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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttacacaagaaccattttattctatgcatgtgaagccttattttccaaaataacttccaaacagtcttaacaatttatttgtatatgcattgaagAACTCGGTGTGCTAGTTGGGAAAGGAGGACTTCATGGCAATGTTTTCAGGATCAAGCCACCAATGTGTTTCTCCAAAGATGATGCAG

Basic information

species Glycine max
transcript GLYMA05G31630.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G31630.1 (Glycine max), 3'ss of exon 7
lower sequence: AT4G39660.1 (Arabidopsis thaliana), 3'ss of exon 7
gttacacaagaaccattttattctatgcatgtgaagccttattttccaaaataacttccaaacagtcttaacaatttatttgtatatgc-attgaagAACTCGGTGTGCTAGTTGGGAAAGGAGGACTTCATGGCAATGTTTTCAGGATCAAGCCACCAATGTGTTTCTCCAAAGATGATGCAG
       ||  | ||||  |  | |        |||| |   |||   ||  | |        |  |  ||   |||  |  | | |   | ||||||||| ||  | || || || ||||||||||||||||| || ||||||||||| |||||||||||||||||| | |||||||||||||
-----gtaaacaacattaaagccaa--------aagcatcgatttgataagcatcagttggttaaccaaaatgttttgctcctttctcttaatgaagAACTTGGCATTCTCGTCGGAAAAGGAGGACTTCATGGGAACGTTTTCAGGATAAAGCCACCAATGTGTTTCACTAAAGATGATGCAG

upper sequence: GLYMA05G31630.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv07s0031g01330.t01 (Vitis vinifera), 3'ss of exon 7
gttacacaagaaccattttattctatgcatgtgaagccttattttccaaaataacttccaaacagtcttaacaatttatttgtatatgcattgaagAACTCGGTGTGCTAGTTGGGAAAGGAGGACTTCATGGCAATGTTTTCAGGATCAAGCCACCAATGTGTTTCTCCAAAGATGATGCAG
            | | |  |   |    | |  ||   | |||        ||| || | ||||  || |   |||||||  | | |  | || |||  ||||| | ||  | || || |||||||| ||||| ||||| ||||| || |||||||| ||||||||| ||||||||||||| |
-------gtttgcaactccaccatgattaagaaaaaattaatt-------gtaatttaccaacacact-acttatttattaattttta-actgtagAGATCGGTATTCTTATCGGAAAGGGAGGACTACATGGAAATGTCTTCAGAATAAAGCCACCTATGTGTTTCACCAAAGATGATGCTG
















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|254331191|gb|GR843310.1|GR843310
EST:     CAAGACACCTGCAAAGGCTGAAACTGCTGTTGTGTTTGAAAAACTCAGAG                         AACTCGGTGTGCTAGTTGGGAAAGGAGGACTTCATGGCAATGTTTTCAGGA
genomic: CAAGACACCTGCAAAGGCTGAAACTGCTGTTGTGTTTGAAAAACTCAGAGgttacacaag ... tgcattgaagAACTCGGTGTGCTAGTTGGGAAAGGAGGACTTCATGGCAATGTTTTCAGGA
EST: gi|254330912|gb|GR842177.1|GR842177
EST:     CAAGACACCTGCAAAGGCTGAAACTGCTGTTGTGTTTGAAAAACTCAGAG                         AACTCGGTGTGCTAGTTGGGAAAGGAGGACTTCATGGCAATGTTTTCAGGA
genomic: CAAGACACCTGCAAAGGCTGAAACTGCTGTTGTGTTTGAAAAACTCAGAGgttacacaag ... tgcattgaagAACTCGGTGTGCTAGTTGGGAAAGGAGGACTTCATGGCAATGTTTTCAGGA
EST: gi|209727818|gb|BW658742.1|BW658742
EST:     CAAGACACCTGCAAAGGCTGAAACTGCTGTTGTGTTTGAAAAACTCAGAG                         AACTCGGTGTGCTAGTTGGGAAAGGAGGACTTCATGGCAATGTTTTCAGGA
genomic: CAAGACACCTGCAAAGGCTGAAACTGCTGTTGTGTTTGAAAAACTCAGAGgttacacaag ... tgcattgaagAACTCGGTGTGCTAGTTGGGAAAGGAGGACTTCATGGCAATGTTTTCAGGA
EST: gi|193626557|gb|FK574405.1|FK574405
EST:     CAAGACACCTGCAAAGGCTGAAACTGCTGTTGTGTTTGAAAAACTCAGAG                         AACTCGGTGTGCTAGTTGGGAAAGGAGGACTTCATGGCAATGTTTTCAGGA
genomic: CAAGACACCTGCAAAGGCTGAAACTGCTGTTGTGTTTGAAAAACTCAGAGgttacacaag ... tgcattgaagAACTCGGTGTGCTAGTTGGGAAAGGAGGACTTCATGGCAATGTTTTCAGGA
EST: gi|6912846|gb|AW394330.1|AW394330
EST:     CAAGACACCTGCAAAGGCTGAAACTGCTGTTGTGTTTGAAAAACTCAGAG                         AACTCGGTGTGCTAGTTGGGAAAGGAGGACTTCATGGCAATGTTTTCAGGA
genomic: CAAGACACCTGCAAAGGCTGAAACTGCTGTTGTGTTTGAAAAACTCAGAGgttacacaag ... tgcattgaagAACTCGGTGTGCTAGTTGGGAAAGGAGGACTTCATGGCAATGTTTTCAGGA
EST: gi|254331192|gb|GR843311.1|GR843311
EST:     CAAGACACCTGCAAAGGCTGAAACTGCTGTTGTGTTTGAAAAACTCAGAG                         AACTCGGTGTGCTAGTTGGGAAAGGAGGACTTCATGGCAATGTTTTCAGGA
genomic: CAAGACACCTGCAAAGGCTGAAACTGCTGTTGTGTTTGAAAAACTCAGAGgttacacaag ... tgcattgaagAACTCGGTGTGCTAGTTGGGAAAGGAGGACTTCATGGCAATGTTTTCAGGA
EST: gi|13790393|gb|BG652984.1|BG652984
EST:     CAAGACACCTGCAAAGGCTGAAACTGCTGTTGTGTTTGAAAAACTCAGAG                         AACTCGGTGTGCTAGTTGGGAAAGGAGGACTTCATGGCAATGTTTTCAGGA
genomic: CAAGACACCTGCAAAGGCTGAAACTGCTGTTGTGTTTGAAAAACTCAGAGgttacacaag ... tgcattgaagAACTCGGTGTGCTAGTTGGGAAAGGAGGACTTCATGGCAATGTTTTCAGGA
EST: gi|7588697|gb|AW704487.1|AW704487
EST:     CAAGACACCTGCAAAGGCTGAAACTGCTGTTGTGTTTGAAAAACTCAGAG                         AACTCGGTGTGCTAGTTGGGAAAGGAGGACTTCATGGCAATGTTTTCAGGA
genomic: CAAGACACCTGCAAAGGCTGAAACTGCTGTTGTGTTTGAAAAACTCAGAGgttacacaag ... tgcattgaagAACTCGGTGTGCTAGTTGGGAAAGGAGGACTTCATGGCAATGTTTTCAGGA
EST: gi|209704503|gb|BW678432.1|BW678432
EST:     CAAGACACCTGCAAAGGCTGAAACTGCTGTTGTGTTTGAAAAACTCAGAG                         AACTCGGTGTGCTAGTTGGGAAAGGAGGACTTCATGGCAATGTTTTCAGGA
genomic: CAAGACACCTGCAAAGGCTGAAACTGCTGTTGTGTTTGAAAAACTCAGAGgttacacaag ... tgcattgaagAACTCGGTGTGCTAGTTGGGAAAGGAGGACTTCATGGCAATGTTTTCAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttccaaaataacttccaaacagtcttaacaatttatttgtatatgcattgaagAACTCGGTGTGCTAGTTGGGAAAGGAGGACTTCATGGCAATGTTTTCAGGATCAAGCCACCAATGTGTTTCTCCAAAGATGATGCAG
                        tcttaac  putative branch site (score: 2)
                        tcttaacaatttattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttacacaagaaccattttattctatgcatgtgaagccttattttccaaaataacttccaaacagtcttaacaatttatttgtatatgcattgaagAACTCGGTGTGCTAGTTGGGAAAGGAGGACTTCATGGCAATGTTTTCAGGATCAAGCCACCAATGTGTTTCTCCAAAGATGATGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG