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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgttgccattattggtatcaatttacagttttgttatatttggtttcatttgtttgcattttgatttaagcatattgcagtcatggcttactaaattgcaatagctttgtcccttgtaattttatagGTGGTCAAGCGAAAACCCTTATGTTTGTACAGCTTAATCCTGATGTTGCTTCATATTCTGAAACTGTAAGCACCTTGAAGTTTGCTGAGCGGGTTTCCGG

Basic information

species Glycine max
transcript GLYMA08G01800.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G01800.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G173700_T01 (Zea mays), 3'ss of exon 14
gtaattgttgccattattggtatcaatttacagttttgttatatttggtttcatttgtttgc-attttgat-ttaagcatattgcagtcatggcttactaaattgcaatagctttgtcccttgtaattttatagGTGGTCAAGCGAAAACCCTTATGTTTGTACAGCTTAATCCTGATGTTGCTTCATATTCTGAAACTGTAAGCACCTTGAAGTTTGCTGAGCGGGTTTCCGG
                                         || |    |  |||| ||| | |  | ||| ||||  |||||   ||  |    | | |||||  |     | |  |  || |  | ||  |||||| ||||| ||||| || |||||||| ||| | |||||||||||||  |||||||| |||||| |||| || || |||||||||||  |||| || ||
----------------------------------------gtaatcaaat--atttatttactacctagatgttaaatatattaatgt--ttatcttccaaatttta-----tgtaccttttattttcttccagGTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGG

upper sequence: GLYMA08G01800.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM5G845682_T02 (Zea mays), 3'ss of exon 4
gtaattgttgccattattggtatcaatttacagttttgt-tatatttggtttcatttgtttgcattttgatttaagcatattgcagtcatggcttactaaattgcaatagctttgtcccttgtaattttatagGTGGTCAAGCGAAAACCCTTATGTTTGTACAGCTTAATCCTGATGTTGCTTCATATTCTGAAACTGTAAGCACCTTGAAGTTTGCTGAGCGGGTTTCCGG
                               | |   || | |||||  |  || |    |  || ||     ||  | |||   || |    ||  |||||   | | |   |  |  |||   | ||  |||||| ||||| ||||| || ||||| || ||  | |||||||||||||  |||||||| |||||| ||||||| || |||||||||||  |||| || ||
-----------------------------gtaatcaagtatttatttactaccagtaaactagatctt-----aaatagatttatgtgaatattt--taaat---atttgtactaccttttgctttcttccagGTGGACAAGCAAAAACTCTAATGTTCGTTCAAATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGCACTTTAAAGTTTGCTGAAAGGGTGTCTGG

upper sequence: GLYMA08G01800.1 (Glycine max), 3'ss of exon 18
lower sequence: AT5G41310.1 (Arabidopsis thaliana), 3'ss of exon 15
gtaattgttgccattattggtatcaatttacagttttgttatatttggtttcatttgtttgcattttgatttaagcatattgcagtcatggcttactaaattgcaatagctttgtcccttgtaattttatagGTGGTCAAGCGAAAACCCTTATGTTTGTACAGCTTAATCCTGATGTTGCTTCATATTCTGAAACTGTAAGCACCTTGAAGTTTGCTGAGCGGGTTTCCGG
                                               ||   ||  | | |  ||       ||  ||||| |     ||   |  |   ||||        |   | || ||||||| |||| || ||||||||||| ||||||||||| ||  ||||||||||||  | ||||||| |||| |||||||| || ||||| ||||| ||  | ||||| ||
-----------------------------------------------gtactataagatagacttcaataaaaaaaatattac----ttgatattgttgcttgcttctttactcctctttttaattttttagGAGGGCAAGCGAAAACTCTTATGTTTGTTCAAATTAATCCTGATGAAGATTCATATGCTGAGACTGTAAGTACTTTGAAATTTGCGGAAAGAGTTTCTGG

upper sequence: GLYMA08G01800.1 (Glycine max), 3'ss of exon 18
lower sequence: Vv02s0025g03480.t01 (Vitis vinifera), 3'ss of exon 18
gtaattgttgccattattggtatcaatttacagttttgttatatttggtttcatt-tgtttgcattttg---atttaagcatattgcagtcatggcttactaaattgcaatagctt---tgtcccttgta---attttatagGTGGTCAAGCGAAAACCCTTATGTTTGTACAGCTTAATCCTGATGTTGCTTCATATTCTGAAACTGTAAGCACCTTGAAGTTTGCTGAGCGGGTTTCCGG
|||  | |     |  ||  |      ||   |||     |||     | ||| | || ||  |  |||   |||| |   | | |  || |    || ||    ||   | | ||    ||  ||| |    | |||||||| ||||||||||| |||||||||||||||||||||||||||||||| | ||| || || |||||| |||| |||||||||||||| ||| | || || ||
gtacatatccttctggtttttga-gtcttgtggttgaaccataccgtttgtcagtgtgctttaagattgggaatttgactttgtagttgttaacattttcttgcctgggcttgtttgaccgtttctttttcctactttatagGAGGTCAAGCGAAGACCCTTATGTTTGTACAGCTTAATCCTGATGTGGATTCCTACTCCGAAACTATAAGTACCTTGAAGTTTGCCGAGAGAGTCTCTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgcagtcatggcttactaaattgcaatagctttgtcccttgtaattttatagGTGGTCAAGCGAAAACCCTTATGTTTGTACAGCTTAATCCTGATGTTGCTTCATATTCTGAAACTGTAAGCACCTTGAAGTTTGCTGAGCGGGTTTCCGG
                tactaaa  putative branch site (score: 1)
                                         ttgtaattttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgttgccattattggtatcaatttacagttttgttatatttggtttcatttgtttgcattttgatttaagcatattgcagtcatggcttactaaattgcaatagctttgtcccttgtaattttatagGTGGTCAAGCGAAAACCCTTATGTTTGTACAGCTTAATCCTGATGTTGCTTCATATTCTGAAACTGTAAGCACCTTGAAGTTTGCTGAGCGGGTTTCCGG

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