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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aataatttgtaggggactactgagtatctgttggaattgcaaactaggacctgccattccaaaactcacatttaatttgtctttttctgctggtatatagCGACTCGGTGCTAAAACATGCATCCAGTGATTTCAAGAAAATGGGGCAACGAATATTTATATTCATTGTTGGTGGAGCAACCAGATCTGAG

Basic information

species Glycine max
transcript GLYMA17G14450.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G14450.1 (Glycine max), 3'ss of exon 18
lower sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 18
aataatttgtaggggactactgagtatctgttggaattgcaaactaggacctgccatt-ccaaaactcac-atttaatttgtctttttctgctggtatat----agCGACTCGGTGCTAAAACATGCATCCAGTGATTTCAAGAAAATGGGGCAACGAATATTTATATTCATTGTTGGTGGAGCAACCAGATCTGAG
      |||   |  || | |   | | | ||     ||  |      |  | ||||| ||  |  | |  || | |    | |  | |||||  | | |    || || ||  | || | |||||||||||||||||||||||||||||| || || || ||| |||| ||||| |||||||| ||  |||| |||
------ttgacagctacaattagttttgttttcctcctgtgactatttaaattccattgccttattttatgatcttacccatttcctgctgcttttttttttttagTGATTCAATACTGAGACATGCATCCAGTGATTTCAAGAAAATGGGCCAGCGCATTTTTGTATTTATTGTAGGTGGAGCTACTCGATCCGAG
















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|209703155|gb|BW673314.1|BW673314
EST:     CGCACACCAACTTGGGCTCGACCTAGAGGCTCTGATGATGGATATTCAAG                         CGACTCGGTGCTAAAACATGCATCCAGTGATTTCAAGAAAATGGGGCAACG
genomic: CGCACACCAACTTGGGCTCGACCTAGAGGCTCTGATGATGGATATTCAAGgttttacttt ... tggtatatagCGACTCGGTGCTAAAACATGCATCCAGTGATTTCAAGAAAATGGGGCAACG
EST: gi|193419802|gb|FK382430.1|FK382430
EST:     CGCACACCAACTTGGGCTCGACCTAGAGGCTCTGATGATGGATATTCAAG                         CGACTCGGTGCTAAAACATGCATCCAGTGATTTCAA
genomic: CGCACACCAACTTGGGCTCGACCTAGAGGCTCTGATGATGGATATTCAAGgttttacttt ... tggtatatagCGACTCGGTGCTAAAACATGCATCCAGTGATTTCAA
EST: gi|213606905|gb|DB974354.1|DB974354
EST:     TTCACACCAACTTGGGCTCGACCTAGAGGCTCTGATGATGGATATTCAAG                         CGACTCGGTTCTAAAACATGCATCCAGTGATTTCAAGAAAATGGGGCAACG
genomic: CGCACACCAACTTGGGCTCGACCTAGAGGCTCTGATGATGGATATTCAAGgttttacttt ... tggtatatagCGACTCGGTGCTAAAACATGCATCCAGTGATTTCAAGAAAATGGGGCAACG
EST: gi|58014859|gb|CX701601.1|CX701601
EST:     CGCACACCAACTTGGGCTCGACCTAGAGGCTCTGATGATGGATATTCAAG                         CGACTCGGTGCTAAAACATGCATCCAGTGATTTCAAGAAAATGGGGCAACG
genomic: CGCACACCAACTTGGGCTCGACCTAGAGGCTCTGATGATGGATATTCAAGgttttacttt ... tggtatatagCGACTCGGTGCTAAAACATGCATCCAGTGATTTCAAGAAAATGGGGCAACG
EST: gi|254340092|gb|GR858217.1|GR858217
EST:     CGCACACCAACTTGGGCTCGACCTAGAGGCTCTGATGATGGATATTCAAG                         CGACTCGGTGCTAAAACATGCATCCAGTGATTTCAAGAAAATGGGGCAACG
genomic: CGCACACCAACTTGGGCTCGACCTAGAGGCTCTGATGATGGATATTCAAGgttttacttt ... tggtatatagCGACTCGGTGCTAAAACATGCATCCAGTGATTTCAAGAAAATGGGGCAACG
EST: gi|208143354|gb|GD943268.1|GD943268
EST:     GGGCTCGACCTAGAGGCTCTGATGATGGATATTCAAG                         CGATTCGGTGCTAAAACACGCATCCAGTGATTTCAAGAAAGTGGGGCAAAG
genomic: GGGCTCGACCTAGAGGCTCTGATGATGGATATTCAAGgttttacttt ... tggtatatagCGACTCGGTGCTAAAACATGCATCCAGTGATTTCAAGAAAATGGGGCAACG
EST: gi|254321303|gb|GR824620.1|GR824620
EST:     CGCACACCAACTTGGGCTCGACCTAGAGGCTCTGATGATGGATATTCAAG                         CGACTCGGTGCTAAAACATGCATCCAGTGATTTCAAGAAAATGGGGCAACG
genomic: CGCACACCAACTTGGGCTCGACCTAGAGGCTCTGATGATGGATATTCAAGgttttacttt ... tggtatatagCGACTCGGTGCTAAAACATGCATCCAGTGATTTCAAGAAAATGGGGCAACG
EST: gi|6666591|gb|AW278050.1|AW278050
EST:     CGCACACCAACTTGGGCTCGACCTAGAGGCTCTGATGATGGATATTCAAG                         CGACTCGGTGCTAAAACATGCATCCAGTGATTTCAAGAAAATGGGGCAACG
genomic: CGCACACCAACTTGGGCTCGACCTAGAGGCTCTGATGATGGATATTCAAGgttttacttt ... tggtatatagCGACTCGGTGCTAAAACATGCATCCAGTGATTTCAAGAAAATGGGGCAACG
EST: gi|208325196|gb|GE123596.1|GE123596
EST:     CGCACACCAACTTGGGCTCGACCTAGAGGCTCTGATGATGGATATTCAAG                         CGACTCGGTGCTAAAACAATGCATCCA
genomic: CGCACACCAACTTGGGCTCGACCTAGAGGCTCTGATGATGGATATTCAAGgttttacttt ... tggtatatagCGACTCGGTGCTAAAACA-TGCATCCA
EST: gi|209720988|gb|BW682467.1|BW682467
EST:     CGCACACCAACTTGGGCTCGACCTAGAGGCTCTGATGATGGATATTCAAG                         CGACTCGGTGCTAAAACATGCATCCAGTGATTTCAAGAAAATGGGGCAACG
genomic: CGCACACCAACTTGGGCTCGACCTAGAGGCTCTGATGATGGATATTCAAGgttttacttt ... tggtatatagCGACTCGGTGCTAAAACATGCATCCAGTGATTTCAAGAAAATGGGGCAACG
EST: gi|208292619|gb|GE093741.1|GE093741
EST:     TGATGGATATTCAAG                         CGACTCGGTGCTAAAACATGCATCCAGTGATTTCAAGAAAATGGGGCAACG
genomic: TGATGGATATTCAAGgttttacttt ... tggtatatagCGACTCGGTGCTAAAACATGCATCCAGTGATTTCAAGAAAATGGGGCAACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggacctgccattccaaaactcacatttaatttgtctttttctgctggtatatagCGACTCGGTGCTAAAACATGCATCCAGTGATTTCAAGAAAATGGGGCAACGAATATTTATATTCATTGTTGGTGGAGCAACCAGATCTGAG
                              tttgtctttttctgct  CT-rich tract
                        atttaatttgtctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aataatttgtaggggactactgagtatctgttggaattgcaaactaggacctgccattccaaaactcacatttaatttgtctttttctgctggtatatagCGACTCGGTGCTAAAACATGCATCCAGTGATTTCAAGAAAATGGGGCAACGAATATTTATATTCATTGTTGGTGGAGCAACCAGATCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - gtagggg
- - - - - - - -actactg
- - - - - - - - - - - - - tctgttg
- - - - - - - - - - - - - - - - - - -tgcaaac
- - - - - - - - - - - - - - - - - - - - - - - - acctgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaaaac