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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttctttcttattggagagtgaacatgacctcagttcactagttggtctgcttgacttttttttttcaattattgtaattttttttgttctgtcttgtaaagTGAGGATCCTGATATTCACTTCAAGTACATTGAGGCCGCTGCTAAAACTGGACAAATTAAGGAGGTAGAGCGTGTAACTAGAGAATCAAACTTTTATGAT

Basic information

species Glycine max
transcript GLYMA11G06720.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 20
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 20
gtatttctttcttattggagagtgaacatgacctcagttcactagttggtctgcttgacttttttttttcaattattgtaatttttt-ttgttc--tgtcttgtaaagTGAGGATCCTGATATTCACTTCAAGTACATTGAGGCCGCTGCTAAAACTGGACAAATTAAGGAGGTAGAGCGTGTAACTAGAGAATCAAACTTTTATGAT
                    ||| |||    ||| |  |   ||  ||    ||   | |||| |  || |  |   | |  ||  | | ||||  |   ||  | ||||||||||| |||||||| ||||| ||||| || || |||||||  |||||||| || || || || || |||||||| || ||||| ||||||||||||
------------------gtagttaactactcctgatgttgatatgtgcgaagc---aattttgtccttaacgtggcgcaccttaatatcgttctttacattcaacagTGAGGATCCAGATATTCATTTCAAATACATAGAAGCAGCTGCTAGGACTGGACAGATCAAAGAAGTTGAACGTGTAACCAGGGAATCCAACTTTTATGAT

upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 20
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 20
gtatttctttcttattggagagtgaacatgacctcagttcactagttggtctgcttgacttttttttttcaattattgtaatttttt-ttgttc--tgtcttgtaaagTGAGGATCCTGATATTCACTTCAAGTACATTGAGGCCGCTGCTAAAACTGGACAAATTAAGGAGGTAGAGCGTGTAACTAGAGAATCAAACTTTTATGAT
                    ||| |||   |||| |  |   ||  ||    ||   | |||| |  || |  |   | |  ||  | | ||||  |   ||  | ||||||||||| |||||||| ||||| ||||| || || |||||||  |||||||| || || || || || |||||||| || ||||| ||||||||||||
------------------gtagttaactacacctgatgttgatatgtgcgaagc---aattttgtccttaacgtggcgcaccttaatatcgttctttacattcaacagTGAGGATCCAGATATTCATTTCAAATACATAGAAGCAGCTGCTAGGACTGGACAGATCAAAGAAGTTGAACGTGTAACCAGGGAATCCAACTTTTATGAT

upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 18
gtatttctttcttattggagagtgaacatgacctcagttcactagttggtctgcttgacttttt--tttttcaattattgtaattttttttgttctgtcttgtaaagTGAGGATCCTGATATTCACTTCAAGTACATTGAGGCCGCTGCTAAAACTGGACAAATTAAGGAGGTAGAGCGTGTAACTAGAGAATCAAACTTTTATGAT
||| ||  |  |  |      ||    ||  | | || |  |         |  |  | || |     |  ||   ||||  |||   |||  | | | ||  | ||||||||||| ||||| || ||||| ||||| || || ||||| | ||||||||| || || || || ||||||||||| ||||| || || || ||||||
gtagttactcttactcctgatgttggtatttcttaaggtggcataccttaatattaaatttctcaacatggcatgcattgatattaaattttctttatatt-catagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGGACAGATCAAAGAAGTTGAGCGTGTAACCAGAGAGTCTAATTTCTATGAT

upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 20
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 20
gtatttctttcttattggagagtgaacatgacctcagttcactagttggtctgcttgacttttttttttcaattattgtaattttttttgttctgtcttgtaaagTGAGGATCCTGATATTCACTTCAAGTACATTGAGGCCGCTGCTAAAACTGGACAAATTAAGGAGGTAGAGCGTGTAACTAGAGAATCAAACTTTTATGAT
|||||||||| | ||   |||   ||| |||| | | ||               || |   |||||| |  ||| || | ||||||    |||  | |   | || ||||| |||||||| |||||||| ||||||||||| ||||||||||||||||||||||||||||| || ||||| ||| | ||||||||||||||||||
gtatttcttt-taataaaagaaaaaac-tgactttaatt---------------ttaagcattttttgtatatt-ttcttatttttcaccttcattttgagacagCGAGGACCCTGATATCCACTTCAAATACATTGAGGCAGCTGCTAAAACTGGACAAATTAAGGAGGTCGAACGTGTGACTCGGGAATCAAACTTTTATGAT

upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 20
lower sequence: EFJ13237 (Selaginella moellendorffii), 3'ss of exon 20
gtatttctttcttattggagagtgaacatgacctcagttcactagttggtctgcttgacttttttttttcaattat-tgtaattttttttgttctgtcttgtaaagTGAGGATCCTGATATTCACTTCAAGTACATTGAGGCCGCTGCTAAAACTGGACAAATTAAGGAGGTAGAGCGTGTAACTAGAGAATCAAACTTTTATGAT
                                                    |  |  |  |  ||||  ||||   ||||||    |       |||||||  || ||||| || |||||||||||||| || ||||| || || |||||||| || ||| | || |||||||||||||| || || ||||| || || ||||||
----------------------------------------------------gtatatccgtggttttaaaattgcatgtaatcaagt-------gtcttgtgcagCGAGGACCCGGATATTCACTTCAAATATATTGAAGCAGCAGCTAAAACGGGCCAACTGAAAGAGGTAGAGCGTGTCACCAGGGAATCGAATTTCTATGAT

upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 20
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 20
gtatttctttcttattggagagtgaacatgacctcagttcactagttggtctgcttgacttttttttttcaattat-tgtaattttttttgttctgtcttgtaaagTGAGGATCCTGATATTCACTTCAAGTACATTGAGGCCGCTGCTAAAACTGGACAAATTAAGGAGGTAGAGCGTGTAACTAGAGAATCAAACTTTTATGAT
                                                    |  |  |  |  ||||  | ||   ||||||   ||       |||||||| || ||||| || |||||||||||||| || ||||| || || |||||||| || ||| | || |||||||||||||| || || ||||| || || ||||||
----------------------------------------------------gtatatccgtggttttaaagttgcatgtaatcaatt-------gtcttgtacagCGAGGACCCGGATATTCACTTCAAATATATTGAAGCAGCAGCTAAAACGGGCCAACTGAAAGAGGTAGAGCGTGTCACCAGGGAATCGAATTTCTATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcttgacttttttttttcaattattgtaattttttttgttctgtcttgtaaagTGAGGATCCTGATATTCACTTCAAGTACATTGAGGCCGCTGCTAAAACTGGACAAATTAAGGAGGTAGAGCGTGTAACTAGAGAATCAAACTTTTATGAT
  gcttgac  putative branch site (score: 4)
                               ttttttttgttctgtc  putative PPT
     tgacttttttttttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttctttcttattggagagtgaacatgacctcagttcactagttggtctgcttgacttttttttttcaattattgtaattttttttgttctgtcttgtaaagTGAGGATCCTGATATTCACTTCAAGTACATTGAGGCCGCTGCTAAAACTGGACAAATTAAGGAGGTAGAGCGTGTAACTAGAGAATCAAACTTTTATGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG