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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCAGGTGCTTTTAAAATTGGTGACACAGCTGGAACAATTGACAATATAATTCAGTGCAAGCTCTACAGGCCTGGATCTGTTGGATTTGTTTCTAAATCTgtatgttgttatttacttcttactcatgtttatgtcatcttcgcattggggatacactttttcttctagtaccactataaagcttttgataatgccaacc...

Basic information

species Glycine max
transcript GLYMA09G04000.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G04000.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os01g19450.2 (Oryza sativa), 5'ss of exon 6
AGCAGGTGCTTTTAAAATTGGTGACACAGCTGGAACAATTGACAATATAATTCAGTGCAAGCTCTACAGGCCTGGATCTGTTGGATTTGTTTCTAAATCTgtatgttgttatttacttcttactcatgtttatgtcatcttcgcattggggatacactttttcttctagtaccactataaagcttttgataatgccaacc------
||| |||||||| || |||||||| || |||||||| |||||||| || ||||| |||||||| |||||||||||||||||||| |||||||||||||| |||||   ||||||  || ||      ||| | ||  | |   ||   |  ||  || ||   | ||| | |   |  | |       |  || | |         
AGCTGGTGCTTTCAAGATTGGTGATACTGCTGGAACCATTGACAACATTATTCAATGCAAGCTTTACAGGCCTGGATCTGTTGGCTTTGTTTCTAAATCGgtatgcatttatttgattttt------gttaaagttgtttgtacaaaagaaatttaccttccgtactatttctgatccataaaaaggcaatattctatttttaaaa

upper sequence: GLYMA09G04000.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G033226_T01 (Zea mays), 5'ss of exon 6
AGCAGGTGCTTTTAAAATTGGTGACACAGCTGGAACAATTGACAATATAATTCAGTGCAAGCTCTACAGGCCTGGATCTGTTGGATTTGTTTCTAAATCTgta-tgttgttatttacttcttactcatgtttatgtcatcttcgcattggggatacactttttcttctagtaccactataaagcttttgataatgccaacc
||| |||||||| || |||||||| || |||||||| ||||| || ||||||||||||||||| |||||||||||||||||||| ||||| |||||||| ||| ||   ||||    ||||| |   | |||   |    |    ||     | |                                              
AGCTGGTGCTTTCAAGATTGGTGATACCGCTGGAACCATTGATAACATAATTCAGTGCAAGCTTTACAGGCCTGGATCTGTTGGTTTTGTGTCTAAATCGgtactgcctttataccattctttcat-tatttggtttgcttgtctatatacaacag---------------------------------------------

upper sequence: GLYMA09G04000.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G002416_T01 (Zea mays), 5'ss of exon 1
AGCAGGTGCTTTTAAAATTGGTGACACAGCTGGAACAATTGACAATATAATTCAGTGCAAGCTCTACAGGCCTGGATCTGTTGGATTTGTTTCTAAATCTgtatgttgttatttacttcttactcatgtttatgtcatcttcgcattggggatacactttttcttctagtaccactataa-agcttttgataatgccaacc----
                                                          ||||| |||||||||||||||||||| ||||| |||||||| |||   ||   ||||| | |      |  ||  || | ||| |  ||| | || |  |    |  | ||  |    | || | |     | |    ||  |    
----------------------------------------------------------AAGCTTTACAGGCCTGGATCTGTTGGTTTTGTGTCTAAATCGgtaa--tgccttttacctttagactgttctttcgtta-ctttgt-ttgtgtat-ctttacaacagcaagagcaggaacaacacccccccacacccacacacacaa

upper sequence: GLYMA09G04000.1 (Glycine max), 5'ss of exon 6
lower sequence: AT3G06650.1 (Arabidopsis thaliana), 5'ss of exon 6
AGCAGGTGCTTTTAAAATTGGTGACACAGCTGGAACAATTGACAATATAATTCAGTGCAAGCTCTACAGGCCTGGATCTGTTGGATTTGTTTCTAAATCTgtatgt----tgttatttacttcttactcatgtttatgtcatcttcgcattggggatacactttttcttctagtaccactataaagcttttgataatgccaacc--------
||| || || |||||||||||||||||||||||||| ||||||||||| || || |||||| | |||||||||||||||||||| ||||| || |||||||||||     ||    ||  || || | ||| ||   |||  | |    |   |  ||  || |||    |  ||     | |     |||   | |  | |          
AGCTGGAGCCTTTAAAATTGGTGACACAGCTGGAACTATTGACAATATCATCCAATGCAAGTTGTACAGGCCTGGATCTGTTGGCTTTGTCTCAAAATCTgtatgagctgtggagattgtttttttcgcattttgtagtctacctaagctcatgattatcctcttttgaatcttaatctgagagtttatttctcattcactattttctatag

upper sequence: GLYMA09G04000.1 (Glycine max), 5'ss of exon 6
lower sequence: AT5G49460.1 (Arabidopsis thaliana), 5'ss of exon 6
AGCAGGTGCTTTTAAAATTGGTGACACAGCTGGAACAATTGACAATATAATTCAGTGCAAGCTCTACAGGCCTGGATCTGTTGGATTTGTTTCTAAATCTgtatgttgttatttacttcttactcatg-tttatgtcatcttcgcattggggatacactttttcttctagtaccactataaagcttttgataatgccaacc
||| || || ||||| |||||||| || || ||||||||||| || || || ||||||||||| ||||| |||||||||||||| ||||| || ||||||||||||  | ||||         ||||  | |   | |   || | |||  |    |   |||  |    |||   | |     ||     |         
AGCTGGAGCCTTTAAGATTGGTGATACTGCAGGAACAATTGATAACATTATCCAGTGCAAGCTATACAGACCTGGATCTGTTGGTTTTGTCTCCAAATCTgtatgtgctgattttgcaaaatttcataatctgcctaaagctcactttgatgtctgagagttttattcgttactcttct----tttcccgcag--------

upper sequence: GLYMA09G04000.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv05s0077g00950.t01 (Vitis vinifera), 5'ss of exon 6
AGCAGGTGCTTTTAAAATTGGTGACACAGCTGGAACAATTGACAATATAATTCAGTGCAAGCTCTACAGGCCTGGATCTGTTGGATTTGTTTCTAAATCTgtatgttgttatttact---tcttactcatgtttatgtcatcttcgcattggggatacactttttcttctagtaccactataaagcttttgataa-tgccaacc
||| || || ||||| || || ||||| || ||||||||||| ||||| ||||||| ||| || ||||||||||| |||||||| |||||||||||||||||| ||  |||||   |     ||| |    || ||  ||| ||     ||   | |  ||  ||||        ||||  || |  | || ||| ||   |  
AGCTGGAGCCTTTAAGATAGGGGACACTGCAGGAACAATTGATAATATCATTCAGTCCAAACTTTACAGGCCTGGCTCTGTTGGTTTTGTTTCTAAATCTgtacgtatttattcgttgaactttatttgctttgattccatatttcttatgtaaaaaacctggttcta--gccttcactgaaatgaatatggtaactggtga--

upper sequence: GLYMA09G04000.1 (Glycine max), 5'ss of exon 6
lower sequence: PP1S46_63V6.2 (Physcomitrella patens), 5'ss of exon 6
AGCAGGTGCTTTTAAAATTGGTGACACAGCTGGAACAATTGACAATATAATTCAGTGCAAGCTCTACAGGCCTGGATCTGTTGGATTTGTTTCTAAATCTgtatgttgttatttacttcttactcatgtttat-gtcatcttcgcattgggg-atacactttttcttctagtaccactataaagcttttgataatgccaacc
 || ||||| || ||||||||||| || || || ||  | |||||||| ||||| |||||||| || || |||||||||||||| ||||| |||||||| ||| |      ||| | || ||| |||  || | |  |     ||| ||    ||   | |       | |  |    || ||     || | | | || | 
GGCTGGTGCATTCAAAATTGGTGATACTGCAGGCACGTTGGACAATATCATTCACTGCAAGCTTTATAGACCTGGATCTGTTGGGTTTGTGTCTAAATCAgtaagca--cgttttcctcgtacccattcttttagataaggctgcagtgaaacatgtgcatggcacgtttgctcgtgaattaactgagtgttcaagacagct

upper sequence: GLYMA09G04000.1 (Glycine max), 5'ss of exon 6
lower sequence: PP1S35_384V6.1 (Physcomitrella patens), 5'ss of exon 6
AGCAGGTGCTTTTAAAATTGGTGACACAGCTGGAACAATTGACAATATAATTCAGTGCAAGCTCTACAGGCCTGGATCTGTTGGATTTGTTTCTAAATCTgtatg----------ttgttattt-acttcttactcatg--------tttatgtcatct------tcgcattggggatacactttttctt--ctagtaccactataaagcttttgataatgccaacc---------------------------------------------------------------
 || ||||| || ||||||||||| ||||| || ||| | ||||| || || || ||||| || ||||| |||||||| ||||||||||| |||||||| ||| |          ||  |||   |||| |   |||||        ||  |||||  |      | |||   || |   || |    ||  | || |  | | |  | ||  |  ||    |                                                                   
GGCTGGTGCATTCAAAATTGGTGATACAGCCGGCACATTGGACAACATCATCCACTGCAAACTTTACAGACCTGGATCCGTTGGATTTGTATCTAAATCAgtacgatcacctaccttactatacgacttttcgatcatgggtgttgattggtgtcaattgagtagttgcaaaaggaaaggacctgcatttggcgagcaaaaatcttcaactcattctaggagctgtttatattggagtgtatctgtgcacaagggttttcactaattagacttcgtgtattgttgaacag

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|9820923|gb|BE556433.1|BE556433
EST:     TTCAGTGCAAGCTCTACAGGCCTGGATCTGTTGGATTTGTTTCTAAATCT                         GGTGGGATGTCCAATGAACTATACAACACTATTGCCCGCGTAACTGATGGG
genomic: TTCAGTGCAAGCTCTACAGGCCTGGATCTGTTGGATTTGTTTCTAAATCTgtatgttgtt ... taaattacagGGTGGGATGTCCAATGAACTATACAACACTATTGCCCGCGTAACTGATGGG
EST: gi|193372338|gb|FK338355.1|FK338355
EST:     TTTCTAAATCT                         GGTGGGATGTCCAATGAACTCTACAACACTATTGCCCGTGTAACTGATGGG
genomic: TTTCTAAATCTgtatgttgtt ... taaattacagGGTGGGATGTCCAATGAACTATACAACACTATTGCCCGCGTAACTGATGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCAGGTGCTTTTAAAATTGGTGACACAGCTGGAACAATTGACAATATAATTCAGTGCAAGCTCTACAGGCCTGGATCTGTTGGATTTGTTTCTAAATCTgtatgttgttatttacttcttactcatgtttatgtcatcttcgcattggggatacactttttcttctagtaccactataaagcttttgataatgccaacc

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT