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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatttacttccttgctacggcttgctgcactggttaattgaatgggatcatattttaaagttggtatttcagGTATTAACAAACCTGATGTCCGCTTTGTAATCCATCATTCCCTCCCAAAATCTATTGAAGGCTATCATCAG

Basic information

species Glycine max
transcript GLYMA08G20070.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G20070.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os04g35420.1 (Oryza sativa), 3'ss of exon 14
gtatatttacttccttgctacggcttgctgcactggttaattgaatgggatcatattttaaagttg--gtatttcagGTATTAACAAACCTGATGTCCGCTTTGTAATCCATCATTCCCTCCCAAAATCTATTGAAGGCTATCATCAG
|||  || | || | |  |  |      |  | | |||  || | |||   |   |  |||   ||  | ||| |||||||||| |||||||||||||| ||||| |||||||||||||| || ||||| |||||||| |||||||||
gtaacttgattttcatagtgtgcaca--tatatttgttgttt-attggtgcctcgtgctaattgtgcaggattgcagGTATTAATAAACCTGATGTCCGTTTTGTTATCCATCATTCCCTGCCCAAATCAATTGAAGGATATCATCAG

upper sequence: GLYMA08G20070.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G319573_T02 (Zea mays), 3'ss of exon 11
gtatattta-cttccttgctacggcttgctgcactggttaattgaatgggatcatattttaaagttggtatttcagGTATTAACAAACCTGATGTCCGCTTTGTAATCCATCATTCCCTCCCAAAATCTATTGAAGGCTATCATCAG
|||  || | ||| |   |  | |  |    ||    ||| |||  ||   ||  || | | ||     | |  |||||| || ||||||||||| |||||||| || |||||||| || || || || |||||||| |||||||||
gtaacttaatctttcaaacacctgtgtataacatctatta-ttgggtgt--tccaatctaataggacaaactgtagGTATCAATAAACCTGATGTTCGCTTTGTTATTCATCATTCACTGCCCAAGTCAATTGAAGGATATCATCAG

upper sequence: GLYMA08G20070.1 (Glycine max), 3'ss of exon 17
lower sequence: AT1G10930.1 (Arabidopsis thaliana), 3'ss of exon 15
gtatatttacttccttgctacggcttgctgcactggttaattgaatgggatcatattttaaagttg-gtatttcagGTATTAACAAACCTGATGTCCGCTTTGTAATCCATCATTCCCTCCCAAAATCTATTGAAGGCTATCATCAG
   || |   ||  ||||||  | |   |  | |  || |   ||||          ||||  |||   |||||||| || ||||| ||||||||||||||||| || ||||| || |||||||| ||||| |||||||||||||||
--gtactggttt--ttgctaatgttgttttaattcattga--aaatgttgctgcccattaacattgcacatttcagGAATCAACAAGCCTGATGTCCGCTTTGTTATTCATCACTCGCTCCCAAAGTCTATAGAAGGCTATCATCAG

upper sequence: GLYMA08G20070.1 (Glycine max), 3'ss of exon 17
lower sequence: AT1G60930.1 (Arabidopsis thaliana), 3'ss of exon 15
gtatatttact--tccttgctacggcttgctgcactggttaattgaatgggatcatattttaaagttggtatttcagGTATTAACAAACCTGATGTCCGCTTTGTAATCCATCATTCCCTCCCAAAATCTATTGAAGGCTATCATCAG
   || ||| |  ||  || ||  |    |  |  || || ||||||          |  ||| |||| ||||||||| || || || |||||||| || |||||||| |||||||| || ||||| || || |||||||||||||||
--gtaattaatggtctctgttatag----ccactttgattgattgaagtttgctgcctgctaacgttgatatttcagGAATCAATAAGCCTGATGTTCGTTTTGTAATTCATCATTCTCTACCAAAGTCCATAGAAGGCTATCATCAG

upper sequence: GLYMA08G20070.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv12s0035g00400.t01 (Vitis vinifera), 3'ss of exon 11
gtatatttacttccttgctacggcttgctgcactggttaattgaatgggatcatattttaa---agttggta------tttcagGTATTAACAAACCTGATGTCCGCTTTGTAATCCATCATTCCCTCCCAAAATCTATTGAAGGCTATCATCAG
     | |  ||  ||  |||   || |   ||| | ||  |||     | ||| | || |   |||   ||      || ||||||| |||||||| |||||||||||||| || |||||||| || |||||||| |||||||| |||||||||
----gtatcattgattattactattttcctgacttggtagctgatgacaaccatgtattgacatagtcactagactcattacagGTATCAACAAACCAGATGTCCGCTTTGTCATTCATCATTCTCTTCCAAAATCAATTGAAGGGTATCATCAG

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|193549141|gb|FK505436.1|FK505436
EST:     GAGCAAAGATGAGATCAATATAATTTGTGCTACTGTGGCATTTGGAATGG                         GTATTAACAAACCTGATGTCCGCTTTGTAATCC
genomic: GAGCAAAGATGAGATCAATATAATTTGTGCTACTGTGGCATTTGGAATGGgtatatttac ... ggtatttcagGTATTAACAAACCTGATGTCCGCTTTGTAATCC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggcttgctgcactggttaattgaatgggatcatattttaaagttggtatttcagGTATTAACAAACCTGATGTCCGCTTTGTAATCCATCATTCCCTCCCAAAATCTATTGAAGGCTATCATCAG
              ggttaat  putative branch site (score: 4)
                             atcatattttaaagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatttacttccttgctacggcttgctgcactggttaattgaatgggatcatattttaaagttggtatttcagGTATTAACAAACCTGATGTCCGCTTTGTAATCCATCATTCCCTCCCAAAATCTATTGAAGGCTATCATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG