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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgtattaccgggtctcaattttcaataattgtgccctctcttgaatgtctatgttttgaaatactaacgagtttttttctccctttttgcatgaacagAATTTCAAAGGATCAGTAGATGCTTTTCATGTTAATACAGTTGATACAACTGGTGCCGGTGATTCCTTTGTTGGTGCTCTATTGTCCAAGATTGTCGATG

Basic information

species Glycine max
transcript GLYMA15G03430.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G03430.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g66940.1 (Oryza sativa), 3'ss of exon 2
-------------------------------------------------------------------------tgtgta-ttaccgggtctcaattttcaataattgt---gccctc-tcttgaatgtctatgttttgaaatactaacgagtttttttctccct---ttttgcatga--acagAATTTCAAAGGATCAGTAGATGCTTTTCATGTTAATACAGTTGATACAACTGGTGCCGGTGATTCCTTTGTTGGTGCTCTATTGTCCAAGATTGTCGATG
                                                                         || ||  ||  |   | | ||||| || | | |||    | | | |  | |    | |    ||  ||  || | |  ||  |     |||    ||   ||||  | || |||||   ||| | ||     | |   | ||  |   |||||||||||| ||||| |||||| | ||||||||||||||  ||   |  |||||| | |
gtaagctgtattcggagtaataaagttgctaaactgctgattgctttttcttttcgttcaaagcagaacccattgagttcttggcttctataaatttgcatttactgttaaactcgcatagtcaccacccagtccttttaaggcttatgctttagtactgacctgaagttactatgattatagGATTTCCGCGGAGCTGTCCCATCCTACAAAGTACAGCAAGTTGATACAACAGGTGCAGGTGATGCGTTTGTTGGTGCTCTGCTGCGAAGAATTGTCCAGG

upper sequence: GLYMA15G03430.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G59480.1 (Arabidopsis thaliana), 3'ss of exon 2
tgtgtattaccgggtctcaattttc-aataattgtgccctctcttgaatgtctatgttttga-aatactaacgagtttttttctccctttttgcatga--acagAATTTCAAAGGATCAGTAGATGCTTTTCATGTTAATACAGTTGATACAACTGGTGCCGGTGATTCCTTTGTTGGTGCTCTATTGTCCAAGATTGTCGATG
             ||     ||||| || | || | |  |||  || || |   | |      |||  ||   |  || | |     | | |  ||||  |||||  |||   ||||| || ||| | || |||||  || |||| |||||||||||||| |||||||| |||||||||||  |  | | ||||||||| ||||
-------------gtaatggttttcgaagagtttttctttcttgtggatttgactttaccattaatgttacttaagttgtgttcttgtatgtatatgattacagAGCTTCCGTGGATCTGTTGATCCCTTCCATGTGGATGCAGTAGATACAACTGGTGCTGGTGATTCATTTGTTGGTGCATTGCTTTGCAAGATTGTTGATG
















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|19453294|gb|BM954704.1|BM954704
EST:     AGTTGCTCCTTGTCACTCTTGGAGAACATGGTTCCAGATACTACACCGAG                         AATTTCAAATGATCAGTAGATGCTTTTCATGTTAATACAGTTGATACAACT
genomic: AGTTGCTCCTTGTCACTCTTGGAGAACATGGTTCCAGATACTACACCGAGgtaaaataaa ... gcatgaacagAATTTCAAAGGATCAGTAGATGCTTTTCATGTTAATACAGTTGATACAACT
EST: gi|26058519|gb|CA801433.1|CA801433
EST:     AGTTGCTCCTTGTCACTCTTGGAGAACATGGTTCCAGATACTACACCGAG                         AATTTCAAAGGATCAGTAGATGCTTTTCATGTTAATACAGTTGATACAACT
genomic: AGTTGCTCCTTGTCACTCTTGGAGAACATGGTTCCAGATACTACACCGAGgtaaaataaa ... gcatgaacagAATTTCAAAGGATCAGTAGATGCTTTTCATGTTAATACAGTTGATACAACT
EST: gi|192313971|gb|FK007675.1|FK007675
EST:     AGTTGCTCCTTGTCACTCTTGGAGAACATGGTTCCAGATACTACACCGAG                         AATTTCAAAGGATCAGTAGATGCTTTTCAGGTTAATACAGTTGATACAACT
genomic: AGTTGCTCCTTGTCACTCTTGGAGAACATGGTTCCAGATACTACACCGAGgtaaaataaa ... gcatgaacagAATTTCAAAGGATCAGTAGATGCTTTTCATGTTAATACAGTTGATACAACT
EST: gi|10231806|gb|BE800694.1|BE800694
EST:     AGTTGCTCCTTGTCACTCTTGGAGAACATGGTTCCAGATACTACACCGAG                         AATTTCAAAGGATCAGTAGATGCTTTTCATGTTAATACAGTTGATACAACT
genomic: AGTTGCTCCTTGTCACTCTTGGAGAACATGGTTCCAGATACTACACCGAGgtaaaataaa ... gcatgaacagAATTTCAAAGGATCAGTAGATGCTTTTCATGTTAATACAGTTGATACAACT
EST: gi|192313972|gb|FK007676.1|FK007676
EST:     AGTTGCTCCTTGTCACTCTTGGAGAACATGGTTCCAGATACTACACCGAG                         AATTTCAAAGGATCAGTAGATGCTTTTCAGGTTAATACAGTTGATACAACT
genomic: AGTTGCTCCTTGTCACTCTTGGAGAACATGGTTCCAGATACTACACCGAGgtaaaataaa ... gcatgaacagAATTTCAAAGGATCAGTAGATGCTTTTCATGTTAATACAGTTGATACAACT
EST: gi|6719605|gb|AW307252.1|AW307252
EST:     AGTTGCTCCTTGTCACTCTTGGAGAACATGGTTCCAGATACTACACCGAG                         AATTTCAAAGGATCAGTAGATGCTTTTCATGTTAATACAGTTGATACAACT
genomic: AGTTGCTCCTTGTCACTCTTGGAGAACATGGTTCCAGATACTACACCGAGgtaaaataaa ... gcatgaacagAATTTCAAAGGATCAGTAGATGCTTTTCATGTTAATACAGTTGATACAACT
EST: gi|19268914|gb|BM885170.1|BM885170
EST:     AGTTGCTCCTTGTCACTCTTGGAGAACATGGTTCCAGATACTACACCGAG                         AATTTCAAAGGATCAGTAGATGCTTTTCATGTTAATACAGTTGATACAACT
genomic: AGTTGCTCCTTGTCACTCTTGGAGAACATGGTTCCAGATACTACACCGAGgtaaaataaa ... gcatgaacagAATTTCAAAGGATCAGTAGATGCTTTTCATGTTAATACAGTTGATACAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgtctatgttttgaaatactaacgagtttttttctccctttttgcatgaacagAATTTCAAAGGATCAGTAGATGCTTTTCATGTTAATACAGTTGATACAACTGGTGCCGGTGATTCCTTTGTTGGTGCTCTATTGTCCAAGATTGTCGATG
                  tactaac  putative branch site (score: 0)
                            tttttttctccctttt  putative PPT
      tatgttttgaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgtattaccgggtctcaattttcaataattgtgccctctcttgaatgtctatgttttgaaatactaacgagtttttttctccctttttgcatgaacagAATTTCAAAGGATCAGTAGATGCTTTTCATGTTAATACAGTTGATACAACTGGTGCCGGTGATTCCTTTGTTGGTGCTCTATTGTCCAAGATTGTCGATG

- - - - - - - - - - - - - - - - - -ccctctc
- - - - - - - - - - - - - - - - - - - - - -tgaatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg