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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcgtcattttttttataaatatcaaggatgtaaccacttgtgtcaacattaatgcttaaacttcccaacatatttgatcaaataattttggaaaatgcagGTACCTCTTGTGGCATCAAATAGGATAGGAAAGGAGATAATTGAGACTGAGCATGGAAAAAGTGAGATAACATTCTATGGAAACTCCTTCATAGCAG

Basic information

species Glycine max
transcript GLYMA08G07960.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G07960.1 (Glycine max), 3'ss of exon 7
lower sequence: AT2G27450.2 (Arabidopsis thaliana), 3'ss of exon 7
----tcgtcattttttttataaatatcaaggatgtaaccacttgtgtcaacattaatgcttaaacttcccaac--atatttgatcaaataattttggaaaatgcagGTACCTCTTGTGGCATCAAATAGGATAGGAAAGGAGATAATTGAGACTGAGCATGGAAAAAGTGAGATAACATTCTATGGAAACTCCTTCATAGCAG
       |  ||| ||   | | |   |  |||   |  |||||   ||| ||   ||||| || |      |  ||   |||   ||||||  |      | ||||||||||| || || |||||| | ||||| ||||| |||||||| ||||||||||||   ||| |||| || ||||| ||||  |||||||| || |
atgtatctagtttgttccgttatttctactgattaga--acttg--ccaaaat--gtgcttcaaatggtttgctaatgagtgaggcaataatactttgggtttcagGTACCTCTAGTAGCCTCAAATCGCATAGGGAAGGAAATAATTGAAACTGAGCATGGACCTAGTCAGATCACTTTCTACGGAACTTCCTTCATTGCCG

upper sequence: GLYMA08G07960.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv06s0080g00560.t01 (Vitis vinifera), 3'ss of exon 7
--tcgtcatttttttta-----taaatatcaaggatgtaaccacttgtgtcaacattaatgcttaaacttcccaacatatttgatcaaataattttggaaaatgcagGTACCTCTTGTGGCATCAAATAGGATAGGAAAGGAGATAATTGAGACTGAGCATGGAAAAAGTGAGATAACATTCTATGGAAACTCCTTCATAGCAG
  | | ||||  || |      | | ||| | |  |  |     | |||||| ||| ||||||   ||| | |||       ||| ||   ||||| |  ||| ||||||||||| || || |||||  | || || ||||| |||||  |||| ||||||||||| | ||| || ||||||||||||||||| || |||||||
gcttgccattaattgtgaagtttgagtatgatgtttacagaagttggtgtca-cataaatgct---actgctcaatggg---gattaatctatttttgttaattcagGTACCTCTAGTAGCTTCAAACCGCATTGGGAAGGAAATAATCCAGACAGAGCATGGAAATACTGAAATCACATTCTATGGAAACTCTTTTATAGCAG
















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|151410591|gb|EV280406.1|EV280406
EST:     CTCGTGACCACTGGAAACGAGTAATGCAAGGACATGCTGGGGCTAATTTG                         GTACCTCTTGTGGCATCAA
genomic: CTCGTGACCACTGGAAACGAGTAATGCAAGGACATGCTGGGGCTAATTTGgtaggttttg ... gaaaatgcagGTACCTCTTGTGGCATCAA
EST: gi|254330222|gb|GR839775.1|GR839775
EST:     CTCGTGACCACTGGAAACGAGTAATGCAAGGACATGCTGGGGCTAATTTG                         GTACCTCTTGTGGCATCAAATAGGATAGGAAAGGAGATAATTGAGACTGAG
genomic: CTCGTGACCACTGGAAACGAGTAATGCAAGGACATGCTGGGGCTAATTTGgtaggttttg ... gaaaatgcagGTACCTCTTGTGGCATCAAATAGGATAGGAAAGGAGATAATTGAGACTGAG
EST: gi|24135848|gb|BU926358.1|BU926358
EST:     CTCGTGACCACTGGAAACGAGTAATGCGAGGACATGCTGAGGCTAATTTG                         GTACCTCTTGGGGCATCAAATAGGATAGGAAAGGAGATAATT
genomic: CTCGTGACCACTGGAAACGAGTAATGCAAGGACATGCTGGGGCTAATTTGgtaggttttg ... gaaaatgcagGTACCTCTTGTGGCATCAAATAGGATAGGAAAGGAGATAATT
EST: gi|6916098|gb|AW397628.1|AW397628
EST:     CTTGTGACCACTGGAAACGAGTAATGCAAGGACATGCTGGGGCTAATTTG                         GTACCTCTTGTGGCATCAAATAGGATAGGAAAGGAGATAATTGAGACTGAG
genomic: CTCGTGACCACTGGAAACGAGTAATGCAAGGACATGCTGGGGCTAATTTGgtaggttttg ... gaaaatgcagGTACCTCTTGTGGCATCAAATAGGATAGGAAAGGAGATAATTGAGACTGAG
EST: gi|192328548|gb|FK023552.1|FK023552
EST:     CTCGTGACCACTGGAAACGAGTAATGCAAGGACATGCTGGGGCTAATTTG                         GTACCTCTTGTGGCATCAAATAGGATAGGAAAGGAGATAATTGAGACTGAG
genomic: CTCGTGACCACTGGAAACGAGTAATGCAAGGACATGCTGGGGCTAATTTGgtaggttttg ... gaaaatgcagGTACCTCTTGTGGCATCAAATAGGATAGGAAAGGAGATAATTGAGACTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acattaatgcttaaacttcccaacatatttgatcaaataattttggaaaatgcagGTACCTCTTGTGGCATCAAATAGGATAGGAAAGGAGATAATTGAGACTGAGCATGGAAAAAGTGAGATAACATTCTATGGAAACTCCTTCATAGCAG
                        atatttgatcaaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcgtcattttttttataaatatcaaggatgtaaccacttgtgtcaacattaatgcttaaacttcccaacatatttgatcaaataattttggaaaatgcagGTACCTCTTGTGGCATCAAATAGGATAGGAAAGGAGATAATTGAGACTGAGCATGGAAAAAGTGAGATAACATTCTATGGAAACTCCTTCATAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - -ccacttg
- - - - - - - - - - - - - - - - - - - - tgtcaac
- - - - - - - - - - - - - - - - - - - - - - - - ttaatgc