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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGATGCTTTGACAACCAAACGTGGTAAAGAAGGTGGTTGGGTTGTTGAACGACTATTGAACCAGgtaaaatatttattagtctttcggaatatgaaaaaacatagccattttaactgataacaacatcgataaatgatacagttatatgaaattgcag

Basic information

species Glycine max
transcript GLYMA08G19920.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G19920.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os06g01980.1 (Oryza sativa), 5'ss of exon 6
ATTGATGCTTTGACAACCAAACGTGGTAAAGAAGGTGGTTGGGTTGTTGAACGACTATTGAACCAGgta-aaata-tttattagtctttcggaatatgaaaaaacatagccattttaactgataacaacatcgataaatgatacagttatatgaaattgcag
 | |||||||||||||| ||| | || ||||| || || |||||||||||||| ||  ||||||||||   |||| ||||  |||   |    || ||    |    | |   |   |  | |       |       |  |  | || | |    |  |||
GTAGATGCTTTGACAACAAAAAGAGGGAAAGAGGGGGGATGGGTTGTTGAACGTCTCCTGAACCAGgtttgaatactttacaagttaatatatatttgcggtagttgatctgctaacaaggttctttttgttctgtgttactctaattgttttgt-tcacag

upper sequence: GLYMA08G19920.1 (Glycine max), 5'ss of exon 6
lower sequence: AT3G01610.1 (Arabidopsis thaliana), 5'ss of exon 6
ATTGATGCTTTGACAACCAAACGTGGTAAAGAAGGTGGTTGGGTTGTTGAACGACTATTGAACCAGgtaaaatatttattagtctttcggaatatgaaaaaacatagccattttaactgataacaacatcgataaatgatacagttatatgaaattgcag
 | |||||||||||||| |  ||||| |||||||||| ||||||||||||||| || ||||||||||||| | |               |  |||  ||     ||||      |  |  | |   ||| ||| ||  || || ||    ||  || |||
GTGGATGCTTTGACAACAAGTCGTGGCAAAGAAGGTGCTTGGGTTGTTGAACGGCTTTTGAACCAGgtaataaac--------------gcttattgaatggtgtagctgcacaatttagtca-ggcattgatcaa--atgcattt---cgatgttccag
















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|21889596|gb|BQ742809.1|BQ742809
EST:     CCAAACGTGGTAAAGAAGGTGGTTGGGTTGTTGAACGACTATTGAACCAG                         TTGCTTGTTGAGTTAGATGGCGCTGAACAACGAAAAGGTGTTTTTGTGATT
genomic: CCAAACGTGGTAAAGAAGGTGGTTGGGTTGTTGAACGACTATTGAACCAGgtaaaatatt ... gaaattgcagTTGCTTGTTGAGTTAGATGGCGCTGAACAACGAAAAGGTGTTTTTGTGATT
EST: gi|298192475|gb|HO036557.1|HO036557
EST:     CCAAACCTGGTAAAGAAGGTGGTTGGGTTGTTGAACGACTATTGAACCAG                         TTGCTTGTTGAGTTAGATGGCGCTGAACAACGAAAAGGTGTTTTTGTGATT
genomic: CCAAACGTGGTAAAGAAGGTGGTTGGGTTGTTGAACGACTATTGAACCAGgtaaaatatt ... gaaattgcagTTGCTTGTTGAGTTAGATGGCGCTGAACAACGAAAAGGTGTTTTTGTGATT
EST: gi|27809133|gb|CB063555.1|CB063555
EST:     CCAAACGTGGTAAAGAAGGTGGTTGGGTTGTTGAACGACTATTGAACCAG                         TTGCTTGTTGAGTTAGATGGCGCTGAACAACGAAAAGGTGTTTTTGTGATT
genomic: CCAAACGTGGTAAAGAAGGTGGTTGGGTTGTTGAACGACTATTGAACCAGgtaaaatatt ... gaaattgcagTTGCTTGTTGAGTTAGATGGCGCTGAACAACGAAAAGGTGTTTTTGTGATT
EST: gi|57574066|gb|CX547041.1|CX547041
EST:     AAACGTGGTAAAGAAGGTGGTTGGGTTGTTGAACGACTATTGAACCAG                         TTGCTTGTTGAGTTAGATGGCGCTGAACAACGAAAAGGTGTTTTTGTGATT
genomic: AAACGTGGTAAAGAAGGTGGTTGGGTTGTTGAACGACTATTGAACCAGgtaaaatatt ... gaaattgcagTTGCTTGTTGAGTTAGATGGCGCTGAACAACGAAAAGGTGTTTTTGTGATT
EST: gi|192294149|gb|FG986238.1|FG986238
EST:     CCAAACGTGGTAAAGAAGGTGGTTGGGTTGTTGAACGACTATTGAACCAG                         TTGCTTGTTGAGTTAGATGGCGCTGAACAACGAAAAGGTGTTTTTGTGATT
genomic: CCAAACGTGGTAAAGAAGGTGGTTGGGTTGTTGAACGACTATTGAACCAGgtaaaatatt ... gaaattgcagTTGCTTGTTGAGTTAGATGGCGCTGAACAACGAAAAGGTGTTTTTGTGATT
EST: gi|209722218|gb|BW659356.1|BW659356
EST:     CCAAACGTGGTAAAGAAGGTGGTTGGGTTGTTGAACGACTATTGAACCAG                         TTGCTTGTTGAGTTAGATGGCGCTGAACAACGAAAAGGTGTTTTTGTGATT
genomic: CCAAACGTGGTAAAGAAGGTGGTTGGGTTGTTGAACGACTATTGAACCAGgtaaaatatt ... gaaattgcagTTGCTTGTTGAGTTAGATGGCGCTGAACAACGAAAAGGTGTTTTTGTGATT
EST: gi|298186613|gb|HO037246.1|HO037246
EST:     CCAAACCTGGTAAAGAAGGTGGTTGGGTTGTTGAACGACTATTGAACCAG                         TTGCTTGTTGAGTTAGATGGCGCTGAACAACGAAAAGGTGTTTTTGTGATT
genomic: CCAAACGTGGTAAAGAAGGTGGTTGGGTTGTTGAACGACTATTGAACCAGgtaaaatatt ... gaaattgcagTTGCTTGTTGAGTTAGATGGCGCTGAACAACGAAAAGGTGTTTTTGTGATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGATGCTTTGACAACCAAACGTGGTAAAGAAGGTGGTTGGGTTGTTGAACGACTATTGAACCAGgtaaaatatttattagtctttcggaatatgaaaaaacatagccattttaactgataacaacatcgataaatgatacagttatatgaaattgcag

- - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - AAGAAG