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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCTATGCACAAGGTCAATTTCGACGCCAAGAGCGAGTATGAGATGATTCAGAACTACAAGGTCCTTCAAGATGTCTTCAATAAACTCAAAATCACCAAGgtaacactctccctctgtattttaattttggacgatcttgaattcaattactgaattgctcgttgtgtttctcag

Basic information

species Glycine max
transcript GLYMA01G39720.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G39720.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os10g35580.1 (Oryza sativa), 5'ss of exon 2
GCCTATGCACAAGGTCAATTTCGACGCCAAGAGCGAGTATGAGATGATTCAGAACTACAAGGTCCTTCAAGATGTCTTCAATAAACTCAAAATCACCAAGgta-------------acactctccctctgtattttaattttggacgatcttgaattcaattactgaattgctcgttgtgtttctcag-------------
||| |||||||||||||| |||||||||||||  ||||| |||||||| ||||||||||| || ||||| || |||||||| || ||||| |||||||||||              |  |   ||| |   ||| |  |      ||      |||     | | | |   |   | ||||  || |              
GCCGATGCACAAGGTCAACTTCGACGCCAAGACGGAGTACGAGATGATCCAGAACTACAAAGTTCTTCAGGACGTCTTCAACAAGCTCAAGATCACCAAGgtgcggccggtttctgattcctacccccctaattcttctccccaccgtgagcaaatcttggttccgtac-acctatcgtgtagctgatttgggcgcgtttg

upper sequence: GLYMA01G39720.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G163409_T01 (Zea mays), 5'ss of exon 2
GCCTATGCACAAGGTCAATTTCGACGCCAAGAGCGAGTATGAGATGATTCAGAACTACAAGGTCCTTCAAGATGTCTTCAATAAACTCAAAATCACCAAGgtaa------------------cactctccctctgtatt-ttaattttggacgatcttgaattcaattactgaa-ttgctcgttgtgtttctcag--------------------------------------------------------
||| |||||||||||||| |||||||||||||  ||||| || ||||| ||||||||||||||||| || ||||| ||||| || ||||| ||||| ||||| |                  | | || |   |||          | |||   | || | || | || ||||| | | | |   ||   |   |                                                        
GCCGATGCACAAGGTCAACTTCGACGCCAAGACGGAGTACGACATGATCCAGAACTACAAGGTCCTGCAGGATGTGTTCAACAAGCTCAAGATCACTAAGgtgaatcacggctttggtttctcgcccttctcttgtgccgcccgcatgggattttttttattttattttctgaaatcgattgaactgccccatcgtgttttgttgctaatatgatcttatttttgttgttttctctgttaatttggcgcag

upper sequence: GLYMA01G39720.1 (Glycine max), 5'ss of exon 2
lower sequence: AT5G67270.1 (Arabidopsis thaliana), 5'ss of exon 2
GCCTATGCACAAGGTCAATTTCGACGCCAAGAGCGAGTATGAGATGATTCAGAACTACAAGGTCCTTCAAGATGTCTTCAATAAACTCAAAATCACCAAGgtaacactctccct--ctgtatttt----aattttggacgatcttgaattca--------attactgaattg--ctcgttgtgtttctcag---------
 || ||||||||||| || || || || ||||| || |||||||||||||||||||| ||||| ||||| ||||| || ||||||||||| ||||| |||||     |    ||  ||  |||||     ||||| |  | | || | |  |        || |  ||| ||   | |||  |||  |  |         
TCCGATGCACAAGGTTAACTTTGATGCGAAGAGTGAATATGAGATGATTCAGAACTATAAGGTTCTTCAGGATGTGTTTAATAAACTCAAGATCACTAAGgtcctctttcttcttccttcatttttatcgatttttgggggttttaattcgaggaggcatataatagaactgactttgtttggttaatttggttgtgtag

upper sequence: GLYMA01G39720.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv07s0129g01080.t01 (Vitis vinifera), 5'ss of exon 2
GCCTATGCACAAGGTCAATTTCGACGCCAAGAGCGAGTATGAGATGATTCAGAACTACAAGGTCCTTCAAGATGTCTTCAATAAACTCAAAATCACCAAGgtaacactctccctctgtattttaattttggacgatcttgaattcaatt--actgaattgctcgttgtgtttctcag-----------------------
 || |||||||| |||||||| || ||||||| |||||| |||||||| ||||| |||||||| |||||||| |||||||| |||||||  ||||||||||||   |||||  |    | |||  |   ||   || ||   |||  ||   |||  ||    |        |  ||                       
TCCCATGCACAAAGTCAATTTTGATGCCAAGAACGAGTACGAGATGATCCAGAATTACAAGGTTCTTCAAGACGTCTTCAACAAACTCAGGATCACCAAGgtatatctctcttttcaaaatttgttacaggggaattttcttttctgttccgctgttttctcagcaaccaaacggaggctaaggatgagagggatttttt

upper sequence: GLYMA01G39720.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ09412 (Selaginella moellendorffii), 5'ss of exon 3
GCCTATGCACAAGGTCAATTTCGACGCCAAGAGCGAGTATGAGATGATTCAGAACTACAAGGTCCTTCAAGATGTCTTCAATAAACTCAAAATCACCAAGgtaacactctccctctgtattttaattttggacgatcttgaattcaattactgaattgctcgttgtgtttctcag
             || || | |||||| |||| ||| ||||| ||||| |||||||||||||| || || ||||| ||||| ||||||||||||| |||||||| |    |  || | ||   |  |   ||  ||||  | ||   | |  || |||   |             
-------------GTGAACTACGACGCTAAGAACGAATATGAAATGATACAGAACTACAAGGTTCTCCAGGATGTTTTCAACAAACTCAAAATCAGCAAGgtaaaa---gcagtcggaat---agatcgtgagaatctaaagtttg-tgaacgatttggcag-------------

upper sequence: GLYMA01G39720.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ12535 (Selaginella moellendorffii), 5'ss of exon 3
GCCTATGCACAAGGTCAATTTCGACGCCAAGAGCGAGTATGAGATGATTCAGAACTACAAGGTCCTTCAAGATGTCTTCAATAAACTCAAAATCACCAAGgt-aacactctccctctgtattttaattttggacgatcttgaattcaattactgaattgctcgttgtgtttctcag
             || ||||| || || |||| ||||||||||||||| ||||||||||| || || ||||| || ||||| || || || || | ||||||     |||   |||     ||      |  ||  |   |  || |  ||| |                      
-------------GTGAATTTTGATGCGAAGAACGAGTATGAGATGATACAGAACTACAAAGTTCTCCAAGAGGTTTTCAACAAGCTTAAGATAAGCAAGgttggttctcatgctcgagtattcgggagttcactctggagcttttatctacag----------------------

upper sequence: GLYMA01G39720.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ10236 (Selaginella moellendorffii), 5'ss of exon 3
GCCTATGCACAAGGTCAATTTCGACGCCAAGAGCGAGTATGAGATGATTCAGAACTACAAGGTCCTTCAAGATGTCTTCAATAAACTCAAAATCACCAAGgt-aacactctccctct-gtattttaattttggacgatcttgaattcaattactgaattgctcgttgtgtttctcag
             || ||||| || || |||| ||||||||||||||| ||||||||||| || || ||||| || ||||| || ||||| || | ||||||     |||   |||  ||||||      |  ||  |      || |  ||| |                      
-------------GTGAATTTTGATGCGAAGAACGAGTATGAGATGATACAGAACTACAAAGTTCTCCAAGAGGTTTTCAACAAGCTCAAGATAAGCAAGgttggttctcatgctcgagtatttcgggaattcactctggaacttttatctacag----------------------

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|151393328|gb|EV263203.1|EV263203
EST:     AGAACTACAAGGTCCTTCAAGATGTCTTCAATAAACTCAAAATCACCAAG                         CACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAG
genomic: AGAACTACAAGGTCCTTCAAGATGTCTTCAATAAACTCAAAATCACCAAGgtaacactct ... tgtttctcagCACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAG
EST: gi|208269719|gb|GE072155.1|GE072155
EST:     AGAACTACAAGGTCCTTCAAGATGTCTTCAATAAACTCAAAATCACCAAG                         CACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAG
genomic: AGAACTACAAGGTCCTTCAAGATGTCTTCAATAAACTCAAAATCACCAAGgtaacactct ... tgtttctcagCACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAG
EST: gi|192301066|gb|FG987991.1|FG987991
EST:     AGAACTACAAGGTCCTTCAAGATGTCTTCAATAAACTCAAAATCACCAAG                         CACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAG
genomic: AGAACTACAAGGTCCTTCAAGATGTCTTCAATAAACTCAAAATCACCAAGgtaacactct ... tgtttctcagCACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAG
EST: gi|208289796|gb|GE088888.1|GE088888
EST:     AGAACTACAAGGTCCTTCAAGATGTCTTCAATAAACTCAAAATCACCAAG                         CACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAG
genomic: AGAACTACAAGGTCCTTCAAGATGTCTTCAATAAACTCAAAATCACCAAGgtaacactct ... tgtttctcagCACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAG
EST: gi|192296790|gb|FG993088.1|FG993088
EST:     AGAACTACAAGGTCCTTCAGGATGTCTTCAATAAACTCAAAATCACCAAG                         CACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAG
genomic: AGAACTACAAGGTCCTTCAAGATGTCTTCAATAAACTCAAAATCACCAAGgtaacactct ... tgtttctcagCACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCTATGCACAAGGTCAATTTCGACGCCAAGAGCGAGTATGAGATGATTCAGAACTACAAGGTCCTTCAAGATGTCTTCAATAAACTCAAAATCACCAAGgtaacactctccctctgtattttaattttggacgatcttgaattcaattactgaattgctcgttgtgtttctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG