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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtctaattcattgctaaactgtttatggttaattttgtctcattactatttattcacaattagtcttgaagcttttgttttgtctgctttctccttgcagTTGAAATCTCCTGTAGTTTCAAGAATGCCATTGCAACCTGATAACAAGAAGCATCCTGATGATGATGATTCTTGTTCAGTTGCTTCAAT

Basic information

species Glycine max
transcript GLYMA20G34780.4
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G34780.4 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0020g04880.t01 (Vitis vinifera), 3'ss of exon 3
gtctaattcattgctaaactgtttatggttaattttgtctcattactatttattcacaattagtcttgaagcttttgttttgtctgctt-----tctccttgcagTTGAAATCTCCTGTAGTTTCAAGAATGCCATTGCAACCTGATAACAAGAAGCATCCTGATGATGATGATTCTTGTTCAGTTGCTTCAAT
    ||  ||  |  ||   |  |||||  || |||||      |  |       |  |  ||  |  |  ||| || | ||    |||     | | |||||||  ||  || | | | ||  |||| | |||| || |||| ||||||||||||||||||||||| || ||||||||||| ||  ||||   
--gaaagacacagg-aattggactatgg--aaatttgttgacaaatcaacctaagattaggagcttgtatacttctgatatggaaacttctacattttcttgcagCAGACCTCACTTTTGGTGCCAAGGAAGCCACTGGAACCAGATAACAAGAAGCATCCTGATGAAGAAGATTCTTGTTCTGTCACTTCCTC
















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|15199929|gb|BI424081.1|BI424081
EST:     CTTTGAACNNNNNNNNTGTGCTATCTCCCAATCTGTTTAAACAGAATCAG                         TTGAAATCTCCTGTAGTTTCAAGAATGCCATTGCAACCTGATAACAAGAAG
genomic: CTTTGAACAAAAAAAATGTGCTATCTCCCAATCTGTTTAAACAGAATCAGgtatatgctg ... ctccttgcagTTGAAATCTCCTGTAGTTTCAAGAATGCCATTGCAACCTGATAACAAGAAG
EST: gi|5687809|gb|AI940881.1|AI940881
EST:     CTTTGAACNNNNNNNNTGTGCTATCTCCCAATCTGTTTAAACAGAATCAG                         TTGAAATCTCCTGTAGTTTCAAGAATGCCATTGCAACCTGATAACAAGAAG
genomic: CTTTGAACAAAAAAAATGTGCTATCTCCCAATCTGTTTAAACAGAATCAGgtatatgctg ... ctccttgcagTTGAAATCTCCTGTAGTTTCAAGAATGCCATTGCAACCTGATAACAAGAAG
EST: gi|192331631|gb|FK023449.1|FK023449
EST:     CTTTGAACNNNNNNNNTGTGCTATCTCCCAATCTGTTTAAACAGAATCAG                         TTGAAATCTCCTGTAGTTTCAAGAATGCCATTGCAACCTGATAACAAGAAG
genomic: CTTTGAACAAAAAAAATGTGCTATCTCCCAATCTGTTTAAACAGAATCAGgtatatgctg ... ctccttgcagTTGAAATCTCCTGTAGTTTCAAGAATGCCATTGCAACCTGATAACAAGAAG
EST: gi|5687837|gb|AI940816.1|AI940816
EST:     CTTTGAACNNNNNNNNTGTGCTATCTCCCAATCTGTTTAAACAGAATCAG                         TTGAAATCTCCTGTAGTTTCAAGAATGCCATTGCAACCTGATAACAAGAAG
genomic: CTTTGAACAAAAAAAATGTGCTATCTCCCAATCTGTTTAAACAGAATCAGgtatatgctg ... ctccttgcagTTGAAATCTCCTGTAGTTTCAAGAATGCCATTGCAACCTGATAACAAGAAG
EST: gi|192309425|gb|FK000941.1|FK000941
EST:     CTTTGAAC-NNNNNNNTGTGCTATCTCCCAATCTGTTTAAACAGAATCAG                         TTGAAATCTCCTGTAGTTTCAAGAATGCCATTGCAACCTGATAACAAGAAG
genomic: CTTTGAACAAAAAAAATGTGCTATCTCCCAATCTGTTTAAACAGAATCAGgtatatgctg ... ctccttgcagTTGAAATCTCCTGTAGTTTCAAGAATGCCATTGCAACCTGATAACAAGAAG
EST: gi|17153596|gb|BM143529.1|BM143529
EST:     CTTTGAACNNNNNNNNTGTGCTATCTCCCAATCTGTTTAAACAGAATCAG                         TTGAAATCTCCTGTAGTTTCAAGAATGCCATTGCAACCTGATAACAAGAAG
genomic: CTTTGAACAAAAAAAATGTGCTATCTCCCAATCTGTTTAAACAGAATCAGgtatatgctg ... ctccttgcagTTGAAATCTCCTGTAGTTTCAAGAATGCCATTGCAACCTGATAACAAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatttattcacaattagtcttgaagcttttgttttgtctgctttctccttgcagTTGAAATCTCCTGTAGTTTCAAGAATGCCATTGCAACCTGATAACAAGAAGCATCCTGATGATGATGATTCTTGTTCAGTTGCTTCAAT
                          cttttgttttgtctgc  CT-rich tract
                           ttttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctaattcattgctaaactgtttatggttaattttgtctcattactatttattcacaattagtcttgaagcttttgttttgtctgctttctccttgcagTTGAAATCTCCTGTAGTTTCAAGAATGCCATTGCAACCTGATAACAAGAAGCATCCTGATGATGATGATTCTTGTTCAGTTGCTTCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC