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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagatcctttcatatctgaactgatataatagtatcaagagattctttcagacttatttatttctatgttaagccctatttacttgcctgctgtggacagTGCTTGCTAGTGAAGGGATGGAAAGGTACAAGTTGGAGTTTCCCTCGTGGAAAAAAGAGCAAAGACGAAGAAGATCATGCATGTTCCATTAGAGAA

Basic information

species Glycine max
transcript GLYMA16G27200.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G27200.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g56210.1 (Oryza sativa), 3'ss of exon 3
-----aagatcctttcatatctgaactgatataatagtatcaagagattctttcagacttatttatttctatgttaagccctatttacttg--cctgctgtggacagTGCTTGCTAGTGAAGGGATGGAAA---GGTACAAGTTGGAGTTTCCCTCGTGGAAAAAAGAGCAAAGACGAAGAAGATCATGCATGTTCCATTAGAGAA
        | ||||  | | || || |     | |  | |  |     | | |||   | |  || |   |    |||    ||| ||||   |    | ||  ||||||||||| ||||||||||||||     |  | || |||||||| ||||||||||| | ||| ||||| |||||||||||| ||||| |  ||||||||
gatctttaacccttgtagacctcaattcgcgcattctttttca----ctttgtca---tcacatactcacaccccaagtttcattcactttttctccttctgtgcagTGCTTGCTTGTGAAGGGATGGAAGTCTAGCGCCAGCTGGAGTTTTCCTCGTGGAAAGAGGAGTAAAGATGAAGAAGATCATACATGTGCTGTTAGAGAA

upper sequence: GLYMA16G27200.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G13570.1 (Arabidopsis thaliana), 3'ss of exon 3
aagatcctttcatatctgaactgatataatagtatcaagagattct-ttcagacttatttatt--tctatgttaagccctatttacttgcctgctgtggacagTGCTTGCTAGTGAAGGGATGGAAAGGTACAAGTTGGAGTTTCCCTCGTGGAAAAAAGAGCAAAGACGAAGAAGATCATGCATGTTCCATTAGAGAA
                          ||| |       | | |  | || ||  ||| |||||  |  ||| | | |||| |||  ||   ||   |   |||||| || | |||||||||||||||||  | || ||||| || || || |||||||||||||| || |||||||| ||||| ||| ||||  | || 
-------------------------gtaagaaccctgtggggtgatatttaggtttacttattagttaatgctta-ccctttttgtttcattgtcattttcagTGCCTGTTGGTGAAGGGATGGAAAGGATCGAGCTGGAGCTTTCCCCGCGGAAAAAAGAGCAAGGATGAAGAAGACCATGCTTGTGCCATACGTGAG

upper sequence: GLYMA16G27200.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0019g04310.t01 (Vitis vinifera), 3'ss of exon 3
aagatcctttcatatctgaactgatataatagtatcaagagattctttcagacttatttatttctatgttaa-gccctatttacttgcctgctgtg-------gacagTGCTTGCTAGTGAAGGGATGGAAAGGTACAAGTTGGAGTTTCCCTCGTGGAAAAAAGAGCAAAGACGAAGAAGATCATGCATGTTCCATTAGAGAA
          |||| | ||  | || ||||||| | |||  | |  |||||   |  || |    || ||    | || |||   | | || | ||        ||||||||| |||||||||||||||||||| ||||| |||||||| || ||||||||||||| |||||| |||||||| ||  | ||| |||||||||||
-------acacataacagagtt-atctaatagtttgaagtaagtgattcagttctccttttaaaaatattgtcacactgttttgatacttgttttgtataattaacagTGCTTACTAGTGAAGGGATGGAAAGGAACAAGCTGGAGTTTTCCCCGTGGAAAAAAGAACAAAGATGAAGAAGACCACACGTGTGCCATTAGAGAA

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|208215038|gb|GE014237.1|GE014237
EST:     TTCGAGTTCCTGTAACTGGGGCAATAATTCTTGATGAAACATATGAAAGG                         TGCTTGCTAAGAGAAGGGATGGAAA
genomic: TTCGAGTTCCTGTAACTGGGGCAATAATTCTTGATGAAACATATGAAAGGgtaagacaag ... ctgtggacagTGCTTGCTA-GTGAAGGGATGGAAA
EST: gi|209716318|gb|BW657464.1|BW657464
EST:     TTCGAGTTCCTGTAACTGGGGCAATAATTCTTGATGAAACATATGAAAGG                         TGCTTGCTAGTGAAGGGATGGAAAGGTACAAGTTGGAGTTTCCCTCGTGGA
genomic: TTCGAGTTCCTGTAACTGGGGCAATAATTCTTGATGAAACATATGAAAGGgtaagacaag ... ctgtggacagTGCTTGCTAGTGAAGGGATGGAAAGGTACAAGTTGGAGTTTCCCTCGTGGA
EST: gi|151410336|gb|EV280151.1|EV280151
EST:     TTCGAGTTCCTGTAACTGGGGCAATAATTCTTGATGAAACATATGAAAGG                         TGCTTGCTAGTGAAGGGATGGAAAGGTACAAGTTGGAGTTTCCCTCGTGGA
genomic: TTCGAGTTCCTGTAACTGGGGCAATAATTCTTGATGAAACATATGAAAGGgtaagacaag ... ctgtggacagTGCTTGCTAGTGAAGGGATGGAAAGGTACAAGTTGGAGTTTCCCTCGTGGA
EST: gi|151409239|gb|EV279047.1|EV279047
EST:     TTCGAGTTCCTGTAACTGGGGCAATAATTCTTGATGAAACATATGAAAGG                         TGCTTGCTAGTGAAGGGATGGAAAGGTACAAGTTGGAGTTTCCCTCGTGGA
genomic: TTCGAGTTCCTGTAACTGGGGCAATAATTCTTGATGAAACATATGAAAGGgtaagacaag ... ctgtggacagTGCTTGCTAGTGAAGGGATGGAAAGGTACAAGTTGGAGTTTCCCTCGTGGA
EST: gi|151410478|gb|EV280293.1|EV280293
EST:     TTCGAGTTCCTGTAACTGGGGCAATAATTCTTGATGAAACATATGAAAGG                         TGCTTGCTAGTGAAGGGATGGAAAGGTACAAGTTGGAGTTTCCCTCGTGGA
genomic: TTCGAGTTCCTGTAACTGGGGCAATAATTCTTGATGAAACATATGAAAGGgtaagacaag ... ctgtggacagTGCTTGCTAGTGAAGGGATGGAAAGGTACAAGTTGGAGTTTCCCTCGTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcagacttatttatttctatgttaagccctatttacttgcctgctgtggacagTGCTTGCTAGTGAAGGGATGGAAAGGTACAAGTTGGAGTTTCCCTCGTGGAAAAAAGAGCAAAGACGAAGAAGATCATGCATGTTCCATTAGAGAA
      acttatttatttctat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagatcctttcatatctgaactgatataatagtatcaagagattctttcagacttatttatttctatgttaagccctatttacttgcctgctgtggacagTGCTTGCTAGTGAAGGGATGGAAAGGTACAAGTTGGAGTTTCCCTCGTGGAAAAAAGAGCAAAGACGAAGAAGATCATGCATGTTCCATTAGAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA