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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttaccattactgtcatatttcttcttttactggatcttataacttttctaatgttaacagctaaacatacttcttatctaattaaatagcgttaaactattttatttgttgattatgctaacatacagcaatttttctggttgcagGTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGACTGCTATTCCCTGCTGATGCAATTGCAAGAGCTAAACACTATCTTTCAT

Basic information

species Glycine max
transcript GLYMA01G03260.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G03260.3 (Glycine max), 3'ss of exon 3
lower sequence: AT1G23310.1 (Arabidopsis thaliana), 3'ss of exon 3
gtttaccattactgtcatatttcttcttttactggatcttataacttttctaatgttaacagctaaacatacttcttatctaattaaatagcgttaaactattttatttgttgattatgctaacatacagcaattttt-ctggttgcagGTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGACTGCTATTCCCTGCTGATGCAATTGCAAGAGCTAAACACTATCTTTCAT
                                                               ||    |   |      | |||| | |||   | ||  ||  || |   | ||  ||  | |||    ||    | |   || ||||| |||||  | ||||||||||| || ||||| ||||| || ||||||||| ||||||| || |||||||| ||||||||||||||||| |||||||| |
--------------------------------------------------------------gtatgtgtgtatagacaattattagacagc--cagac--ttcaatctccggcttgagcctaaatagtaaaacgaataccaattacagGTGGTTGCGCTTTGCCAAGCTCCGTTTCTACTAGATGACCCAAATGTTGGAATGCTATTTCCAGCTGATGCTATTGCAAGAGCTAAACATTATCTTTCCT

upper sequence: GLYMA01G03260.3 (Glycine max), 3'ss of exon 3
lower sequence: AT1G70580.1 (Arabidopsis thaliana), 3'ss of exon 3
gtttaccattactgtcatatttcttcttttactggatcttataacttttctaatgttaacagctaaacatacttcttatctaattaaatagcgttaaactattttatttgttgattatgctaacatacagcaatttttctggttgcagGTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGACTGCTATTCCCTGCTGATGCAATTGCAAGAGCTAAACACTATCTTTCAT
                                                                         |  |||  ||||     |  ||   | |   |||   || |       ||||||  | ||          ||||||| ||| |||| |||||||| ||||| ||  | |||||||| ||||||||  || ||||||| || ||||| |||||||||||||| || |||||||| |
----------------------------------------------------------------------gtataatatgcaattctcatgttttttgccaagctatagatttaa-gcctaaacatattgaaaacc-----aatgcagGTGGTTTCTTTATGCCAAGCACCATTTCTGTTAGATGATCCAAATGTTGGTATGATATTCCCAGCAGATGCTATTGCAAGAGCTAAGCATTATCTTTCCT
















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|19053398|gb|BM732065.1|BM732065
EST:     TGAGCTTCCCTCGTCAG                         GTTGTTGCTTTGTGACAAGCTCCATTCCTACTTGATGATCCTAATGTTGGA
genomic: TGAGCTTCCCTCGTCAGgtttaccatt ... ctggttgcagGTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGA
EST: gi|120529201|gb|EH257335.1|EH257335
EST:     TTGGCAACCCACATGCATTGGGACAGAAACCACTGAGCTTCCCTCGTCAG                         GTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGA
genomic: TTGGCAACCCACATGCATTGGGACAGAAACCACTGAGCTTCCCTCGTCAGgtttaccatt ... ctggttgcagGTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGA
EST: gi|14205452|gb|BG839130.1|BG839130
EST:     TTGGCAACCCACATGCATTGGGACAGAAACCACTGAGCTTCCCTCGTCAG                         GTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGA
genomic: TTGGCAACCCACATGCATTGGGACAGAAACCACTGAGCTTCCCTCGTCAGgtttaccatt ... ctggttgcagGTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGA
EST: gi|15285990|gb|BI469890.1|BI469890
EST:     TTGGCAACCCACATGCATTGGGACAGAAACCACTGAGCTTCCCTCGTCAG                         GTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGA
genomic: TTGGCAACCCACATGCATTGGGACAGAAACCACTGAGCTTCCCTCGTCAGgtttaccatt ... ctggttgcagGTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGA
EST: gi|7283746|gb|AW596349.1|AW596349
EST:     TTGGCAACCCACATGCATTGGGACAGAAACCACTGAGCTTCCCTCGTCAG                         GTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGA
genomic: TTGGCAACCCACATGCATTGGGACAGAAACCACTGAGCTTCCCTCGTCAGgtttaccatt ... ctggttgcagGTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGA
EST: gi|21887563|gb|BQ740776.1|BQ740776
EST:     TTGGCAACCCACATGCATTGGGACAGAAACCACTGAGCTTCCCTCGTCAG                         GTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGA
genomic: TTGGCAACCCACATGCATTGGGACAGAAACCACTGAGCTTCCCTCGTCAGgtttaccatt ... ctggttgcagGTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGA
EST: gi|23052838|gb|BU577329.1|BU577329
EST:     TTGGCAACCCACATGCATTGGGACAGAAACCACTGAGCTTCCCTCGTCAG                         GTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGA
genomic: TTGGCAACCCACATGCATTGGGACAGAAACCACTGAGCTTCCCTCGTCAGgtttaccatt ... ctggttgcagGTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGA
EST: gi|13481869|gb|BG511212.1|BG511212
EST:     TTGGCAACCCACATGCATTGGGACAGAAACCACTGAGCTTCCCTCGTCAG                         GTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGA
genomic: TTGGCAACCCACATGCATTGGGACAGAAACCACTGAGCTTCCCTCGTCAGgtttaccatt ... ctggttgcagGTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGA
EST: gi|23056339|gb|BU577717.1|BU577717
EST:     CCACATGCATTGGGACAGAAACCACTGAGCTTCCCTCGTCAG                         GTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGA
genomic: CCACATGCATTGGGACAGAAACCACTGAGCTTCCCTCGTCAGgtttaccatt ... ctggttgcagGTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGA
EST: gi|298167407|gb|HO012670.1|HO012670
EST:     TTGGCAACCCACATGCATTGGGACAGAAACCACTGAGCTTCCCTCGTCAG                         GTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGA
genomic: TTGGCAACCCACATGCATTGGGACAGAAACCACTGAGCTTCCCTCGTCAGgtttaccatt ... ctggttgcagGTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGA
EST: gi|120491572|gb|EH219739.1|EH219739
EST:     TTGGCAACCCACATGCATTGGGACAGAAACCACTGAGCTTCCCTCGTCAG                         GTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGA
genomic: TTGGCAACCCACATGCATTGGGACAGAAACCACTGAGCTTCCCTCGTCAGgtttaccatt ... ctggttgcagGTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGA
EST: gi|14205590|gb|BG839268.1|BG839268
EST:     TTGGCAACCCACATGCATTGGGACAGAAACCACTGAGCTTCCCTCGTCAG                         GTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGA
genomic: TTGGCAACCCACATGCATTGGGACAGAAACCACTGAGCTTCCCTCGTCAGgtttaccatt ... ctggttgcagGTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGA
EST: gi|15285988|gb|BI469879.1|BI469879
EST:     TTGGCAACCCACATGCATTGGGACAGAAACCACTGAGCTTCCCTCGTCAG                         GTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGA
genomic: TTGGCAACCCACATGCATTGGGACAGAAACCACTGAGCTTCCCTCGTCAGgtttaccatt ... ctggttgcagGTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGA
EST: gi|10847451|gb|BF070138.1|BF070138
EST:     TTGGCAACCCACATGCATTGGGACAGAAACCACTGAGCTTCCCTCGTCAG                         GTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGA
genomic: TTGGCAACCCACATGCATTGGGACAGAAACCACTGAGCTTCCCTCGTCAGgtttaccatt ... ctggttgcagGTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGA
EST: gi|213588415|gb|DB959735.1|DB959735
EST:     TTGGCAACCCACATGCATTGGGACAGAAACCACTGAGCTTCCCTCGTCAG                         GTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGA
genomic: TTGGCAACCCACATGCATTGGGACAGAAACCACTGAGCTTCCCTCGTCAGgtttaccatt ... ctggttgcagGTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaactattttatttgttgattatgctaacatacagcaatttttctggttgcagGTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGACTGCTATTCCCTGCTGATGCAATTGCAAGAGCTAAACACTATCTTTCAT
                        tgctaac  putative branch site (score: 1)
                                        tttttct  putative PPT
      tattttatttgttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttaccattactgtcatatttcttcttttactggatcttataacttttctaatgttaacagctaaacatacttcttatctaattaaatagcgttaaactattttatttgttgattatgctaacatacagcaatttttctggttgcagGTTGTTGCTTTGTGCCAAGCTCCATTCCTACTTGATGATCCTAATGTTGGACTGCTATTCCCTGCTGATGCAATTGCAAGAGCTAAACACTATCTTTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT