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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATGGCACAGATGACCACAAAAAAGGAACTCAACTTTTGGAGGTATATGCTGTAGAGATTCAAATGTACACAGAGACCAAGAACAACAAAAAACTTAAGgtcaggatttcttttacagaagaaactcttgttcttgcatgacttaagtaattatgtcttttcaattgcttttagtgtgtttgcctgcaatttatcattg...

Basic information

species Glycine max
transcript GLYMA05G14170.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G14170.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os01g17180.1 (Oryza sativa), 5'ss of exon 6
AGATGGCACAGATGACCACAAAAAAGGAACTCAACTTTTGGAGGTATATGCTGTAGAGATTCAAATGTACACAGAGACCAAGAACAACAAAAAACTTAAGgtcaggatttcttttacagaagaaactcttgttcttgcatgact-taagtaattatgtcttttcaattgcttttagtgtgtttgcctgcaatttatcattg
||||||  | ||||| || || ||||| || ||||||||||| || |||||| | ||||| ||||||||||| || || ||||||||||||||| | ||||| ||   |  | | |        || | || |  |    || |  | || | ||    |    | ||  | | ||| | ||   |   | |  |  | | 
AGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAATGTACACTGAAACAAAGAACAACAAAAAATTGAAGgtaagacatattgtcagtctttttacacgtgattattttggattacaggttactactgttcaagattttgtgtcagtttcttgttcaatattgcagtact-

upper sequence: GLYMA05G14170.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv08s0040g00430.t01 (Vitis vinifera), 5'ss of exon 6
AGATGGCACAGATGACCACAAAAAAGGAACTCAACTTTTGGAGGTATATGCTGTAGAGATTCAAATGTACACAGAGACCAAGAACAACAAAAAACTTAAGgtcaggatttcttttacagaagaaactcttgttcttgcatgacttaagtaattatgtcttttcaattgcttttagtgtgtttgcctgcaatttatcattg-
|||||| |||||||| || || |||||||| ||||||||||| ||||||||  | |||||||||||||| || ||||||||||| ||||||||||| ||||||||| ||||||  |  |        | | ||  |   | | | |  |  ||  ||  |||    |  || ||  || |||   | | ||   | |    
AGATGGTACAGATGATCAAAAGAAAGGAACCCAACTTTTGGAAGTATATGCAATTGAGATTCAAATGTATACTGAGACCAAGAATAACAAAAAACTCAAGgtcagggtttcttgaat-gtttgtttccatattgatttgtaaatcatttttttcagtaattttgtatatttctatagtatttaagttccatgagttaaaat

upper sequence: GLYMA05G14170.1 (Glycine max), 5'ss of exon 6
lower sequence: PP1S124_47V6.1 (Physcomitrella patens), 5'ss of exon 6
AGATGGCACAGATGACCACAAAAAAGGAACTCAACTTTTGGAGGTATATGCTGTAGAGATTCAAATGTACACAGAGACCAAGAACAACAAAAAACTTAAGgtca--------ggatttcttttacagaagaaactcttgttcttgcatgacttaagtaattatgtcttttcaattgcttttagtgtgtttgcctgcaatttatcattg
|||||| ||||||||||| || || || || ||| |  ||||||| |||||  |||||||||| ||||| |||||||||||||||||||| || || ||||| |        || |  || ||| ||   |     || | |||  | ||   || | |||||||  ||| |  | ||   | | |   |   |       |||||| 
AGATGGTACAGATGACCAGAAGAAGGGCACACAATTGCTGGAGGTGTATGCGATAGAGATTCAGATGTATACAGAGACCAAGAACAACAAGAAGCTCAAGgttatttcaactggctccctgttatagtctatcgcattctgcttagacgaaacaatttattatgttcttttagct-ctcccactataaatcttta------atcatt-

upper sequence: GLYMA05G14170.1 (Glycine max), 5'ss of exon 6
lower sequence: PP1S105_216V6.1 (Physcomitrella patens), 5'ss of exon 6
AGATGGCACAGATGACCACAAAAAAGGAACTCAACTTTTGGAGGTATATGCTGTAGAGATTCAAATGTACACAGAGACCAAGAACAACAAAAAACTTAAGgtcag-------gatttcttttacagaag-----------aaactcttgt------tcttgcatgacttaagtaattatgtcttttcaattgcttttagtgtgtttg--cctgcaatttatcattg-------------------------------------------------------------
|||||||||||||||||| || || || || || ||  |||| || |||||  | || ||||| ||||| |||||||| ||||||||||||||||||||||| ||       ||   |||  |  |||            || ||||  |      ||| |    ||| ||  |||||  | ||     |||   ||   |   | |   ||  || |  | | ||                                                             
AGATGGCACAGATGACCAGAAGAAGGGCACGCAGCTGCTGGAAGTTTATGCGATTGAAATTCAGATGTATACAGAGACTAAGAACAACAAAAAACTTAAGgttagttcaagtgaaaccttcaattgaaattctgtgacctaagctctgctaccagatctagtggaactaaaaaaattaattattcattcttgacattgtagcaataggatctcgaagtcgttagtgttggaatctcgtatattggtataagagttagtatttattctttttagcgtgaaccttgcag

upper sequence: GLYMA05G14170.1 (Glycine max), 5'ss of exon 6
lower sequence: PP1S90_192V6.1 (Physcomitrella patens), 5'ss of exon 6
AGATGGCACAGATGACCACAAAAAAGGAACTCAACTTTTGGAGGTATATGCTGTAGAGATTCAAATGTACACAGAGACCAAGAACAACAAAAAACTTAAGgtcag---gatttcttttacagaagaaact---cttgttcttgcatgacttaagtaattatgtctt-ttcaattgcttttagtgtgtttgcctgcaatttatcattg-----------------------------------------------------------------------------------------
|||||| |||||||| || || || || || ||| |  | ||||| |||||  |||||||||| ||||| |||||||||||||||||||| || || |||||       |     ||  ||   | |      |||||| |    |||   ||  | |||| |  | || ||    | |||   |     |   |||    |||||                                                                                          
AGATGGTACAGATGATCAGAAGAAGGGCACACAATTGCTCGAGGTTTATGCGATAGAGATTCAGATGTATACAGAGACCAAGAACAACAAGAAGCTCAAGgttttttcaaccagattcccacgtgcagtctaccttgttttgatttgatgaaacaatttatattctgtttaagccgtgttatcataggatctctcaacccttcattttcggtgtcaaaatttatagttgtgggtaagtggttaatatgtttactttttagggtttgtgctgattctctctggtataaactttgcag

upper sequence: GLYMA05G14170.1 (Glycine max), 5'ss of exon 6
lower sequence: EFJ29478 (Selaginella moellendorffii), 5'ss of exon 6
AGATGGCACAGATGACCACAAAAAAGGAACTCAACTTTTGGAGGTATATGCTGTAGAGATTCAAATGTACACAGAGACCAAGAACAACAAAAAACTTAAGgtcaggatttcttttacagaagaaactcttgttcttgcatgacttaagtaattatgtcttttcaattgcttttagtgtgtttgcctgcaatttatcattg
||||||| | ||||| || || ||||||||||| ||| |||| ||||| ||  | |||||||| |||||||| ||||| ||||||||||| || || |||||    ||    ||      |  |  | ||| |    |  | | | ||                                                    
AGATGGCTCTGATGATCAGAAGAAAGGAACTCAGCTTCTGGAAGTATACGCCATTGAGATTCAGATGTACACGGAGACAAAGAACAACAAGAAGCTAAAGgtatctatgcagttctttttatgatattttgctgaacctcggcctcag----------------------------------------------------

upper sequence: GLYMA05G14170.1 (Glycine max), 5'ss of exon 6
lower sequence: EFJ28052 (Selaginella moellendorffii), 5'ss of exon 6
AGATGGCACAGATGACCACAAAAAAGGAACTCAACTTTTGGAGGTATATGCTGTAGAGATTCAAATGTACACAGAGACCAAGAACAACAAAAAACTTAAGgtcaggatttcttttacagaagaaactcttgttcttgcatgacttaagtaattatgtcttttcaattgcttttagtgtgtttgcctgcaatttatcattg
||||||| | ||||| || || ||||||||||| ||| |||| ||||| ||  | |||||||| |||||||| ||||| ||||||||||| || || |||||    ||    |||     |  |  |  |  |    |  | | | ||                                                    
AGATGGCTCTGATGATCAGAAGAAAGGAACTCAGCTTCTGGAAGTATACGCCATTGAGATTCAGATGTACACGGAGACAAAGAACAACAAGAAGCTAAAGgtatctatgcagttttttttatgatattctactgaacctcggcctcag----------------------------------------------------

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|8283183|gb|BE020744.1|BE020744
EST:     CTGTAGAGATTCAAATGTACACAGAGACCAAGAACAACAAAGAACTTAAG                         CAACTGTACCAGAAAGCACTCACTATTAAGTCAGCAATTCCGCATCCAAGG
genomic: CTGTAGAGATTCAAATGTACACAGAGACCAAGAACAACAAAAAACTTAAGgtcaggattt ... ttaaatacagCAACTTTACCAGAAAGCACTCACTATTAAGTCAGCAATTCCCCATCCAAGG
EST: gi|18690841|gb|BM519689.1|BM519689
EST:     CTGTAGAGATTCAAATGTACACAGAGACCAAGAACAACAAAAAACTTAAG                         CAACTTTACCAGAAAGCACTCACTATTAAGTCAGCAATT
genomic: CTGTAGAGATTCAAATGTACACAGAGACCAAGAACAACAAAAAACTTAAGgtcaggattt ... ttaaatacagCAACTTTACCAGAAAGCACTCACTATTAAGTCAGCAATT
EST: gi|9898913|gb|BE607881.1|BE607881
EST:     CTGTAGAGATTCAAATGTACACAGAGACCAAGAACAACAAAAAACTTAAG                         CAACTTTACCAGAAAGCACTCACTATTAAGTCAGCAATTCCCCATCCAAGG
genomic: CTGTAGAGATTCAAATGTACACAGAGACCAAGAACAACAAAAAACTTAAGgtcaggattt ... ttaaatacagCAACTTTACCAGAAAGCACTCACTATTAAGTCAGCAATTCCCCATCCAAGG
EST: gi|9899182|gb|BE608080.1|BE608080
EST:     CTGTAGAGATTCAAATGTACACAGAGACCAAGAACAACAAAAAACTTAAG                         CAACTTTACCAGAAAGCACTCACTATTAAGTCAGCAATTCCCCATCCAAGG
genomic: CTGTAGAGATTCAAATGTACACAGAGACCAAGAACAACAAAAAACTTAAGgtcaggattt ... ttaaatacagCAACTTTACCAGAAAGCACTCACTATTAAGTCAGCAATTCCCCATCCAAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATGGCACAGATGACCACAAAAAAGGAACTCAACTTTTGGAGGTATATGCTGTAGAGATTCAAATGTACACAGAGACCAAGAACAACAAAAAACTTAAGgtcaggatttcttttacagaagaaactcttgttcttgcatgacttaagtaattatgtcttttcaattgcttttagtgtgtttgcctgcaatttatcattg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaagaaa