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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaaacacagaatacataagacgcaatttcttaatcttaagcacttgttattttgttattaagctattattatgcttccttgatttttttttaattctcatcaataactgcgtttttgttgcgcagTTTGCTCATAGAGATTGCATACAGAGATGGTGCAACGAAAAAGGAAATACAACCTGTGAAATATGTCTCCAG

Basic information

species Glycine max
transcript GLYMA19G40340.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G40340.2 (Glycine max), 3'ss of exon 1
lower sequence: AT1G02610.1 (Arabidopsis thaliana), 3'ss of exon 1
gtaagtaaacacagaatacataagacgcaatttcttaatcttaagcacttgttattttgttattaagctattattatgcttccttgatttttttttaattct-catcaataactgcgtttttgttgcgc--agTTTGCTCATAGAGATTGCATACAGAGATGGTGCAACGAAAAAGGAAATACAACCTGTGAAATATGTCTCCAG
                                                |   |||    || |  |  |||| || || ||    |||| ||||  ||  |   ||  ||   |  | ||| ||||     |||| ||||| ||||||||||||||  |||||||  | || |||||||| ||||  |||||||| |||||||||
-----------------------------------------------gtaaatatcgaattctagatttatttttttgttt----gattcttttgaaaaccgatattgattgttttggtttcgttggatttagTTCGCTCACAGAGATTGCATACAACGATGGTGTGATGAGAAAGGAAACACAATTTGTGAAATTTGTCTCCAG

upper sequence: GLYMA19G40340.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv07s0005g01360.t01 (Vitis vinifera), 3'ss of exon 1
gtaagtaaacacagaatacataagacgcaatttcttaatcttaagcacttgttattttgttattaagctattattatgcttccttgatttttttttaattctcatcaataactgcgtttttgttgcgcagTTTGCTCATAGAGATTGCATACAGAGATGGTGCAACGAAAAAGGAAATACAACCTGTGAAATATGTCTCCAG
    ||||| | ||||     | |  | | ||||||  | ||  ||  | |  |||| |   ||  |  ||| || || ||  | | |||| ||||                |  || |||       ||||||||||||||||||| |||||||| |||||||| |||||||| || ||||| |||||||| |||||||||
----gtaaagaaagaa-----agggggtattttcttggtttt--gctttcggaattt-gaggtttggtgatttttctgatt--tgggttttgtttt----------------tttgtcttt-------agTTTGCTCATAGAGATTGTATACAGAGGTGGTGCAATGAAAAAGGGAACACAACTTGTGAAATCTGTCTCCAG
















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|298188637|gb|HO035330.1|HO035330
EST:     AAAGCGTAGAAACCTTGGAAGCACCTTGTGCTTGTTCTGGGACCGTTAAG                         TTTGCTCATAGAGATCGCATACAGAGATGGTGCAACGAAAAAGGAAATACA
genomic: AAAGCGTAGAAACCTTGGAAGCACCTTGTGCTTGTTCTGGGACCGTTAAGgtaagtaaac ... tgttgcgcagTTTGCTCATAGAGATTGCATACAGAGATGGTGCAACGAAAAAGGAAATACA
EST: gi|213614284|gb|DB964944.1|DB964944
EST:     AAAGCGTAGAAACCTTGGAAGCACCTTGTGCTTGTTCTGGGACCGTTAAG                         TTTGCTCATAGAGATTGCATACAGAGATGGTGCAACGAAAAAGGAAATACA
genomic: AAAGCGTAGAAACCTTGGAAGCACCTTGTGCTTGTTCTGGGACCGTTAAGgtaagtaaac ... tgttgcgcagTTTGCTCATAGAGATTGCATACAGAGATGGTGCAACGAAAAAGGAAATACA
EST: gi|151407045|gb|EV276860.1|EV276860
EST:     AAAGCGTAGAAACCTTGGAAGCACCTTGTGCTTGTTCTGGGACCGTTAAG                         TTTGCTCATAGAGATTGCATACAGAGATGGTGCAACGAAAAAGGAAATACA
genomic: AAAGCGTAGAAACCTTGGAAGCACCTTGTGCTTGTTCTGGGACCGTTAAGgtaagtaaac ... tgttgcgcagTTTGCTCATAGAGATTGCATACAGAGATGGTGCAACGAAAAAGGAAATACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcttccttgatttttttttaattctcatcaataactgcgtttttgttgcgcagTTTGCTCATAGAGATTGCATACAGAGATGGTGCAACGAAAAAGGAAATACAACCTGTGAAATATGTCTCCAG
                              caataac  putative branch site (score: 2)
                                         tttttgtt  putative PPT
        ttgatttttttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtaaacacagaatacataagacgcaatttcttaatcttaagcacttgttattttgttattaagctattattatgcttccttgatttttttttaattctcatcaataactgcgtttttgttgcgcagTTTGCTCATAGAGATTGCATACAGAGATGGTGCAACGAAAAAGGAAATACAACCTGTGAAATATGTCTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA