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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAATgtaagtttgaaactttatcttgtattgtactgcatctgcatgtgcaaatcggtttgtttatatggtctcagtctcagtattttgtgatcaacttccaaaa...

Basic information

species Glycine max
transcript GLYMA16G08200.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G08200.1 (Glycine max), 5'ss of exon 2
lower sequence: AT4G17730.2 (Arabidopsis thaliana), 5'ss of exon 2
CCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAATgtaagtttgaaactttatcttgtattgtactgcatctgcatgtgcaaatcggtttgtttatatggtctcagtctcagtattttgtgatcaacttccaaaa
 || ||||||||| || ||||||| || || ||||||||||||||||||||||||||  |||| ||||| | |||||| ||    |  || ||||| |||   |    | ||   | |   | ||   ||| | | ||| | |    ||| |||   ||  |  |  |   |  || |                
GCATAAGACAAGATTATATATTGGACAGTTAGTGAAAGATACATCAGCTAAACTTAAAGAAGCTAGTGAAACTGATCATCAAAGAGGTGTAAATgtgagtc--atttatgataaaggaagattcttgttcttcttctgctacttctgttgattaataggaatttgattggttggttag----------------

upper sequence: GLYMA16G08200.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv02s0012g01850.t01 (Vitis vinifera), 5'ss of exon 2
CCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAATgtaagtttgaaactttatcttgtattg-tactgcatctgcatg----tgcaaatcggtttgtttatatggtctcagtctcagtattttgtgatcaacttccaaaa
 |||||||| || |||||||||||||| || || || ||||| || ||||||||||||||||| || || |  ||||| ||||||||||||| ||||||||||    || ||  |    |  || ||  | |||| |    |     ||  ||| ||  |||    |    ||||| | || |||   |||||   |  
GCACAAGACGAGGCTACATATTGGGCAGTTAGTCAAGGATACCTCTGCTAAACTTAAGCAAGCTAGCGAAACAGATCATCATGCTGAAGTTAGTgtaagtttgc--tttcatgatacgatactattgattttgcaagaatttctctctccctttcttactatttatttgtactcagcaatt-gtggcaaacttatca--
















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|6666502|gb|AW277896.1|AW277896
EST:     CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAAT                         GCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
genomic: CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAATgtaagtttga ... attattgcagGCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
EST: gi|298189796|gb|HO038199.1|HO038199
EST:     CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAAT                         GCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
genomic: CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAATgtaagtttga ... attattgcagGCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
EST: gi|298185952|gb|HO031113.1|HO031113
EST:     CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAAT                         GCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
genomic: CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAATgtaagtttga ... attattgcagGCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
EST: gi|15662381|gb|BI699752.1|BI699752
EST:     CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAAT                         GCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
genomic: CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAATgtaagtttga ... attattgcagGCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
EST: gi|193552638|gb|FK506161.1|FK506161
EST:     CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAAT                         GCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
genomic: CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAATgtaagtttga ... attattgcagGCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
EST: gi|37994080|gb|CF805826.1|CF805826
EST:     CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAAT                         GCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
genomic: CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAATgtaagtttga ... attattgcagGCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
EST: gi|7686453|gb|AW757101.1|AW757101
EST:     CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAAT                         GCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
genomic: CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAATgtaagtttga ... attattgcagGCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
EST: gi|209725412|gb|BW651556.1|BW651556
EST:     CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAAT                         GCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
genomic: CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAATgtaagtttga ... attattgcagGCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
EST: gi|298196583|gb|HO041326.1|HO041326
EST:     CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAAT                         GCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
genomic: CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAATgtaagtttga ... attattgcagGCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
EST: gi|193483117|gb|FK448440.1|FK448440
EST:     CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAAT                         GCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
genomic: CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAATgtaagtttga ... attattgcagGCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
EST: gi|208150896|gb|GD946013.1|GD946013
EST:     CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAAT                         GCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTC
genomic: CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAATgtaagtttga ... attattgcagGCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTC
EST: gi|192299164|gb|FG992895.1|FG992895
EST:     CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAAT                         GCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
genomic: CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAATgtaagtttga ... attattgcagGCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
EST: gi|207829398|gb|GD804016.1|GD804016
EST:     TTGATCACCATGCTGAAGTTAAT                         GCAAGCAAGAAGATAGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
genomic: TTGATCACCATGCTGAAGTTAATgtaagtttga ... attattgcagGCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
EST: gi|209702008|gb|BW683185.1|BW683185
EST:     CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAAT                         GCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
genomic: CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAATgtaagtttga ... attattgcagGCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
EST: gi|192296912|gb|FG990258.1|FG990258
EST:     CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAAT                         GCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
genomic: CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAATgtaagtttga ... attattgcagGCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
EST: gi|193488148|gb|FK453185.1|FK453185
EST:     CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAAT                         GCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
genomic: CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAATgtaagtttga ... attattgcagGCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
EST: gi|192315290|gb|FK009610.1|FK009610
EST:     CAGTGACATTGATCACCATGCTGAAGTTAAT                         GCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGACTTTCAGGCAGTG
genomic: CAGTGACATTGATCACCATGCTGAAGTTAATgtaagtttga ... attattgcagGCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
EST: gi|19452417|gb|BM953827.1|BM953827
EST:     CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAAT                         GCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
genomic: CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAATgtaagtttga ... attattgcagGCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
EST: gi|21255947|gb|BQ452835.1|BQ452835
EST:     CATCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAAT                         GCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
genomic: CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAATgtaagtttga ... attattgcagGCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
EST: gi|9565390|gb|BE474899.1|BE474899
EST:     CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAAT                         GCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG
genomic: CAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAATgtaagtttga ... attattgcagGCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAATgtaagtttgaaactttatcttgtattgtactgcatctgcatgtgcaaatcggtttgtttatatggtctcagtctcagtattttgtgatcaacttccaaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG