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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaatgttcaagagatcccgaaagctctttttaattttcagttgtgtttgctttttcattgtatgatgatgtatgctaaattgagttttaactttggcagCCAATAATTTAGAGGTGGATGCGCTTTTTGTGTACACAAAGACAGGGCACATGGCGTCTCTATTGTCTCGTTGCCGTCCTGACTGCCCAATCTTTGCTTT

Basic information

species Glycine max
transcript GLYMA20G35400.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G35400.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv05s0020g04480.t01 (Vitis vinifera), 3'ss of exon 5
ctaatgttcaagagatcccgaaagctctttttaattttca-gttgtgtttgctttttca--ttgtatgatgatgtatgc-taaattgagttttaactttggcagCCAATAATTTAGAGGTGGATGCGCTTTTTGTGTACACAAAGACAGGGCACATGGCGTCTCTATTGTCTCGTTGCCGTCCTGACTGCCCAATCTTTGCTTT
   ||    | ||||     |  |   || |  ||  |   ||||    |  |||  ||  || | |   ||| |     |   |||| || | | ||   |||| || ||||||| |||||| ||||||||||| ||||||||||| ||||| ||||| |||||  |||| |||||||| |||||||||||||||||||| ||
-ctatcacgaggagaaagatatggtgtttctggatgctagtgttggaacttttttcccactttttctctcgatattgatgtgggttgaattgttattt---cagCGAACAATTTAGCGGTGGACGCGCTTTTTGTTTACACAAAGACCGGGCATATGGCATCTCTCCTGTCACGTTGCCGACCTGACTGCCCAATCTTTGCATT
















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|16342800|gb|BI968395.1|BI968395
EST:     TTTTTCAGAAAAGATATCTGAAGAAATCTGCAATTCAGCTGCTAAGATGG                         CCAATAATTTAGAGGTGGATGCGCTTTTTGTGTACACAAAGACAGGGCACA
genomic: TTTTTCAGAAAAGATATCTGAAGAAATCTGCAATTCAGCTGCTAAGATGGgtaagctgtc ... actttggcagCCAATAATTTAGAGGTGGATGCGCTTTTTGTGTACACAAAGACAGGGCACA
EST: gi|209718962|gb|BW657891.1|BW657891
EST:     TTTTTCAGAAAAGATATCTGAAGAAATCTGCAATTCAGCTGCTAAGATGG                         CCAATAATTTAGAGGTGGATGCGCTTTTTGTGTACACAAAGACAGGGCACA
genomic: TTTTTCAGAAAAGATATCTGAAGAAATCTGCAATTCAGCTGCTAAGATGGgtaagctgtc ... actttggcagCCAATAATTTAGAGGTGGATGCGCTTTTTGTGTACACAAAGACAGGGCACA
EST: gi|58016539|gb|CX703281.1|CX703281
EST:     TTTTTCAGAAAAGATATCTGAAGAAATCTGCAATTCAGCTGCTAAGATGG                         CCAATAATTTAGAGGTGGATGCGCTTTTTGTGTACACAAAGACAGGGCACA
genomic: TTTTTCAGAAAAGATATCTGAAGAAATCTGCAATTCAGCTGCTAAGATGGgtaagctgtc ... actttggcagCCAATAATTTAGAGGTGGATGCGCTTTTTGTGTACACAAAGACAGGGCACA
EST: gi|42723116|gb|CK769015.1|CK769015
EST:     TTTTTCAGAAAAGATATCTGAAGAAATCTGCAATTCAGCTGCTAAGATGG                         CCAATAATTTAGAGGTGGATGCGCTTTTTGTGTACACAAAGACAGGGCACA
genomic: TTTTTCAGAAAAGATATCTGAAGAAATCTGCAATTCAGCTGCTAAGATGGgtaagctgtc ... actttggcagCCAATAATTTAGAGGTGGATGCGCTTTTTGTGTACACAAAGACAGGGCACA
EST: gi|6227927|gb|AW156589.1|AW156589
EST:     TCAGAAAAGATATCTGAAGAAATCTGCAATTCAGCTGCTAAGATGG                         CCAATAATTTAGAGGTGGATGCGCTTTTTGTGTACACAAAGACAGGGCACA
genomic: TCAGAAAAGATATCTGAAGAAATCTGCAATTCAGCTGCTAAGATGGgtaagctgtc ... actttggcagCCAATAATTTAGAGGTGGATGCGCTTTTTGTGTACACAAAGACAGGGCACA
EST: gi|192307675|gb|FK001619.1|FK001619
EST:     TTTTTCAGAAAAGATATCTGAAGAAATCTGCAATTCAGCTGCTAAGATGG                         CCAATAATTTAGAGGTGGATGCGCTTTTTGTGTACACAAAGACAGGACACA
genomic: TTTTTCAGAAAAGATATCTGAAGAAATCTGCAATTCAGCTGCTAAGATGGgtaagctgtc ... actttggcagCCAATAATTTAGAGGTGGATGCGCTTTTTGTGTACACAAAGACAGGGCACA
EST: gi|9984631|gb|BE658739.1|BE658739
EST:     TGAAGAAANCTGCAATTCAGCTNNNNNGATGG                         NCAATAATTTAGAGGTGGATGCGCTTTTTGTGTACACAAAGACAGGGCACA
genomic: TGAAGAAATCTGCAATTCAGCTGCTAAGATGGgtaagctgtc ... actttggcagCCAATAATTTAGAGGTGGATGCGCTTTTTGTGTACACAAAGACAGGGCACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgctttttcattgtatgatgatgtatgctaaattgagttttaactttggcagCCAATAATTTAGAGGTGGATGCGCTTTTTGTGTACACAAAGACAGGGCACATGGCGTCTCTATTGTCTCGTTGCCGTCCTGACTGCCCAATCTTTGCTTT
                                        ttttaac  putative branch site (score: 2)
                               taaattgagttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctaatgttcaagagatcccgaaagctctttttaattttcagttgtgtttgctttttcattgtatgatgatgtatgctaaattgagttttaactttggcagCCAATAATTTAGAGGTGGATGCGCTTTTTGTGTACACAAAGACAGGGCACATGGCGTCTCTATTGTCTCGTTGCCGTCCTGACTGCCCAATCTTTGCTTT

- - - - - - - - - - - - - - - - - - - -agttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtatgct