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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggaccagaggaactgaaacattatgaataccttgttaccagtagaatggttctccaagtttctagtttcttaatgcatgctagtttcttatgagatgttttatacagATGATGCAGAATCTGCTTTTGCAAGAGGGAGACATCGTAAGAGTGAAATTCGTATCACTTCCAAAGGGAACATATGTTAAATTACAGCCACACACAAAGG

Basic information

species Glycine max
transcript GLYMA04G00980.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G00980.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G037185_T01 (Zea mays), 3'ss of exon 5
gtaggaccagaggaactgaaacattatgaataccttgttaccagtagaatggttctccaagtttctagtttcttaatgcatgctagtttcttatgagatgttttatacagATGATGCAGAATCTGCTTTTGCAAGAGGGAGACATCGTAAGAGTGAAATTCGTATCACTTCCAAAGGGAACATATGTTAAATTACAGCCACACACAAAGG
                              ||  |    | |  ||| ||| |  | ||  | | ||  |  | |   ||    || |   | |  |  || ||   ||||||||||| ||||| ||||||||||||||||| || ||     | |||   |     || || ||||| |||||||| || || ||||| || ||||  |
-----------------------------gtatgtcaagatc--taggatgctgttgcacttctttatatcatcatgtcaacgaagctaactttacgtggtctt---cagATGATGCAAAATCTTCTTTTGCAAGAGGGAGATATGGTGTTCATAAAAAATGCCAACCTCCCCAAGGGCACATATGTGAAGTTGCAGCCTCATACAACAG

upper sequence: GLYMA04G00980.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G38930.2 (Arabidopsis thaliana), 3'ss of exon 6
gtaggaccagaggaactgaaacattatgaataccttgttaccagtagaatggttctccaagtttctagtttcttaatgcatgctagtttcttatgagatgttttatacagATGATGCAGAATCTGCTTTTGCAAGAGGGAGACATCGTAAGAGTGAAATTCGTATCACTTCCAAAGGGAACATATGTTAAATTACAGCCACACACAAAGG
           | |||  ||||| ||        || | |||| || || | | ||| |  | ||| ||  |||||       |  || ||| ||            ||||||||||||||| |||| |||||||| |||||||| || ||||| | |   ||  | |||||||||||||| || || ||| | || || |||||||  |
-----------gtaac--aaacagtagcttgtttttatcaccaatacaa-gatactcga--tatcttgtgacttaaaatcgattgtttgcttttg------------cagATGATGCAGAATTTGCTGTTGCAAGAAGGAGACATGGTGAGAGTTAGAAATGTCACTCTTCCAAAGGGAACCTACGTGAAACTGCAACCCCACACAACAG

upper sequence: GLYMA04G00980.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G21270.3 (Arabidopsis thaliana), 3'ss of exon 6
gtaggaccagaggaactgaaacattatgaataccttgttaccagtagaatg--gttctccaagtt-tctagtttcttaatgcatgctagtttcttatgagatgttttatacagATGATGCAGAATCTGCTTTTGCAAGAGGGAGACATCGTAAGAGTGAAATTCGTATCACTTCCAAAGGGAACATATGTTAAATTACAGCCACACACAAAGG
                 | || | |     | |||  ||    ||  |  |  || |||    |  | | |  |    |  |    |  || ||| |  ||| |   || ||||||||||||||||||||  ||||||| |||||||| || ||||| | |   ||  | |||||||||||||| || |||||| ||||||| |||||||  |
-----------------gtaagaat-cagtttcctctttgtttgtgaatcgaagtactctggatcatgtggacttaccagactgattgtttgcttctttgatat--aatccagATGATGCAGAATCTGCTGCTGCAAGAAGGAGACATTGTGAGAGTTAGAAATGTCACTCTTCCAAAGGGAACTTACGTTAAACTACAGCCCCACACAACAG

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|23051392|gb|BU577079.1|BU577079
EST:     GGGTTCTGGAGTTCATTGCAGATGAAGGAACTATATATATGCCATACTGG                         ATGATGCAGAATCTGCTTTTGCAAGAGGGAGACATCGTAAGAGTGAAATTC
genomic: GGGTTCTGGAGTTCATTGCAGATGAAGGAACTATATATATGCCATACTGGgtaggaccag ... ttttatacagATGATGCAGAATCTGCTTTTGCAAGAGGGAGACATCGTAAGAGTGAAATTC
EST: gi|151397776|gb|EV267649.1|EV267649
EST:     GGGTTCTGGAGTTCATTGCAGATGAAGGAACTATATATATGCCATACTGG                         ATGATGAAGAATCTGCTTTTGCAAGAGGGAGACATCGTAAGAGTGAAATTC
genomic: GGGTTCTGGAGTTCATTGCAGATGAAGGAACTATATATATGCCATACTGGgtaggaccag ... ttttatacagATGATGCAGAATCTGCTTTTGCAAGAGGGAGACATCGTAAGAGTGAAATTC
EST: gi|192302630|gb|FG994882.1|FG994882
EST:     GGGTTCTGGAGTTCATTGCAGATGAAGGAACTATATATATGCCATACTGG                         ATGATGCAGAATCTGCTTTTGCAAGAGGGAGACATCGTAAGAGTGAAATTC
genomic: GGGTTCTGGAGTTCATTGCAGATGAAGGAACTATATATATGCCATACTGGgtaggaccag ... ttttatacagATGATGCAGAATCTGCTTTTGCAAGAGGGAGACATCGTAAGAGTGAAATTC
EST: gi|213620291|gb|DB961436.1|DB961436
EST:     GGGTTCTGGAGTTCATTGCAGATGAAGGAACTATATATATGCCATACTGG                         ATGATGCAGAATCTGCTTTTGCAAGAGGGAGACATCGTAAGAGTGAAATTC
genomic: GGGTTCTGGAGTTCATTGCAGATGAAGGAACTATATATATGCCATACTGGgtaggaccag ... ttttatacagATGATGCAGAATCTGCTTTTGCAAGAGGGAGACATCGTAAGAGTGAAATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccaagtttctagtttcttaatgcatgctagtttcttatgagatgttttatacagATGATGCAGAATCTGCTTTTGCAAGAGGGAGACATCGTAAGAGTGAAATTCGTATCACTTCCAAAGGGAACATATGTTAAATTACAGCCACACACAAAGG
               tcttaat  putative branch site (score: 3)
                                          atgttttata  TA-rich tract