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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttcttaagaaacaatgtacatgacatcagttctccacacaaactattgcttttctagttttctatttacttttttaattttggctttttattctgtcttgtacagCGAGGATCCTGATATTCACTTCAAGTATATCGAAGCAGCTGCTAAAACTGGACAAATTAAGGAGGTGGAGCGTGTTACTCGGGAATCAAACTTTTATGAT

Basic information

species Glycine max
transcript GLYMA02G39360.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 20
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 20
gtatttcttaagaaacaatgtacatgacatcagttctccacacaaactattgcttttctagttttctatttacttttttaattttggctttttattctgtcttgtacagCGAGGATCCTGATATTCACTTCAAGTATATCGAAGCAGCTGCTAAAACTGGACAAATTAAGGAGGTGGAGCGTGTTACTCGGGAATCAAACTTTTATGAT
                   |||  | ||  |   ||   |     |    |||    | | |||    || || |     |  ||    |  |  | |   ||  |||| |||||||| |||||||| ||||| || || |||||||||||||  |||||||| || || || || || ||||| ||  ||||||| ||||||||||||
-------------------gtagttaactac---tcctgatgttgatatgtgcgaagcaattttgtccttaacgtggcgcaccttaatatcgttctttacattcaacagTGAGGATCCAGATATTCATTTCAAATACATAGAAGCAGCTGCTAGGACTGGACAGATCAAAGAAGTTGAACGTGTAACCAGGGAATCCAACTTTTATGAT

upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 20
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 20
gtatttcttaagaaacaatgtacatgacatcagttctccacacaaactattgcttttctagttttctatttacttttttaattttggctttttattctgtcttgtacagCGAGGATCCTGATATTCACTTCAAGTATATCGAAGCAGCTGCTAAAACTGGACAAATTAAGGAGGTGGAGCGTGTTACTCGGGAATCAAACTTTTATGAT
                   |||  | ||  ||   |   |     |    |||    | | |||    || || |     |  ||    |  |  | |   ||  |||| |||||||| |||||||| ||||| || || |||||||||||||  |||||||| || || || || || ||||| ||  ||||||| ||||||||||||
-------------------gtagttaactaca---cctgatgttgatatgtgcgaagcaattttgtccttaacgtggcgcaccttaatatcgttctttacattcaacagTGAGGATCCAGATATTCATTTCAAATACATAGAAGCAGCTGCTAGGACTGGACAGATCAAAGAAGTTGAACGTGTAACCAGGGAATCCAACTTTTATGAT

upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM2G453474_T01 (Zea mays), 3'ss of exon 4
gtatttcttaagaaacaatgtacatgacatcagttctccacacaaactattgcttttct--agttttctatttacttttttaattttggcttt-------ttattctgtcttgtacagCGAGGATCCTGATATTCACTTCAAGTATATCGAAGCAGCTGCTAAAACTGGACAAATTAAGGAGGTGGAGCGTGTTACTCGGGAATCAAACTTTTATGAT----
                      || |  ||   |  | |  |||    | ||| |||||  | |||| | | |  || |  || |    |          ||  | |   |   |||||||||| || ||||| || |||||||| || |||||||| || | |||||||||||| || || || || | ||| ||  | || |||||||| ||||||    
----------------------caggtaatttctcttgctgacagcggaatgcctttctcaaattttgtgtgtctttctcaaaatgcaacacacctgaggtttctttacatgcaacagcgagGACCCAGATATCCATTTCAAGTACATAGAAGCAGCAGCAAGAACTGGACAAATCAAAGAAGTTGAACATGTAACCAGAGAGTCAAACTTATATGATGCTG

upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 20
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 20
gtatttcttaagaaacaatgtacatgacatcagttctccacacaaactattgcttttctagttttctatttacttttttaattttggctttttattctgtcttgtacagCGAGGATCCTGATATTCACTTCAAGTATATCGAAGCAGCTGCTAAAACTGGACAAATTAAGGAGGTGGAGCGTGTTACTCGGGAATCAAACTTTTATGAT
                  | |   |   |  |       | ||  ||| |   |||     |||| | | || ||| ||| ||||  | ||  ||| ||      |||||||||| |||||||| |||||||| || || || |||||||||||||||||||||||||||||||| || ||||| ||||||||||||||||||||||||
-----------------gtatttcttttaataaaagaaaaaactgactttaattttaagcattttttgtatattttcttatttttcaccttc-attttg----agacagCGAGGACCCTGATATCCACTTCAAATACATTGAGGCAGCTGCTAAAACTGGACAAATTAAGGAGGTCGAACGTGTGACTCGGGAATCAAACTTTTATGAT

upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 20
lower sequence: EFJ13237 (Selaginella moellendorffii), 3'ss of exon 20
gtatttcttaagaaacaatgtacatgacatcagttctccacacaaactattgcttttctagttttctatttacttttttaattttggctttttattc--tgtcttgtacagCGAGGATCCTGATATTCACTTCAAGTATATCGAAGCAGCTGCTAAAACTGGACAAATTAAGGAGGTGGAGCGTGTTACTCGGGAATCAAACTTTTATGAT
                                                                | |||      ||||||  ||| | | | ||    |||||||| ||||||||| || |||||||||||||| ||||| |||||||| |||||||| || ||| | || ||||| |||||||| ||  ||||||| || || ||||||
---------------------------------------------------------------gtatatccgtggttttaaaattg-catgtaatcaagtgtcttgtgcagCGAGGACCCGGATATTCACTTCAAATATATTGAAGCAGCAGCTAAAACGGGCCAACTGAAAGAGGTAGAGCGTGTCACCAGGGAATCGAATTTCTATGAT

upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 20
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 20
gtatttcttaagaaacaatgtacatgacatcagttctccacacaaactattgcttttctagttttctatttacttttttaattttggctttttatt--ctgtcttgtacagCGAGGATCCTGATATTCACTTCAAGTATATCGAAGCAGCTGCTAAAACTGGACAAATTAAGGAGGTGGAGCGTGTTACTCGGGAATCAAACTTTTATGAT
                                                                | |||      ||||||  ||| | | | ||    |||||||||||||||||| || |||||||||||||| ||||| |||||||| |||||||| || ||| | || ||||| |||||||| ||  ||||||| || || ||||||
---------------------------------------------------------------gtatatccgtggttttaaagttg-catgtaatcaattgtcttgtacagCGAGGACCCGGATATTCACTTCAAATATATTGAAGCAGCAGCTAAAACGGGCCAACTGAAAGAGGTAGAGCGTGTCACCAGGGAATCGAATTTCTATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctagttttctatttacttttttaattttggctttttattctgtcttgtacagCGAGGATCCTGATATTCACTTCAAGTATATCGAAGCAGCTGCTAAAACTGGACAAATTAAGGAGGTGGAGCGTGTTACTCGGGAATCAAACTTTTATGAT
                     ttttaat  putative branch site (score: 3)
                                 ctttttattctgtctt  putative PPT
       ttttctatttactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttcttaagaaacaatgtacatgacatcagttctccacacaaactattgcttttctagttttctatttacttttttaattttggctttttattctgtcttgtacagCGAGGATCCTGATATTCACTTCAAGTATATCGAAGCAGCTGCTAAAACTGGACAAATTAAGGAGGTGGAGCGTGTTACTCGGGAATCAAACTTTTATGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG