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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggttcatatggatgacctttgatggatatataattgtgaagcttttaaagttgtgggatcttcattagctgaatttgttgttttcgggttacatgatagGAAGAAGACCTGAAGGAATTCCGACAATGGGGGAGCAGGACTCCTGGACATCCTGAGAACTTTGAGACAGTTGGAATTGAAGTGACTACAG

Basic information

species Glycine max
transcript GLYMA20G38720.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38720.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G45290.1 (Arabidopsis thaliana), 3'ss of exon 1
--------------------------------------------------------------------------------aggttcatatggatgacc-tttgatggatatataattgtgaagcttttaaagttgtgggatcttcattagctgaattt--gttgttttcgggttacatgatagGAAGAAGACCTGAAGGAATTCCGACAATGGGGGAGCAGGACTCCTGGACATCCTGAGAACTTTGAGACAGTTGGAATTGAAGTGACTACAG
                                                                                 | | | | |   ||  | |||| ||  | |   | | |  || ||| | | |||| | | |  | | || |    |   |  || ||   |||   |  ||||| |||||  |||||   ||||| |||||||| || | |||||| |||||||||||||| ||||||||   |||  ||||||  ||||| |
gtttgtgttctcttactctgcttattaagtttgtatccttttagtttacattattgagattacatagtaaatacacagattgttccgtttccctgctcatttggtgatttttggagtcttgagattt-agaattgtagaaccaacttaagatttgctgaagcagtgttgaagttttttattagGAGGAAGATTTGAAGAGCTTCCGTCAATGGGGAAGTAAGACTCCAGGACATCCTGAGAATTTTGAGACTCCTGGTGTTGAAGCCACTACTG

upper sequence: GLYMA20G38720.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G60750.1 (Arabidopsis thaliana), 3'ss of exon 1
------------------------------------------aggttcat--atggatgacctttgatggatatataattgtgaagcttttaaagttgtgggat--cttcattagctgaatttgttgt-------tttcgggttacatgatagGAAGAAGACCTGAAGGAATTCCGACAATGGGGGAGCAGGACTCCTGGACATCCTGAGAACTTTGAGACAGTTGGAATTGAAGTGACTACAG
                                             || ||  ||| |  | ||||  |||||| ||  |      | ||| | | |  |  |||  || | | |  |  |||   ||        ||| |  ||   |  ||||| |||||  ||||| | ||||| |||||||| |||| ||| || |||||||||||||| || |||||   |||||||||||| ||||| |
gtctgtgatctcttctctgtttaattgctttcgatctgatcgtaattgatgaatgtagtaactttagtggatagat--tgaatctgttttgatattcatctgatggctgcttgaagtagattcactgaaaaggtgtttggatttgtttattagGAGGAAGATTTGAAGCAGTTCCGTCAATGGGGAAGCAAGACACCAGGACATCCTGAGAATTTCGAGACTCCTGGAATTGAAGTCACTACTG
















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|213617212|gb|DB971303.1|DB971303
EST:     GCATGCTCCAATATGCTCTCCTTCACCTTGCAGGCTATGACAGTGTTCTG                         GAAGAAGACCTGAAGGAATTCCGACAATGGGGGAGCAGGACTCCTGGACAT
genomic: GCATGCTCCAATATGCTCTCCTTCACCTTGCAGGCTATGACAGTGTTCTGgtcagctttt ... tacatgatagGAAGAAGACCTGAAGGAATTCCGACAATGGGGGAGCAGGACTCCTGGACAT
EST: gi|15287320|gb|BI471211.1|BI471211
EST:     GCATGCTCCAATATGCTCTCCTTCACCTTGCAGGCTATGACAGTGTTCTG                         GAAGAAGACCTGAAGGAATTCCGACAATGGGGGAGCAGGACTCCTGGACAT
genomic: GCATGCTCCAATATGCTCTCCTTCACCTTGCAGGCTATGACAGTGTTCTGgtcagctttt ... tacatgatagGAAGAAGACCTGAAGGAATTCCGACAATGGGGGAGCAGGACTCCTGGACAT
EST: gi|8826649|gb|BE210379.1|BE210379
EST:     GCATGCTCCAATATGCTCTCCTTCACCTTGCAGGCTATGACAGTGTTCTG                         GAAGAAGACCTGAAGGAATTCCGACAATGGGGGAGCAGGACTCCTGGACAT
genomic: GCATGCTCCAATATGCTCTCCTTCACCTTGCAGGCTATGACAGTGTTCTGgtcagctttt ... tacatgatagGAAGAAGACCTGAAGGAATTCCGACAATGGGGGAGCAGGACTCCTGGACAT
EST: gi|7326487|gb|AW620296.1|AW620296
EST:     GCATGCTCCAATATGCTCTCCTTCACCTTGCAGGCTATGACAGTGGTCTG                         GGAGAAAACCTGAAAGAATT
genomic: GCATGCTCCAATATGCTCTCCTTCACCTTGCAGGCTATGACAGTGTTCTGgtcagctttt ... tacatgatagGAAGAAGACCTGAAGGAATT
EST: gi|209723701|gb|BW662583.1|BW662583
EST:     GCATGCTCCAATATGCTCTCCTTCACCTTGCAGGCTATGACAGTGTTCTG                         GAAGAAGACCTGAAGGAATTCCGACAATGGGGGA
genomic: GCATGCTCCAATATGCTCTCCTTCACCTTGCAGGCTATGACAGTGTTCTGgtcagctttt ... tacatgatagGAAGAAGACCTGAAGGAATTCCGACAATGGGGGA
EST: gi|18848458|gb|BM567678.1|BM567678
EST:     GCATGCTCCAATATGCTCTCCTTCACCTTGCAGGCTATGACAGTGTTCTG                         GAAGAAGACCTGAAGGAATTCCGACAATGGGGGAGCAGGACTCCTGGACAT
genomic: GCATGCTCCAATATGCTCTCCTTCACCTTGCAGGCTATGACAGTGTTCTGgtcagctttt ... tacatgatagGAAGAAGACCTGAAGGAATTCCGACAATGGGGGAGCAGGACTCCTGGACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaagttgtgggatcttcattagctgaatttgttgttttcgggttacatgatagGAAGAAGACCTGAAGGAATTCCGACAATGGGGGAGCAGGACTCCTGGACATCCTGAGAACTTTGAGACAGTTGGAATTGAAGTGACTACAG
                           aatttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggttcatatggatgacctttgatggatatataattgtgaagcttttaaagttgtgggatcttcattagctgaatttgttgttttcgggttacatgatagGAAGAAGACCTGAAGGAATTCCGACAATGGGGGAGCAGGACTCCTGGACATCCTGAGAACTTTGAGACAGTTGGAATTGAAGTGACTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - -acctttg
- - - - - - - - - - - - - - - - - - - - - - - - - -ttgtggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgtt