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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGAAGACAATCAAGAAGAAACTTATTAGGAAAGCCCTTGATATGATCCGCAGGATTGCTGATGAGGATCCTGACGAGTCAACTGACAAAGAAAAGAAAGgtatggtttaatagttatgagtttcatctgttggaatccctatttttttatgggctaaggttgaccaaaacacgtgtaattgtgtttgctttgttataccatttcaaaatgtaaggtgtttcttgaattctgttcattgactttgtacttccatcttaaatattgatgcacagaag

Basic information

species Glycine max
transcript GLYMA14G40320.3
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G40320.3 (Glycine max), 5'ss of exon 11
lower sequence: AT4G24190.1 (Arabidopsis thaliana), 5'ss of exon 11
CTGAAGACAATCAAGAAGAAACTTATTAGGAAAGCCCTTGATATGATCCGCAGGATTGCTGATGAGGATCCTGACGAGTCAACTGACAAAGAAAAGAAAGgtatggtttaatagttatgagtttcatctgttggaatccctatttttttatgggctaaggttgaccaaaacacgtgtaattgtgtttgctttgttataccatttcaaaatgtaaggtgtttcttgaattctgttcattgactttgtacttccatcttaaatattgatgcacagaag
 | |||||||| |||||||| |||||  | || || |||||||||||||||| | ||||||| || |||||||| ||      |||  | || || ||||||||    |||     |  ||||||     |||| |||  |    ||| |  |    |  ||     |    | | |  | |  |   |||| | | ||    || ||   ||  |  ||  | | |  | |                                            
TTAAAGACAATTAAGAAGAAGCTTATCCGAAAGGCGCTTGATATGATCCGCAAGCTTGCTGAAGAAGATCCTGATGAAATCCATGATGATGAGAAAAAAGgtattccataa----aacaagtttc-----ttggtatcaatccactttgaccgttccacttttttttac---catttggtagcttcatctttctgaaacatggtctaagcttattgacttgttggcacgcag--------------------------------------------

upper sequence: GLYMA14G40320.3 (Glycine max), 5'ss of exon 11
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 5'ss of exon 11
CTGAAGACAATCAAGAAGAAACTTATTAGGAAAGCCCTTGATATGATCCGCAGGATTGCTGATGAGGATCCTGACGAGTCAACTGACAAAGAAAAGAAAGgtatggt----ttaatagttatgagtttcatctg--ttggaatccctatttttttatgggctaaggttgacc---aaaacacgtgtaattg-tgtttgctttgttataccatttcaaaatgtaaggtgtttcttgaattctgttcattgactttgtacttccatcttaaatattgatgcacagaag
 |||| ||||| |||||||| |||||  | || |||||||||||||| || | ||| || |||||||||||||| ||||| | ||| ||||| ||||||||||||||    ||||| || |  |  ||  |||   ||  |     ||||||| |    |      ||  |    |||       | |||| ||  |   |||  ||   |||  |  |  |   |    |||   |||    |      ||||     |  || || | |    ||  |  | ||
TTGAAAACAATTAAGAAGAAGCTTATCCGCAAGGCCCTTGATATGATTCGTAAGATCGCCGATGAGGATCCTGATGAGTCTAATGATAAAGACAAGAAAGgtatggtgtcgttaat-gtcacaatcttgttctaacttccagaaaatatttttctcccagaagcaatttgcttttaaattttaattgattgctgcctatcttgcaatgg-attctagtaactgttgctgctctctcatttctcttgccatcttta----ttgatgttgagttccaatatattgcag
















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|23059035|gb|BU578351.1|BU578351
EST:     CAGGATTGCTGATGAGGATCCTGACGAGTCAACTGACAAAGAAAAGAAAG                         AAGATGCATCCTCTGACAATGATGAGAAGAAAGGTCAATATTCTAAGTTCT
genomic: CAGGATTGCTGATGAGGATCCTGACGAGTCAACTGACAAAGAAAAGAAAGgtatggttta ... tgcacagaagA---TGCATCCTCTGACAATGATGAGAAGAAAGGTCAATATTCTAAGTTCT
EST: gi|192301679|gb|FG997621.1|FG997621
EST:     CAGGATTGCTGATGAGGATCCTGACGAGTCAACTGACAAAGAAAAGAAAG                         AAGATGCATCCTCTGACAATGATGAGAAGAAAGGTCAATATTCTAAGTTCT
genomic: CAGGATTGCTGATGAGGATCCTGACGAGTCAACTGACAAAGAAAAGAAAGgtatggttta ... tgcacagaagA---TGCATCCTCTGACAATGATGAGAAGAAAGGTCAATATTCTAAGTTCT
EST: gi|15661681|gb|BI699052.1|BI699052
EST:     CAGGATTGCTGATGAGGATCCTGACGAGTCAACTGACAAAGAAAAGAAAGAAG                       
genomic: CAGGATTGCTGATGAGGATCCTGACGAGTCAACTGACAAAGAAAAG--A-AAGgtatggttta ... tgcacaga
EST: gi|208126857|gb|GD926087.1|GD926087
EST:     CAGGATTGCTGATGAGGATCCTGACGAGTCAACTGACAAAGAAAAGAAAG                         AAGATGCATCCTCTGACAATGATGAGAAGAAAGGTCAATATTCTAAGTTCT
genomic: CAGGATTGCTGATGAGGATCCTGACGAGTCAACTGACAAAGAAAAGAAAGgtatggttta ... tgcacagaagA---TGCATCCTCTGACAATGATGAGAAGAAAGGTCAATATTCTAAGTTCT
EST: gi|213592217|gb|DB965980.1|DB965980
EST:     CAGGATTGCTGATGAGGATCCTGACGAGTCAACTGACAAAGAAAAGAAAG                         AAGATGCATCCTCTGACAATGATGAGAAGAAAGGTCAATATTCTAAGTT
genomic: CAGGATTGCTGATGAGGATCCTGACGAGTCAACTGACAAAGAAAAGAAAGgtatggttta ... tgcacagaagA---TGCATCCTCTGACAATGATGAGAAGAAAGGTCAATATTCTAAGTT
EST: gi|193358348|gb|FK324064.1|FK324064
EST:     CAGGATTGCTGATGAGGATCCTGACGAGTCAACTGACAAAGAAAAGAAAG                         AAGATGCATCCTCTGACAATGATGAGAAGAAAGGTCAATATTCTAAGTTCT
genomic: CAGGATTGCTGATGAGGATCCTGACGAGTCAACTGACAAAGAAAAGAAAGgtatggttta ... tgcacagaagA---TGCATCCTCTGACAATGATGAGAAGAAAGGTCAATATTCTAAGTTCT
EST: gi|7233546|gb|AW568951.1|AW568951
EST:     CAGGATTGCTGATGAGGATCCTGACGAGTCAACTGACAAAGAAAAGAAAG                         AAGATGCATCCTCTGACAATGATGAGAAGAAAGGTCAATATTCTAAGTTCT
genomic: CAGGATTGCTGATGAGGATCCTGACGAGTCAACTGACAAAGAAAAGAAAGgtatggttta ... tgcacagaagA---TGCATCCTCTGACAATGATGAGAAGAAAGGTCAATATTCTAAGTTCT
EST: gi|193630999|gb|FK579526.1|FK579526
EST:     CAGGATTGCTGATGAGGATCCTGACGAGTCAACTGACAAAGAAAAGAAAG                         AAGATGCATCCTCTGACAATGATGAGAAGAAAGGTCAATATTCTAAGTTCT
genomic: CAGGATTGCTGATGAGGATCCTGACGAGTCAACTGACAAAGAAAAGAAAGgtatggttta ... tgcacagaagA---TGCATCCTCTGACAATGATGAGAAGAAAGGTCAATATTCTAAGTTCT
EST: gi|192313364|gb|FK005136.1|FK005136
EST:     CAGGATTGCTGATGAGGATCCTGACGAGTCAACTGACAAAGAAAAGAAAGAAG                       
genomic: CAGGATTGCTGATGAGGATCCTGACGAGTCAACTGACAAAGAAAAG--A-AAGgtatggttta ... tgcacaga
EST: gi|208176347|gb|GD979030.1|GD979030
EST:     CAGGATTGCTGATGAGGATCCTGACGAGTCAACTGACAAAGAAAAGAAAGAAG                       
genomic: CAGGATTGCTGATGAGGATCCTGACGAGTCAACTGACAAAGAAAAG--A-AAGgtatggttta ... tgcacaga
EST: gi|193311042|gb|FK275050.1|FK275050
EST:     CAGGATTGCTGATGAGGATCCTGACGAGTCAACTGACAAAGAAAAGAAAG                         ATGCATCCTCTGACAATGATGAGAAGAAAGGTCAATATTCTAAGTTCTGGA
genomic: CAGGATTGCTGATGAGGATCCTGACGAGTCAACTGACAAAGAAAAGAAAGgtatggttta ... tgcacagaagATGCATCCTCTGACAATGATGAGAAGAAAGGTCAATATTCTAAGTTCTGGA
EST: gi|192313365|gb|FK005137.1|FK005137
EST:     CAGGATTGCTGATGAGGATCCTGACGAGTCAACTGACAAAGAAAAGAAAGAAG                       
genomic: CAGGATTGCTGATGAGGATCCTGACGAGTCAACTGACAAAGAAAAG--A-AAGgtatggttta ... tgcacaga

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGAAGACAATCAAGAAGAAACTTATTAGGAAAGCCCTTGATATGATCCGCAGGATTGCTGATGAGGATCCTGACGAGTCAACTGACAAAGAAAAGAAAGgtatggtttaatagttatgagtttcatctgttggaatccctatttttttatgggctaaggttgaccaaaacacgtgtaattgtgtttgctttgttataccatttcaaaatgtaaggtgtttcttgaattctgttcattgactttgtacttccatcttaaatattgatgcacagaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA