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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgtaggaggtgtaagaagattactccttttattttcatgatacttactgtgatggttatgtgaacctctggaaaatttaaatatttttttctctgtccagGTTATGGCATTAATTGCATACTTGATGGAGTTTAAAGGAAACTATGGCCCACATCTTATAATAGTCCCAAATGCTGTTATGGTTAACTGGAAG

Basic information

species Glycine max
transcript GLYMA18G46930.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G46930.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g02290.1 (Oryza sativa), 3'ss of exon 6
---------------------------------cgtaggaggtgtaagaagattactccttttattttcatgatacttactgtgatggttatgtgaacctctggaaaatttaaatattttt---ttctctgtccagGTTATGGCATTAATTGCATACTTGATGGAGTTTAAAGGAAACTATGGCCCACATCTTATAATAGTCCCAAATGCTGTTATGGTTAACTGGAAG
                                 | |  |   | | | || |||     || |  | ||||    ||  |  |     ||       |   |   |  |||   |         ||   |    |||||||| |  | ||||||||||||||||| |||||||| || ||||| |||||||| ||||| || || ||||||||  |||| |||||||||
gtgtggatttcttattccgttctacctgctagacttttgctatttcacaatattttcttttattatctcatttgcctccccatttccttttgccctgctagtaacatctttttgtggccaccaattgaataaatagGTTATGTCTCTGATTGCATACTTGATGGAATTTAAAGGGAATTATGGACCACATCTCATAATTGTACCGAATGCTGTCTTGGTCAACTGGAAG

upper sequence: GLYMA18G46930.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G163849_T01 (Zea mays), 3'ss of exon 6
---------------------cgtaggaggtgtaagaagattactc-------cttttattttcat-gatacttactgtgatggttatgtgaacctctggaaa---atttaaatattttt-ttctctgtc----cagGTTATGGCATTAATTGCATACTTGATGGAGTTTAAAGGAAACTATGGCCCACATCTTATAATAGTCCCAAATGCTGTTATGGTTAACTGGAAG
                       ||     ||||      ||| ||        ||||||| || |  || ||| || |  |  ||     ||   |  | ||   ||||  || | | |  | | |||      |||| ||||||||  |||| ||| ||||||| |||||||| || |||||||| ||||| |||||||| |||||||||||  | || || ||||||
gtcattccttgcttattcttgtttactttctgtactcctgttattcatgatattttttattatcgtcaatgcttcctcttttcattcgaccaatggccaggaacttatttgtatgtctatgctatttgttgtaatagGTCATGGCATTGGTTGCGTACCTGATGGAATTTAAAGGGAATTATGGCCCTCATCTCATAATAGTGCCAAATGCTGTCTTAGTCAATTGGAAG

upper sequence: GLYMA18G46930.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv15s0046g02290.t01 (Vitis vinifera), 3'ss of exon 6
-------cgtaggaggtgtaagaagattactccttttattttcatgatacttactgtgatggttatgtgaacctctggaaaatttaaatatttttttctctgtccagGTTATGGCATTAATTGCATACTTGATGGAGTTTAAAGGAAACTATGGCCCACATCTTATAATAGTCCCAAATGCTGTTATGGTTAACTGGAAG
         |      |       |  |||| |   || |||||   |   |  | | |   ||| |      | || |   ||| | | ||| ||| | ||  ||||| |||||||||||||| || ||||||||||| |||||||||||||| ||||||||||| || || || ||||||||| |||| |||||||||
gtgaatttctgcatattccttatggcatactgcaactactttcaaattttatgtt-taacaattaag--ggtttgtgcagtgtttgattgtttctttat-tggacagGTAATGGCATTAATTGCTTATTTGATGGAGTTCAAAGGAAACTATGGTCCACATCTTATTATTGTTCCTAATGCTGTTCTGGTAAACTGGAAG

upper sequence: GLYMA18G46930.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ33371 (Selaginella moellendorffii), 3'ss of exon 2
cgtaggaggtgtaagaagattactccttttattttcatgatacttactgtgatggttatgtgaacctctggaaaatttaaatatttttttctctgtccagGTTATGGCATTAATTGCATACTTGATGGAGTTTAAAGGAAACTATGGCCCACATCTTATAATAGTCCCAAATGCTGTTATGGTTAACTGGAAG
                                               |    | ||  | |||    | ||    | | |  || ||||     ||||||||||||||  | |||||||||||||||||||| |||||||| || || ||||||||||| || || || || || || || || |||||||||
---------------------------------------------gttagctttgtattttgaggtccgggcttgtctgag-atgttttc----gtccagGTTATGGCGCTCATTGCATACTTGATGGAGTTCAAAGGAAATTACGGACCACATCTTATTATTGTTCCCAACGCAGTCATAGTGAACTGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgtgatggttatgtgaacctctggaaaatttaaatatttttttctctgtccagGTTATGGCATTAATTGCATACTTGATGGAGTTTAAAGGAAACTATGGCCCACATCTTATAATAGTCCCAAATGCTGTTATGGTTAACTGGAAG
 tacttac  putative branch site (score: 1)
                                    tatttttttctctgtc  putative PPT
                          aaaatttaaatatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgtaggaggtgtaagaagattactccttttattttcatgatacttactgtgatggttatgtgaacctctggaaaatttaaatatttttttctctgtccagGTTATGGCATTAATTGCATACTTGATGGAGTTTAAAGGAAACTATGGCCCACATCTTATAATAGTCCCAAATGCTGTTATGGTTAACTGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - ggaggtg
- - - - - - - - - - - - - - - - -ttcatga
- - - - - - - - - - - - - - - - - - - - - - - - gtgatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctgga