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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggattaattaagcatgcatattgcctatagggtaacagttttgaaaatgtgcttttttttttttaatttttaaaattggttatttgtttccaccatgcagATTCAGTATCTTGTGTCTCGTTGGGGATCAGATATAAATTCACTAGGTTCATATAGCTATGATGCAGTTGGGAAACCCCATGAACTATATGAGAGGCTAC

Basic information

species Glycine max
transcript GLYMA08G41570.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G41570.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv12s0028g01120.t01 (Vitis vinifera), 3'ss of exon 9
-ggattaattaagcatgcatattgcctatagg-gtaacagttttgaaaatgtgctt--ttttttttttaatttttaaaattggttatttgtttccaccatgcagATTCAGTATCTTGTGTCTCGTTGGGGATCAGATATAAATTCACTAGGTTCATATAGCTATGATGCAGTTGGGAAACCCCATGAACTATATGAGAGGCTAC
 | |  ||     || |   | | ||  | |   | | | |||      |||  |     ||   ||   ||||  ||| |  || ||  |||      ||||||||||||||||||| ||||| |||||  |||||   |||||||| || || || | |||||||||||| |||||||||||||| || |||||||||||| 
tgaagaaaaagtacacgacaaatcccggtggatatgataatttcatgtgtgtagtgggcattgccttgggttttctaaagtttttgttcattt----ggtgcagATTCAGTATCTTGTTTCTCGGTGGGGCACAGATGAGAATTCACTTGGATCCTACACCTATGATGCAGTAGGGAAACCCCATGATCTGTATGAGAGGCTAA
















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|17400285|gb|BM177067.1|BM177067
EST:     ACTTCGCTTTCATGCAGCTCAAGAAGATTTTTCCAGATGCTTCTTCACCG                         ATTCAGTATCTTGTGTCTCGTTGGGGATCAGATATAAATTCACTAGGTTCA
genomic: ACTTCGCTTTCATGCAGCTCAAGAAGATTTTTCCAGATGCTTCTTCACCGgtagccatac ... caccatgcagATTCAGTATCTTGTGTCTCGTTGGGGATCAGATATAAATTCACTAGGTTCA
EST: gi|6952167|gb|AW424235.1|AW424235
EST:     ACTTCGCTTTCATGCAGCTCAAGAAGATTTTTCCAGATGCTTCTTCACCG                         ATTCAGTATCTTGTGTCTCGTTGGGGATCAGATATAAATTCACTAGGTTCA
genomic: ACTTCGCTTTCATGCAGCTCAAGAAGATTTTTCCAGATGCTTCTTCACCGgtagccatac ... caccatgcagATTCAGTATCTTGTGTCTCGTTGGGGATCAGATATAAATTCACTAGGTTCA
EST: gi|151394677|gb|EV264548.1|EV264548
EST:     ACTTCGCTTTCATGCAGCTCAAGAAGATTTTTCCAGATGCTTCTTCACCG                         ATTCAGTATCTTGTGTCTCGTTGGGGATCAGATATAAATTCACTAGGTTCA
genomic: ACTTCGCTTTCATGCAGCTCAAGAAGATTTTTCCAGATGCTTCTTCACCGgtagccatac ... caccatgcagATTCAGTATCTTGTGTCTCGTTGGGGATCAGATATAAATTCACTAGGTTCA
EST: gi|9985097|gb|BE659205.1|BE659205
EST:     ACTTCGCTTTCATGCAGCTCAAGAAGATTTTTCCAGATGCTTCTTCACCG                         ATTCAGTATCTTGTGTCTCGTTGGGGATCAGATATAAATTCACTAGGTTCA
genomic: ACTTCGCTTTCATGCAGCTCAAGAAGATTTTTCCAGATGCTTCTTCACCGgtagccatac ... caccatgcagATTCAGTATCTTGTGTCTCGTTGGGGATCAGATATAAATTCACTAGGTTCA
EST: gi|9903014|gb|BE611982.1|BE611982
EST:     GCTTCTT-ACCG                         ATTCAGTATCTTGTGTCTCGTTGGGGATCAGATATAAATTCACTAGGTTCA
genomic: GCTTCTTCACCGgtagccatac ... caccatgcagATTCAGTATCTTGTGTCTCGTTGGGGATCAGATATAAATTCACTAGGTTCA
EST: gi|19452964|gb|BM954374.1|BM954374
EST:     ACTTCGCTTTCATGCAGCTCAAGAAGATTTTTCCAGATGCTTCTTCACCG                         ATTCAGTATCTTGTGTCTCGTTGGGGATCAGATATAAATTCACTAGGTTCA
genomic: ACTTCGCTTTCATGCAGCTCAAGAAGATTTTTCCAGATGCTTCTTCACCGgtagccatac ... caccatgcagATTCAGTATCTTGTGTCTCGTTGGGGATCAGATATAAATTCACTAGGTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgtgcttttttttttttaatttttaaaattggttatttgtttccaccatgcagATTCAGTATCTTGTGTCTCGTTGGGGATCAGATATAAATTCACTAGGTTCATATAGCTATGATGCAGTTGGGAAACCCCATGAACTATATGAGAGGCTAC
               ttttaat  putative branch site (score: 3)
                                     tttgtttcc  putative PPT
       ttttttttttttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggattaattaagcatgcatattgcctatagggtaacagttttgaaaatgtgcttttttttttttaatttttaaaattggttatttgtttccaccatgcagATTCAGTATCTTGTGTCTCGTTGGGGATCAGATATAAATTCACTAGGTTCATATAGCTATGATGCAGTTGGGAAACCCCATGAACTATATGAGAGGCTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG