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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGCTTACCCTTTGGCGGATGCCCAACTCTCAATAACCATACTAGACCTTGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAGgtatatagctcattttctttcattttattatcacttctcactgtgtgtgctaagtaaaatagtgtacttgctgtgttgcag

Basic information

species Glycine max
transcript GLYMA17G12430.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G12430.1 (Glycine max), 5'ss of exon 2
lower sequence: AT5G20160.1 (Arabidopsis thaliana), 5'ss of exon 2
AAAGCTTACCCTTTGGCGGATGCCCAACTCTCAATAACCATACTAGACCTTGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAGgtatatagctcattttctttcattttattatcactt-ctcactgtgtgtgctaagtaaaatagtgtacttgctgtgttgcag--------------
||||| || ||  | || ||| | ||  | || ||||| || || ||||| |||||||||||| | ||||||||||||||||| || |||||||||||||||||     |  |  || |   | ||  | || |||  | | || || |  |   |   |   ||| | || | | ||  |               
AAAGCGTATCCGCTTGCAGATTCTCAGTTATCGATAACAATTCTTGACCTCGTTCAACAAGCTACTAACTACAAGCAGCTCAAGAAGGGTGCTAATGAAGgtatccgcttgttactcatgtgtgtttgtctctcttatttattgagtttaatgtttgtgaagttgttcctgatttatttaaatttgttcatttcag

upper sequence: GLYMA17G12430.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv13s0019g02650.t01 (Vitis vinifera), 5'ss of exon 2
AAAGCTTACCCTTTGGCGGATGCCCAACTCTCAATAACCATACTAGACCTTGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAGgtatatagc-tcattttctttcattttattatcacttctcactgtgtgtgctaagtaaaatagtgtacttgctgtgttgcag--------------
||||| |||||| | || ||||| || ||  | || || || || || ||  | || ||||| ||||||||||| ||||||||||| ||||| |||||||||  ||  | | | | |  || |||||||  |  |||||  ||   | |  | | |  |||  | |     ||  ||| ||               
AAAGCATACCCTCTCGCCGATGCTCAGCTGACTATTACAATTCTCGATCTCATCCAGCAAGCAGCCAACTACAAACAGCTCAAAAAGGGTGCCAATGAAGgttcatttcattactataattgattttat-gtttcttct-gctcaatttctttattttaatgttttttccccttggtttcaatctttcgcttttag

upper sequence: GLYMA17G12430.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv11s0016g05140.t01 (Vitis vinifera), 5'ss of exon 2
AAAGCTTACCCTTTGGCGGATGCCCAACTCTCAATAACCATACTAGACCTTGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAGgtatatagctcattttctttcattttattatcacttctcactgtgtgtgctaagtaaaatagtgtacttgctgtg---ttgcag
||||| |||||  | |||||||| |||||| | ||||| || || || ||  |||||||||||||||||||||||||||||||||| || ||||||||||||   |  ||    |   |  ||||   || | |   |   | | | |  |   ||| ||  | ||| |||| ||   || |||
AAAGCATACCCACTTGCGGATGCGCAACTCACCATAACTATTCTGGATCTCATTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAGGGCGCTAATGAAGgtccctttctgcaataactctatttatatagctcgatttgttttttctatttcataatatt-tatacgtgctttgaaatttcag

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|298182539|gb|HO031274.1|HO031274
EST:     TGTTCAACAAGCAGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAG                         CCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
genomic: TGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAGgtatatagct ... tgtgttgcagCCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
EST: gi|298180380|gb|HO025581.1|HO025581
EST:     TGTTCAACAAGCAGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAG                         CCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
genomic: TGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAGgtatatagct ... tgtgttgcagCCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
EST: gi|6725768|gb|AW310167.1|AW310167
EST:     TGTTCAACAAGCTGCCAACTACAAGCAGCTCAANAAAGGTGCTAATGAAG                         CCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
genomic: TGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAGgtatatagct ... tgtgttgcagCCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
EST: gi|208173600|gb|GD970263.1|GD970263
EST:     TGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAG                         CCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTG
genomic: TGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAGgtatatagct ... tgtgttgcagCCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTG
EST: gi|298185053|gb|HO030266.1|HO030266
EST:     TGTTCAACAAGCAGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAG                         CCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
genomic: TGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAGgtatatagct ... tgtgttgcagCCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
EST: gi|298171220|gb|HO016252.1|HO016252
EST:     TGTTCAACAAGCAGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAG                         CCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
genomic: TGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAGgtatatagct ... tgtgttgcagCCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
EST: gi|298195944|gb|HO044335.1|HO044335
EST:     TGTTCAACAAGCAGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAGG                         CCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
genomic: TGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAGgtatatagct ... tgtgttgcagCCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
EST: gi|6566245|gb|AW233926.1|AW233926
EST:     TGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAG                         CCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
genomic: TGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAGgtatatagct ... tgtgttgcagCCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
EST: gi|26059372|gb|CA802286.1|CA802286
EST:     TGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAG                         CCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
genomic: TGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAGgtatatagct ... tgtgttgcagCCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
EST: gi|298189335|gb|HO037738.1|HO037738
EST:     TGTTCAACAAGCAGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAG                         CCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
genomic: TGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAGgtatatagct ... tgtgttgcagCCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
EST: gi|18039291|gb|BM307585.1|BM307585
EST:     TGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAG                         CCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
genomic: TGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAGgtatatagct ... tgtgttgcagCCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
EST: gi|298164419|gb|HO014064.1|HO014064
EST:     TGTTCAACAAGCAGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAG                         CCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
genomic: TGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAGgtatatagct ... tgtgttgcagCCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGCTTACCCTTTGGCGGATGCCCAACTCTCAATAACCATACTAGACCTTGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAGgtatatagctcattttctttcattttattatcacttctcactgtgtgtgctaagtaaaatagtgtacttgctgtgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA