATATGTAGAAGAAAAACTAGCTGTCAAG
genomic: ACAAGATTCATCCTACCTCGATTATCAGTGGATATAGAgtaagtgtct ... ttctgtatagCTTGCTATGCGAGAGGCTTGTAAATATGTAGAAGAAAAACTAGCTGTCAAG
EST: gi|120533836|gb|EH261969.1|EH261969
EST:     ACCTTGTCAGGAACAAGATTCATCCTACCTCGATTATCAGTGGATATAGA                         CTTGCTATGCGAGAGGCTTGTAAATATGTAGAAGAAAAACTAGCTGTCAAG
genomic: ACCTTGTCAGGAACAAGATTCATCCTACCTCGATTATCAGTGGATATAGAgtaagtgtct ... ttctgtatagCTTGCTATGCGAGAGGCTTGTAAATATGTAGAAGAAAAACTAGCTGTCAAG
EST: gi|18040032|gb|BM308326.1|BM308326
EST:     ACCTCGTCAGGAACAAGATTCATCCTACCTCGATTATCAGTGGATATAGA                         CTTGCTATGCGAGAGGCTTGTAAATATGTAGAAGAAAAACTAGCTGTCAAG
genomic: ACCTTGTCAGGAACAAGATTCATCCTACCTCGATTATCAGTGGATATAGAgtaagtgtct ... ttctgtatagCTTGCTATGCGAGAGGCTTGTAAATATGTAGAAGAAAAACTAGCTGTCAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGGCAAATGACCTTGTCAGGAACAAGATTCATCCTACCTCGATTATCAGTGGATATAGAgtaagtgtcttttaataatttcttaaacttaactaactgtttattgctatttttaaactttgtagctaccattatggagtttttgtgttctgctatttgaattgcgaatttgcatggtttaactaacttctctttttgttgattattctgtatag

- - - - - - - - - - - - - - - - - - - - - - - - AGTGGA