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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgcaagtccattctggccaagaagatcatcacaaaatgttctctgcatctattttttcaagtaattaaatttttaacaagtttgtcatgcttctgcagGTTTTCTTTGCCCAGCTCATGCTTGCTGACATGAATAAAGAACTTAAAGGATTAAG

Basic information

species Glycine max
transcript GLYMA08G20930.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G20930.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G015289_T02 (Zea mays), 3'ss of exon 7
-------------------------------------------cttgcaagt-ccat-----tctggccaagaagatcatcacaaaatgttct--ctgcatc--tattttttcaagtaattaaatttttaacaagtttgtcatgcttctgcagGTTTTCTTTGCCCAGCTCATGCTTGCTGACATGAATAAAGAACTTAAAGGATTAAG
                                             ||   || | ||     | |  | |  || ||         ||||  |  ||| | |  | |  ||      | | |||   |  |  |  |  |  |   | ||||||| || ||||| |  ||  | |||||||| ||||||||||| ||||||||||||||
gtaaagtgctaccttaattttcgtttggctggagatagtgtgttctgtgggtgctatagttgtttcacaagtaatatttctgttgcatgtgttgactggaccattgtccttgttcaaagtgaaacactatatgaaatcattctatctatgcagGTGTTTTTTGCACGTCTTTTACTTGCTGAAATGAATAAAGAGCTTAAAGGATTAAG

upper sequence: GLYMA08G20930.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G015289_T01 (Zea mays), 3'ss of exon 7
-------------------------------------------cttgcaagt-ccat-----tctggccaagaagatcatcacaaaatgttct--ctgcatc--tattttttcaagtaattaaatttttaacaagtttgtcatgcttctgcagGTTTTCTTTGCCCAGCTCATGCTTGCTGACATGAATAAAGAACTTAAAGGATTAAG--------------------------------------------
                                             ||   || | ||     | |  | |  || ||         ||||  |  ||| | |  | |  ||      | | |||   |  |  |  |  |  |   | ||||||| || ||||| |  ||  | |||||||| ||||||||||| ||||||||||||||                                            
gtaaagtgctaccttaattttcgtttggctggagatagtgtgttctgtgggtgctatagttgtttcacaagtaatatttctgttgcatgtgttgactggaccattgtccttgttcaaagtgaaacactatatgaaatcattctatctatgcagGTGTTTTTTGCACGTCTTTTACTTGCTGAAATGAATAAAGAGCTTAAAGGATTAAGGTTTCTTACATTGATCCACTAAATGTTTCTTTGTTATAATTTAG

upper sequence: GLYMA08G20930.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv09s0002g02530.t01 (Vitis vinifera), 3'ss of exon 7
cttgcaagtccattctggccaagaagatcatcacaaaatgttctctgcatctattttttcaagtaattaaatt----tttaacaagtttgtcatgcttctgcagGTTTTCTTTGCCCAGCTCATGCTTGCTGACATGAATAAAGAACTTAAAGGATTAAG
  |     |   |  |  |  |     || | |    ||  | ||| ||| | | ||||    | |  |||||    ||| |||| |    ||||| | |||||||||| || ||||| || |||||||| ||||||||||||||||| || ||||||||
--tagtcttttttcataccagatttactctttatgtcatcatttcttcatttgtgttttttgttgaacaaattggaatttcacaaatcc--catgcctttgcagGTTTTTTTCGCCCAACTTATGCTTGCGGACATGAATAAAGAACTCAAGGGATTAAG

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|7924271|gb|AW830297.1|AW830297
EST:     TATTTTGGTCTGGCTCCAGTCTTCGACCTGAAGCCACTGGCTATGGGCTG                         GTTTTCTTTGCCCAGCTCATGCTTGCTGACATGAATAAAGAACTTAAAGGA
genomic: TATTTTGGTCTGGCTCCAGTCTTCGACCTGAAGCCACTGGCTATGGGCTGgtaatttcaa ... gcttctgcagGTTTTCTTTGCCCAGCTCATGCTTGCTGACATGAATAAAGAACTTAAAGGA
EST: gi|193386749|gb|FK352082.1|FK352082
EST:     TATTTTGGTCTGGCTCCAGTCTTCGACCTGAAGCCACTGGCTATGGGCTG                         GTTTTCTTTGCCCAGCTCATGCTTGCTGACATGAATAAAGAACTTAAAGGA
genomic: TATTTTGGTCTGGCTCCAGTCTTCGACCTGAAGCCACTGGCTATGGGCTGgtaatttcaa ... gcttctgcagGTTTTCTTTGCCCAGCTCATGCTTGCTGACATGAATAAAGAACTTAAAGGA
EST: gi|207749540|gb|GD720958.1|GD720958
EST:     TTGGTTCTTGGTCTTCCAGTCTTCGACCTGAAGCCACTGGCTATGGGCTG                         GTTTTCTTTGCCCAGCTCATGCTTGCTGACATGAATAAAGAACTTAAAGGA
genomic: TTGG-TC-TGG-C-TCCAGTCTTCGACCTGAAGCCACTGGCTATGGGCTGgtaatttcaa ... gcttctgcagGTTTTCTTTGCCCAGCTCATGCTTGCTGACATGAATAAAGAACTTAAAGGA
EST: gi|16997272|gb|BM086644.1|BM086644
EST:     TATTTTGGTCTGGCTCCAGTCTTCGACCTGAAGCCACTGGCTATGGGCTG                         GTTTTCTTTGCCCAGCTCATGCTTGCTGACATGAATAAAGAACTTAAAGGA
genomic: TATTTTGGTCTGGCTCCAGTCTTCGACCTGAAGCCACTGGCTATGGGCTGgtaatttcaa ... gcttctgcagGTTTTCTTTGCCCAGCTCATGCTTGCTGACATGAATAAAGAACTTAAAGGA
EST: gi|193653480|gb|FK599478.1|FK599478
EST:     TATTTTGGTCTGGCTCCAGTCTTCGACCTGAAGCCACTGGCTATGGGCTG                         GTTTTCTTTGCCCAGCTCATGCTTGCTGACATGAATAAAGAACTTAAAGGA
genomic: TATTTTGGTCTGGCTCCAGTCTTCGACCTGAAGCCACTGGCTATGGGCTGgtaatttcaa ... gcttctgcagGTTTTCTTTGCCCAGCTCATGCTTGCTGACATGAATAAAGAACTTAAAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatctattttttcaagtaattaaatttttaacaagtttgtcatgcttctgcagGTTTTCTTTGCCCAGCTCATGCTTGCTGACATGAATAAAGAACTTAAAGGATTAAG
                           ttttaac  putative branch site (score: 2)
                                            tgcttct  putative PPT
      tattttttcaagtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgcaagtccattctggccaagaagatcatcacaaaatgttctctgcatctattttttcaagtaattaaatttttaacaagtttgtcatgcttctgcagGTTTTCTTTGCCCAGCTCATGCTTGCTGACATGAATAAAGAACTTAAAGGATTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC