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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGATCCGACCCTTGCTGTTGTTGCTTACCGAAGAGGGCAATGTGATGATGAGCTTGTTAATGTTACTAATAAAAATTCCTTGTTCAAACTTCAAGCAAGgtgtgtactgtgagcttcagcaggaagttgtcattgtatttcatatttttataatgctagtctgagacactcatgttattttctaatgtttgtgtcag

Basic information

species Glycine max
transcript GLYMA01G38580.1
intron # 23
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G38580.1 (Glycine max), 5'ss of exon 23
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 23
GGGATCCGACCCTTGCTGTTGTTGCTTACCGAAGAGGGCAATGTGATGATGAGCTTGTTAATGTTACTAATAAAAATTCCTTGTTCAAACTTCAAGCAAGgtgtgta--ctgtgagcttcagcaggaagttgtcattgtatttcatat---ttttataatgctagtctgagacactcatgttattttctaatgtttgtgtcag
||||||| ||||||||||||||||||||| || | || || ||||||||||| ||| ||||||| || |||||||| ||  ||||||| || ||||| |||| || |   |||     |       |  || | ||| |||||| | |   | ||  ||| |   | |      || |  |     || | |     || |||
GGGATCCTACCCTTGCTGTTGTTGCTTACAGACGTGGACAGTGTGATGATGAACTTATTAATGTCACCAATAAAAACTCACTGTTCAAGCTGCAAGCTAGgtatgcaaattgtttttattcttcataccttttaattttatttcttctgaatctttaaatccatctattgattgcttacatagaaatcgatttgaattgccag

upper sequence: GLYMA01G38580.1 (Glycine max), 5'ss of exon 23
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 23
GGGATCCGACCCTTGCTGTTGTTGCTTACCGAAGAGGGCAATGTGATGATGAGCTTGTTAATGTTACTAATAAAAATTCCTTGTTCAAACTTCAAGCAAGgtgtgtactgtgagcttcagcagga-agttgtcattgtatttcat----atttttataatgctagtctgagacactcatgttattttctaatgtttgtgtcag
||||||| ||||||||||||||||||||| || | || || ||||||||||| ||| ||||||| || |||||||| ||  ||||||| || ||||| |||| || |   ||   ||   |   | | || | ||| |||||| |    || |||| |    | |  |||    || |  |     || | |     || |||
GGGATCCTACCCTTGCTGTTGTTGCTTACAGACGTGGACAGTGTGATGATGAACTTATTAATGTCACCAATAAAAACTCACTGTTCAAGCTGCAAGCTAGgtatgcaaattgtttttattcttcatacttttaattttatttcttctgaatctttaaatccatcgattgat-tgcttacatagaaatcgatttgaattgccag

upper sequence: GLYMA01G38580.1 (Glycine max), 5'ss of exon 23
lower sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 21
GGGATCCGACCCTTGCTGTTGTTGCTTACCGAAGAGGGCAATGTGATGATGAGCTTGTTAATGTTACTAATAAAAATTCCTTGTTCAAACTTCAAGCAAGgtgtgtact---gtgagcttcagcaggaagttgtcattgtatttcatatttttata-atgctagtctgagacactcatgttattttctaatg--ttt---gtgtcag
| ||||| || |||||||||||||||||  || | ||||||||||| || |||||| ||||||| ||||| ||||| || |||||||| || ||||| |||| | || |    |  | | | |       |     |||| | |   | |  | || ||  |   |   | | | | || |  | ||  ||   |||    | ||||
GAGATCCTACACTTGCTGTTGTTGCTTATAGACGTGGGCAATGTGACGACGAGCTTATTAATGTCACTAACAAAAACTCATTGTTCAAGCTACAAGCTAGgtatataattatttttgttcctgttactgatgccttttgtttgttccagtcctctatatattgagcaatggctcgcttggtcatgtcacataaatttaaaatttcag

upper sequence: GLYMA01G38580.1 (Glycine max), 5'ss of exon 23
lower sequence: GRMZM2G111355_T01 (Zea mays), 5'ss of exon 3
GGGATCCGACCCTTGCTGTTGTTGCTTACCGAAGAGGGCAATGTGATGATGAGCTTGTTAATGTTACTAATAAAAATTCCTTGTTCAAACTTCAAGCAAGgtgtgtactgtgagcttcagcaggaagttgtcat-tgtatttcat-atttttataatgctagtctgagacactcatgttattttctaatgtttgtgtcag-------
||||||| || |||||||||||||||||| || | ||||| |||||  |||| ||| |||| || ||||| || ||||| || ||||| || ||||| |||| |||| |      |   |  |  | |||| |    | |||||  || |  | |    | ||||||   ||| |  |  |  | |    ||| | | |        
GGGATCCTACACTTGCTGTTGTTGCTTACAGACGTGGGCAGTGTGACTATGAACTTATTAACGTCACTAACAAGAATTCGTTATTCAAGCTGCAAGCTAGgtatgtaataatttttattgttgtgacttgtgacacctgtttcaagatgtccacatcaattgtctgacg-acttacatgttcatattgcatttatttaaaatgacag

upper sequence: GLYMA01G38580.1 (Glycine max), 5'ss of exon 23
lower sequence: GRMZM2G325285_T01 (Zea mays), 5'ss of exon 12
GGGATCCGACCCTTGCTGTTGTTGCTTACCGAAGAGGGCAATGTGATGATGAGCTTGTTAATGTTACTAATAAAAATTCCTTGTTCAAACTTCAAGCAAGgtgtgtactgtgagcttcagcaggaagttgtcat-tgtatttcat-atttttataatgctagtctgagacactcatgttattttctaatgtttgtgtcag-------
  ||||| || |||||||||||||||||  || | ||||| ||||| ||||| ||| |||| || ||||| || ||||| || ||||| || ||||| |||| |||| |      |   |  |  | |||| |    | |||||  || |  | |    | ||||||   ||| |  |  |  | |    ||| | | |        
--GATCCTACACTTGCTGTTGTTGCTTATAGACGTGGGCAGTGTGACGATGAACTTATTAACGTCACTAACAAGAATTCGTTATTCAAGCTGCAAGCTAGgtatgtaataatttttattgttgtgacttgtgacacctgtttcaagatgtccacatcaattgtctgacg-acttacatgttcatattgcatttatttaaaatgacag

upper sequence: GLYMA01G38580.1 (Glycine max), 5'ss of exon 23
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 23
GGGATCCGACCCTTGCTGTTGTTGCTTACCGAAGAGGGCAATGTGATGATGAGCTTGTTAATGTTACTAATAAAAATTCCTTGTTCAAACTTCAAGCAAGgtgtgtactgtgagcttcagcaggaagttgtcattgtatttcatatttttataatgctagtctgagacactcatgttattttctaatgtttgtgtcag
||||||| || ||||| |||||||||||||| ||||| || ||||||||||| ||| | |||||||| |||||||| || ||||||||||| || || |||| |||  | | |   | |     |||  ||| |||  |  ||||        |   |  | |    |  | || || |    |  | ||  | | ||
GGGATCCCACTCTTGCAGTTGTTGCTTACCGCAGAGGACAGTGTGATGATGAACTTATCAATGTTACAAATAAAAACTCTTTGTTCAAACTGCAGGCCAGgtttgt-ttatcatgctgatggttaagaggtctttgcttcacataaagcctgcagatttttattgacctattattttttcccttttttttgttattag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|193544457|gb|FK499786.1|FK499786
EST:     GAGCTTGTTAATGTTACTAATAAAAATTCCTTGTTCAAACTTCAAGCAAG                         ATATGTTGTCGAAAGGATGGACTCCGACCTCTGGGAGAAAGTTCTTAATCC
genomic: GAGCTTGTTAATGTTACTAATAAAAATTCCTTGTTCAAACTTCAAGCAAGgtgtgtactg ... tttgtgtcagATATGTTGTCGAAAGGATGGACTCCGACCTCTGGGAGAAAGTTCTTAATCC




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGATCCGACCCTTGCTGTTGTTGCTTACCGAAGAGGGCAATGTGATGATGAGCTTGTTAATGTTACTAATAAAAATTCCTTGTTCAAACTTCAAGCAAGgtgtgtactgtgagcttcagcaggaagttgtcattgtatttcatatttttataatgctagtctgagacactcatgttattttctaatgtttgtgtcag

- - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG