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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctttccccttctttcttctcttgtcttgtcttgtctttagtagtgtgagtaatgaatgattttcttttttacttgctaactgcttgtttcctattatagAGAATTGTTGATTGGCTGGCTTCCAACTTCAAGAGAGATGAAGGCATAGACCTTTTGAAAGACAAACAAGCTCTTCAGCGTCTCACTGAGACAGCCGAGA

Basic information

species Glycine max
transcript GLYMA16G00410.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G00410.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os12g14070.1 (Oryza sativa), 3'ss of exon 3
gtacctttccccttctttcttctcttgtcttgtcttgtctttagtagtgtgagtaatgaatgattttcttttttacttgctaactgcttgtttcctattatagAGAATTGTTGATTGGCTGGCTTCCAACTTCAAGAGAGATGAAGGCATAGACCTTTTGAAAGACAAACAAGCTCTTCAGCGTCTCACTGAGACAGCCGAGA
        |  | |   | |    |   ||  |  | |   |   ||| ||    ||  ||  |||| ||||| | |||     |     |    |||  |||| | |||| |||||||| |||  |||||| |||| |||||||||||| || ||| |||||||||||||||| || ||||| ||||||||| |||| ||||
-ccatggacaacatacctatcagttgaactgattcttttactgacagtatgctatatttattgtttt-tttttaatttgaatgttatccttgaattat-gtagAAAGTTGTGGATTGGCTTGCTAGCAACTTTAAGAAAGATGAAGGCATTGATCTTCTGAAAGACAAACAAGCCCTGCAGCGACTCACTGAGGCAGCAGAGA

upper sequence: GLYMA16G00410.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G001500_T01 (Zea mays), 3'ss of exon 3
gtacctttccccttctttcttctcttgtcttgtcttgtctttagtagtgtgagtaatgaatgattttcttttttacttgctaactgcttgtttcctattatagAGAATTGTTGATTGGCTGGCTTCCAACTTCAAGAGAGATGAAGGCATAGACCTTTTGAAAGACAAACAAGCTCTTCAGCGTCTCACTGAGACAGCCGAGA
  | | |      | |           |    || |   ||  | | | | |     || |  || ||   | || |     | |     |  | | ||  ||||||| || |||||||| |||  ||||||||||| ||||||| | || || ||| |||| || |||||||| |||||| | || |||||| |||| ||||
-gatcatatggaatgtcaaaatctaactaacttcatactttatgcaattttaagggaga-tagttctcaactatattgatatattatccttgacttgtt-cagAGAATAGTAGATTGGCTTGCTAGCAACTTCAAGAAAGATGAACGTATTGATCTTCTGAAGGATAAACAAGCCCTTCAGAGGCTTACTGAGGCAGCAGAGA

upper sequence: GLYMA16G00410.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv17s0000g03310.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------------gtacctttccccttctttc-ttctcttgtcttgtct-tgtctttag-tagtgtgag-taatgaatgattttctttt-ttacttgctaactgcttgtttcctattatagAGAATTGTTGATTGGCTGGCTTCCAACTTCAAGAGAGATGAAGGCATAGACCTTTTGAAAGACAAACAAGCTCTTCAGCGTCTCACTGAGACAGCCGAGA
                                          || |||   |||||||  ||||||    || ||| | ||   |  || | | || |  ||| || ||        | | ||   |  ||  |      |   | ||||| |||| |||||| ||||| | |  || |||| |||||| || ||||| ||| | || ||||||||||||||||||||||| || |||||||| ||||
gttgagaatatttgaatagcctgcaatgaacaatgttatgtcacattttgtcttctttagttctctctctttctctctatccacatctaatattaggttttgattggttagagcaaatcatttatcatttgtcttaccattcaaacagAGAGTTGTGGATTGGTTGGCTGCAAGTTTTAAGAAAGATGAGGGTATAGATCTTCTCAAGGACAAACAAGCTCTTCAGCGTCTAACAGAGACAGCTGAGA

upper sequence: GLYMA16G00410.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ32911 (Selaginella moellendorffii), 3'ss of exon 4
gtacctttccccttctttcttctcttgtcttgtcttgtctttagtagtgtgagtaatgaatgattttcttttttacttgctaactgcttgtttcctattatagAGAATTGTTGATTGGCTGGCTTCCAACTTCAAGAGAGATGAAGGCATAGACCTTTTGAAAGACAAACAAGCTCTTCAGCGTCTCACTGAGACAGCCGAGA
                                           ||     ||   || ||| |   |||||||   ||  |||||  || |   |    | ||||||||||||| ||||| || ||||||||||||| ||| ||||| || || ||| | || ||||| ||||| |||||  | || || ||||| || ||||
-------------------------------------------gtgccacgaa-gatcaattaagatctttttattttcttaactctttttcgtcgtaaacagAGAATTGTTGACTGGCTAGCGTCCAACTTCAAGAAAGACGAAGGAATCGATCTTCTCAAGGACAAGCAAGCACTTCAAAGGCTGACAGAGACTGCAGAGA

upper sequence: GLYMA16G00410.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ15775 (Selaginella moellendorffii), 3'ss of exon 3
gtacctttccccttctttcttctcttgtcttgtcttgtctttagtagtgtgagtaatgaatgattttcttttttacttgctaactgcttgtttcctattatagAGAATTGTTGATTGGCTGGCTTCCAACTTCAAGAGAGATGAAGGCATAGACCTTTTGAAAGACAAACAAGCTCTTCAGCGTCTCACTGAGACAGCCGAGA
                                           ||     ||   ||  || |   |||||||   ||  |||||  || |   |    | ||||||||||||| ||||| || ||||||||||||| ||| ||||| || || ||| | || ||||| ||||| |||||  | || || ||||| || ||||
-------------------------------------------gtgccacgaa-gatcgattaagatctttttattttcttaactctttttcgtcgtaaacagAGAATTGTTGACTGGCTAGCGTCCAACTTCAAGAAAGACGAAGGAATCGATCTTCTCAAGGACAAGCAAGCACTTCAAAGGCTGACAGAGACTGCAGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgagtaatgaatgattttcttttttacttgctaactgcttgtttcctattatagAGAATTGTTGATTGGCTGGCTTCCAACTTCAAGAGAGATGAAGGCATAGACCTTTTGAAAGACAAACAAGCTCTTCAGCGTCTCACTGAGACAGCCGAGA
                             tgctaac  putative branch site (score: 1)
                                      cttgtttcct  putative PPT
     taatgaatgattttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacctttccccttctttcttctcttgtcttgtcttgtctttagtagtgtgagtaatgaatgattttcttttttacttgctaactgcttgtttcctattatagAGAATTGTTGATTGGCTGGCTTCCAACTTCAAGAGAGATGAAGGCATAGACCTTTTGAAAGACAAACAAGCTCTTCAGCGTCTCACTGAGACAGCCGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT