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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATGAAGGACTTTATGAATGAGACCAATGGCTCTGACTATGTACCCACATATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGAgtcagtgccccttcattcattcatttccttttctttctttaattatcaacctatttaatactacctttttttgacaatttcacag

Basic information

species Glycine max
transcript GLYMA20G36790.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G36790.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os12g40890.1 (Oryza sativa), 5'ss of exon 3
GGATGAAGGACTTTATGAATGAGACCAATGGCTCTGACTATGTACCCACATATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGAgtcagtg----ccccttcattcattcatttccttttcttt----ctttaattat--caacct-atttaa--tactacctt---tttttgaca--atttcacag-----------------------------------------------------
    ||   |  ||    ||  |  ||| |||||||| ||||| || || || || ||||||||||| ||||||||||||||||| || || || |||||||||||     |  ||| | |  |  |||  ||  | | |     ||||||| |   ||||| | ||||  |||||   |   | | ||| |  | | ||                                                        
ACGAGAGCAAGATTGCTGATCTGCTCAACGGCTCTGAATATGTGCCAACCTACGAGGACAAGGACGGCGACTGGATGCTCGTCGGCGACGTCCCATGGGAgtcagtaatctctacttaaattttctattatctaatatctaagtgtttaattttaataacctgaattaaggtactagtctgaatctctgatatgagtccatgctctgcatctgtgttctgaattctgaccattttgtttggaaatggaaatttcag

upper sequence: GLYMA20G36790.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os03g43400.1 (Oryza sativa), 5'ss of exon 3
GGATGAAGGACTTTATGAATGAGACCAATGGCTCTGACTATGTACCCACATATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGAgtcagtgccccttcattcattcatttccttttctttctttaattatcaacctatttaatactacctttt---tttgacaatttcacag--------------
 | |||||||    |  ||   ||   ||| |   || || || || || || || ||||||||||| ||||||||||||||||| || || || ||||||| ||  || |  | |      |       | |    | |||| || || |    | |    | ||      |  ||    |  |  |              
AGCTGAAGGAGAGCAATAAGCTGAGAGATGACCTGGAGTACGTGCCGACGTACGAGGACAAGGACGGCGACTGGATGCTCGTCGGCGACGTCCCGTGGGAgtaag--cctcgccgtcgcgataagcataatcccagttctaataattaatccccatcagctaagctagcagatcggatggatcgatcgagtaactgatcaac

upper sequence: GLYMA20G36790.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G138268_T01 (Zea mays), 5'ss of exon 3
GGATGAAGGACTTTATGAATGAGACCAATGGCTCTGACTATGTACCCACATATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGAgtcagtgcc-ccttcattcattcatttcc------ttttctttctttaattatcaacctattt---aatactacctttttttgacaatttcacag
    ||   |  |  || ||  |  ||| ||||| || || || || || || || ||||||||||| ||||||||||||||||| |||||||| ||||||| ||  |  | | ||| |  |  || |       |  || || ||  |||||   |  ||     |||| ||    |||        ||  |||
ACGAGAGCAAGCTGGTGGATCTGCTCAACGGCTCCGAGTACGTGCCGACCTACGAGGACAAGGACGGGGACTGGATGCTCGTCGGCGATGTGCCGTGGGAgtgagcactgcatgcatgcgcttcttcctgcactatactccttattatattattgcctaatcggaaaataataataatttccatttcattttcag

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|21594765|gb|BQ610259.1|BQ610259
EST:     TATGAAGACAAGGACTGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGA                         GATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
genomic: TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGAgtcagtgccc ... aatttcacagGATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
EST: gi|254339868|gb|GR857993.1|GR857993
EST:     TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGA                         GATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
genomic: TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGAgtcagtgccc ... aatttcacagGATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
EST: gi|254339867|gb|GR857992.1|GR857992
EST:     TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGA                         GATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
genomic: TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGAgtcagtgccc ... aatttcacagGATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
EST: gi|21600987|gb|BQ611327.1|BQ611327
EST:     TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGNGA                         GATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
genomic: TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGAgtcagtgccc ... aatttcacagGATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
EST: gi|26057410|gb|CA800324.1|CA800324
EST:     TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGNGA                         GATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
genomic: TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGAgtcagtgccc ... aatttcacagGATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
EST: gi|151396677|gb|EV266550.1|EV266550
EST:     TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGA                         GATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
genomic: TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGAgtcagtgccc ... aatttcacagGATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
EST: gi|151398070|gb|EV267948.1|EV267948
EST:     TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGA                         GATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
genomic: TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGAgtcagtgccc ... aatttcacagGATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
EST: gi|192317984|gb|FK009464.1|FK009464
EST:     TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGA                         GATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
genomic: TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGAgtcagtgccc ... aatttcacagGATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
EST: gi|21602083|gb|BQ612414.1|BQ612414
EST:     TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGA                         GATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
genomic: TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGAgtcagtgccc ... aatttcacagGATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
EST: gi|51335090|gb|CO978956.1|CO978956
EST:     TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGA                         GATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
genomic: TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGAgtcagtgccc ... aatttcacagGATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
EST: gi|58024615|gb|CX711356.1|CX711356
EST:     TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGA                         GATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
genomic: TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGAgtcagtgccc ... aatttcacagGATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
EST: gi|192317983|gb|FK009463.1|FK009463
EST:     TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGA                         GATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
genomic: TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGAgtcagtgccc ... aatttcacagGATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
EST: gi|42722983|gb|CK768882.1|CK768882
EST:     TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGA                         GATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
genomic: TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGAgtcagtgccc ... aatttcacagGATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
EST: gi|192324558|gb|FK018714.1|FK018714
EST:     TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGA                         GATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
genomic: TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGAgtcagtgccc ... aatttcacagGATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
EST: gi|208178460|gb|GD977797.1|GD977797
EST:     TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGA                         GATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
genomic: TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGAgtcagtgccc ... aatttcacagGATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
EST: gi|192297650|gb|FG992758.1|FG992758
EST:     TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGA                         GATGTTCGTTGAATCATGCAAGCGTTTTCGCATAATGAAAGGTTCCGAGGC
genomic: TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGAgtcagtgccc ... aatttcacagGATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
EST: gi|214008573|gb|DB986750.1|DB986750
EST:     ATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGA                         GATGTTCGTTGAATCATGCAAGATTCAACGCATAATGAAAGGCTCCGAGGC
genomic: ATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGAgtcagtgccc ... aatttcacagGATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
EST: gi|57576038|gb|CX549009.1|CX549009
EST:     TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGA                         GATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
genomic: TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGAgtcagtgccc ... aatttcacagGATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
EST: gi|26058652|gb|CA801566.1|CA801566
EST:     TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGNGA                         GATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
genomic: TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGAgtcagtgccc ... aatttcacagGATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
EST: gi|10236738|gb|BE805626.1|BE805626
EST:     TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGA                         GATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
genomic: TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGAgtcagtgccc ... aatttcacagGATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGC
EST: gi|151405757|gb|EV275571.1|EV275571
EST:     TATGAAGACAAGGACGGAGACTGGATGCTCGCCGGTGATGTGCCCTGGGA                         GATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATG
genomic: TATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGAgtcagtgccc ... aatttcacagGATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATGAAGGACTTTATGAATGAGACCAATGGCTCTGACTATGTACCCACATATGAAGACAAGGACGGAGACTGGATGCTCGTCGGTGATGTGCCCTGGGAgtcagtgccccttcattcattcatttccttttctttctttaattatcaacctatttaatactacctttttttgacaatttcacag

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