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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGGtattgctttcatttctttttattgttttttatgcaaatatttttaccttgaagcatgaaaatctctttccatggtcctatcaggttaatatccacacaga...

Basic information

species Glycine max
transcript GLYMA18G08230.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G08230.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G112672_T01 (Zea mays), 5'ss of exon 3
-AAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGGtattgctttcatttctttttattgttttttatgcaaatatttttaccttgaagcatgaaaatctct--ttccatggtcctatcaggttaatatccacacaga----
 | ||||||||| ||||  |||||||||| ||||| || |||||| |||||||||||||||||  |||    || | |  | || | | ||||||   | ||| ||| ||| ||      |||      |    | |  |||| ||  || ||| ||  ||      
GAGGAGTTTCAGCTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGGgtaaggctact-ttgcatactgtt-tctgttatgc---tctttgtactttgtagttgtccaatgaaaaatattgtagcactattag--tagtattcagtcatgatca

upper sequence: GLYMA18G08230.1 (Glycine max), 5'ss of exon 5
lower sequence: AT5G55990.1 (Arabidopsis thaliana), 5'ss of exon 5
-AAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGGtattgctttcatttc----tttttattgttttttatgcaaatatttttaccttgaagcatgaaaatctctttccatggtcctatcaggttaatatccacacaga
 |||||||||||||||| ||||| ||||||||||||||||| ||| ||||||| ||||||||| || ||   | |     || | | |||| || |  | | | || | |   | |||  |  ||       |  |   |   ||   |||  ||          
GAAGAGTTTCAGTTGGCTTTGTTTAAGACAAATAAAAAAGAGAGTTTGTTTGCAGATCGGgtaatgtttctttcttcacattataagtgttcttaaacccatttttgtcaagatcaagtttagaagaaatgctgaaatatgtgattttgtttctag---------

upper sequence: GLYMA18G08230.1 (Glycine max), 5'ss of exon 5
lower sequence: AT4G26570.1 (Arabidopsis thaliana), 5'ss of exon 5
-AAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGGtattgctttcatttctttttattgttttttatgcaaatatttttaccttgaagcatgaaaatctctttccatggtcctatcaggttaatatcca-cacaga
 |||| |||||||| || ||||||||||||||||||||||| ||  ||||||| || |||||||         ||||| ||     |||| ||  ||| | |||    |  |      || |||  |||  |  |   || |  |  | || | | ||||| 
GAAGAATTTCAGTTAGCCTTGTTCAAGACAAATAAAAAAGAGAGCTTGTTTGCAGACCGGgtatg--------ttcttctt-----ttttaatcaaaagactttgttatccatttgccaagatcctttttgaaaga--taacttgacagtaccaatcacag-

upper sequence: GLYMA18G08230.1 (Glycine max), 5'ss of exon 5
lower sequence: AT4G26570.2 (Arabidopsis thaliana), 5'ss of exon 5
-AAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGGtattgctttcatttctttttattgttttttatgcaaatatttttaccttgaagcatgaaaatctctttccatggtcctatcaggttaatatccacacaga
 |||| |||||||| || ||||||||||||||||||||||| ||  ||||||| || |||||||         ||||| ||     |||| ||  ||| | |||    |  |      || |||  |||  |  |   || |  |  |             
GAAGAATTTCAGTTAGCCTTGTTCAAGACAAATAAAAAAGAGAGCTTGTTTGCAGACCGGgtatg--------ttcttctt-----ttttaatcaaaagactttgttatccatttgccaagatcctttttgaaaga--taacttgacag------------

upper sequence: GLYMA18G08230.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv19s0015g01070.t01 (Vitis vinifera), 5'ss of exon 3
-AAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGGtattgctttcatttctt--tttattgttttttatgcaaatatttttaccttgaagcatgaaaatctctttccatggtcctatcaggttaatatccacacaga
 |||||||||| ||||| |||||||| ||||| ||||| |||||  | ||||||||||||||| |  ||   |||  |   | || ||||||  | | | |  ||  |  || |           |       ||  ||  |  |      |||| | | |  
GAAGAGTTTCAATTGGCTTTGTTCAAAACAAACAAAAAGGAAAGCTTATTTGCTGATCGGgtactttttctctttgataactcatagtttttcttccta-tccttggattttcagcagcagtctacaaaccatatattctcacaaatagtctatcaaaaaa--

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|151397479|gb|EV267352.1|EV267352
EST:     GTTGGCATCGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGG                         TATTTGATTTATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGT
genomic: GTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGGtattgctttc ... ctctattaggTATTTGATTTATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGT
EST: gi|16349164|gb|BI974759.1|BI974759
EST:     GTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGG                         TATTTGATTTATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGT
genomic: GTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGGtattgctttc ... ctctattaggTATTTGATTTATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGT
EST: gi|192298955|gb|FG987700.1|FG987700
EST:     GTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGG                         TATTTGATTTATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGT
genomic: GTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGGtattgctttc ... ctctattaggTATTTGATTTATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGT
EST: gi|18848425|gb|BM567661.1|BM567661
EST:     GTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGG                         TATTTGATTTATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGT
genomic: GTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGGtattgctttc ... ctctattaggTATTTGATTTATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGT
EST: gi|8284959|gb|BE022518.1|BE022518
EST:     GTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGG                         TATTTGATTTATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGT
genomic: GTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGGtattgctttc ... ctctattaggTATTTGATTTATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGT
EST: gi|13791269|gb|BG653860.1|BG653860
EST:     GTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGG                         TATTTGATTTATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGT
genomic: GTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGGtattgctttc ... ctctattaggTATTTGATTTATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGT
EST: gi|8283189|gb|BE020750.1|BE020750
EST:     GTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGGTTGCTGATCGGG                         TATTTGATTTATTTGACACAAAGCACAATGGGATACTANGGTTT
genomic: GTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGGtattgctttc ... ctctattaggTATTTGATTTATTTGACACAAAGCACAATGGGATACTA-GGTTT
EST: gi|192334402|gb|FK025551.1|FK025551
EST:     GTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGG                         TATTTGATTTATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGT
genomic: GTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGGtattgctttc ... ctctattaggTATTTGATTTATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGT
EST: gi|209718662|gb|BW674764.1|BW674764
EST:     GTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGG                         TATTTGATTTATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGT
genomic: GTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGGtattgctttc ... ctctattaggTATTTGATTTATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGT
EST: gi|254347752|gb|GR854001.1|GR854001
EST:     GTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGG                         TATTTGATTTATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGT
genomic: GTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGGtattgctttc ... ctctattaggTATTTGATTTATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGT
EST: gi|192320225|gb|FK014239.1|FK014239
EST:     GTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGG                         TATTTGATTTATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGT
genomic: GTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGGtattgctttc ... ctctattaggTATTTGATTTATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGT
EST: gi|213592918|gb|DB966023.1|DB966023
EST:     GTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGG                         TATTTGATTTATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGT
genomic: GTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGGtattgctttc ... ctctattaggTATTTGATTTATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGT
EST: gi|254324275|gb|GR840592.1|GR840592
EST:     GTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGG                         TATTTGATTTATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGT
genomic: GTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGGtattgctttc ... ctctattaggTATTTGATTTATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGT
EST: gi|308098080|gb|HO761251.1|HO761251
EST:     GTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTACTGATCGGG                         TATTTGATTTATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGT
genomic: GTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGGtattgctttc ... ctctattaggTATTTGATTTATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGGtattgctttcatttctttttattgttttttatgcaaatatttttaccttgaagcatgaaaatctctttccatggtcctatcaggttaatatccacacaga

- - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctttcc