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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGAAGTTGGACCGCTACAGGAATCCTTGGCTTGAATTGAAGATACAATATGGACAAAACAAAGGAAAGTTATACAATGAAGAATGTGACCGATTCATGgtgtgaattttatttccttttgtttttatttttgcccaaattcatttctttttgttcatgttcagttccttgtttagtctggtgttttccgaacagaattcttgtgttgtctgactttacttaaaacttgcag

Basic information

species Glycine max
transcript GLYMA17G02640.1
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G02640.1 (Glycine max), 5'ss of exon 22
lower sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 22
GAAGAAGTTGGACCGCTACAGGAATCCTTGGCTTGAATTGAAGATACAATATGGACAAAACAAAGGAAAGTTATACAATGAAGAATGTGACCGATTCATGgtgtgaattttatttccttttgtttttatttttgcccaaattcatttctttttgttcatgttcagttccttgtttagtctggtgttttccgaacagaattcttgtgttgtctgactttacttaaaacttgcag
||||||||| |||||||||| ||| || ||| | || ||||| || |||||||| ||||| ||||| ||||| || ||||| ||||||||||| || ||||| ||     |    | | || | ||||| | ||    | | ||| |  | |     | | |  ||  |   ||    ||  ||  |   | ||| |   ||||  |                          
GAAGAAGTTAGACCGCTACAAGAACCCATGGTTAGAGTTGAAAATTCAATATGGCCAAAATAAAGGGAAGTTCTATAATGAGGAATGTGACCGCTTTATGgtatgttccct-caccatattatgtttatctatgt--gagtacatgttatgtctactaagctgggtgtcacattccagctt-tgcatggtgcacaaa---cttggat--------------------------

upper sequence: GLYMA17G02640.1 (Glycine max), 5'ss of exon 22
lower sequence: AT3G06400.3 (Arabidopsis thaliana), 5'ss of exon 22
GAAGAAGTTGGACCGCTACAGGAATCCTTGGCTTGAATTGAAGATACAATATGGACAAAACAAAGGAAAGTTATACAATGAAGAATGTGACCGATTCATGgtgtgaattttatttccttttgtttttatttttgcccaaattcatttctttttgttcatgttcagttccttgtttagtctggtgttttccgaacagaattcttgtgttgtctgactttacttaaaacttgcag
||||||  |||| |||||||| || |||||||| ||| ||||||| |||||||| || |||||||| ||| | ||||||||||| |||||||| |||||||| ||  ||||      | | ||||   |||||||     |   | || ||   |  ||  | |  |  |||  |  |  ||   |||        ||  |                                
GAAGAAACTGGATCGCTACAGAAACCCTTGGCTGGAACTGAAGATTCAATATGGTCAGAACAAAGGCAAGCTGTACAATGAAGAGTGTGACCGTTTCATGgtatgtctttt------tctcgtttccctttttgct--gttctgtctcattaattatatcatgaagtttttgactgttgaggaactttggtggtgaaaaacag------------------------------

upper sequence: GLYMA17G02640.1 (Glycine max), 5'ss of exon 22
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 5'ss of exon 22
GAAGAAGTTGGACCGCTACAGGAATCCTTGGCTTGAATTGAAGATACAATATGGACAAAACAAAGGAAAGTTATACAATGAAGAATGTGACCGATTCATGgtgtgaattttatttccttttgtttttatttttgcccaaattcatttctttttgttcatgttcagttccttgtttagtctggtgttttccgaacagaattcttgtgttgtctgactttacttaaaacttgcag
||||||  |||| |||||||| || || ||||| ||| ||||||| |||||||| || |||||||| ||| | ||||||||||| || ||||| |||||||| |||  | |||||       |     | ||||   | |||   || || |||||  | |||           || | || | ||  ||  |  ||| |  ||  || || |                    
GAAGAAACTGGATCGCTACAGAAACCCGTGGCTGGAACTGAAGATTCAATATGGTCAGAACAAAGGGAAGCTGTACAATGAAGAGTGCGACCGTTTCATGgtatgacatctattt------atcaaactctttgttgagatttcattgttattgttt-tattc-----------taatatgatattgacccgat-gaacttgtg-attatcag--------------------

upper sequence: GLYMA17G02640.1 (Glycine max), 5'ss of exon 22
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 5'ss of exon 22
GAAGAAGTTGGACCGCTACAGGAATCCTTGGCTTGAATTGAAGATACAATATGGACAAAACAAAGGAAAGTTATACAATGAAGAATGTGACCGATTCATGgtgtgaattttatttccttttgtttttatttttgcccaaat--tcatttctttttgttc-atgttcagttccttgtttagtctggtgttttccgaacagaattcttgtgttgtctgactttacttaaaacttgcag
|||||||||||| ||||||| |||||| ||||| ||| | ||||| || ||||| ||||||||||| ||||| |||||||||||||| || || || |||||| |||||  | |    | | |  ||  |||    |||||  |  | | ||||||||  | | |   |     |  |    |  ||  | |     | | ||| |||                            
GAAGAAGTTGGATCGCTACAAGAATCCATGGCTGGAACTAAAGATCCAGTATGGGCAAAACAAAGGGAAGTTGTACAATGAAGAATGCGATCGTTTTATGgtgagaattgcaatcatctctctagtttgtttgatacaaatgttggtgtgtttttgtttgacgattgatcttccgagtgtattcatgcctcc-----atacttcatgtag--------------------------

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|193594415|gb|FK545434.1|FK545434
EST:     ATGGACAAAACAAAGGGAAGTTATACAATGAAGAATGTGACCGATTCATG                         ATTTGTATGATTCACAAACTTGGCTATGGTAATTGGGATGAGTTGAAGGCA
genomic: ATGGACAAAACAAAGGAAAGTTATACAATGAAGAATGTGACCGATTCATGgtgtgaattt ... aaacttgcagATATGTATGATTCACAAACTTGGCTATGGTAATTGGGATGAGTTGAAGGCA
EST: gi|23734541|gb|BU765507.1|BU765507
EST:     ATGGACAAAACAAAGGAAAGTTATACAATGAAGAATGTGACCGATTCATG                         ATATGTATGATTCACAAACTTGGCTATGGTAATTGGGATGAGTTGAAGGCA
genomic: ATGGACAAAACAAAGGAAAGTTATACAATGAAGAATGTGACCGATTCATGgtgtgaattt ... aaacttgcagATATGTATGATTCACAAACTTGGCTATGGTAATTGGGATGAGTTGAAGGCA
EST: gi|13790494|gb|BG653094.1|BG653094
EST:     GGAAAGTTATACAATGAAGAATGTGACCGATTCATG                         ATATGTATGATTCACAAACTTGGCTATGGTAATTGGGATGAGTTGAAGGCA
genomic: GGAAAGTTATACAATGAAGAATGTGACCGATTCATGgtgtgaattt ... aaacttgcagATATGTATGATTCACAAACTTGGCTATGGTAATTGGGATGAGTTGAAGGCA
EST: gi|193367197|gb|FK330315.1|FK330315
EST:     ATGGACAAAACAAAGGAAAGTTATACAATGAAGAATGTGACCGATTCATG                         ATATGTATGATTCACAAACTTGGCTATGGTAAATTGGGATGAG
genomic: ATGGACAAAACAAAGGAAAGTTATACAATGAAGAATGTGACCGATTCATGgtgtgaattt ... aaacttgcagATATGTATGATTCACAAACTTGGCTATGGTAA-TTGGGATGAG
EST: gi|208242340|gb|GE043298.1|GE043298
EST:     GAAAGTTATACAATGAAGAATGTGACCGATTCATG                         ATATGTATGATTCACAAACTTGGCTATGGTAATTGGGA
genomic: GAAAGTTATACAATGAAGAATGTGACCGATTCATGgtgtgaattt ... aaacttgcagATATGTATGATTCACAAACTTGGCTATGGTAATTGGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGAAGTTGGACCGCTACAGGAATCCTTGGCTTGAATTGAAGATACAATATGGACAAAACAAAGGAAAGTTATACAATGAAGAATGTGACCGATTCATGgtgtgaattttatttccttttgtttttatttttgcccaaattcatttctttttgttcatgttcagttccttgtttagtctggtgttttccgaacagaattcttgtgttgtctgactttacttaaaacttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA