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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attcttgaaacttgatagatatttaaaatccagtttttttcatgatcttcatagagaagaaacttattcatgttcccttggtttcttaactgtgactcagGAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTAGATCGTGATTGTTTAAGTGGCTGGGGTGGACATGTTTATGTTGT

Basic information

species Glycine max
transcript GLYMA04G42830.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G42830.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G21720.1 (Arabidopsis thaliana), 3'ss of exon 5
attcttgaaacttgatagatatttaa-aatccagtttttttcatgat-cttcatagagaag----aaacttattcat-gttcccttggtttcttaactgtga---ctcagGAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTAGATCGTGATTGTTTAAGTGGCTGGGGTGGACATGTTTATGTTGT
          | |||  | | ||||| | ||     || ||    || || ||| |         | ||||||  || |   |  ||| ||   |  || |     ||||||| | || ||||||||||||||||| || |||||||| || |||||||| || ||||||||| | ||||| ||||| || ||||||||  ||||
--------ggcatga--ggtgtttaatagtctgagcttgttagccatactccattgtactactctagacttatgtatcgagactctggcttaacacatgaggattttcagGAAGCTGAGGAATTGTTCGAGACAATATCGCAAGCACTTCTCTCATCTGTTGACCGTGATTGTCTGAGTGGTTGGGGAGGGCATGTTTACATTGT

upper sequence: GLYMA04G42830.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0001g02260.t01 (Vitis vinifera), 3'ss of exon 5
attct--tgaaacttgatagatatttaaaatccagtttttttcatgatcttcatagagaagaaacttattcatgttcccttggtttcttaactgtgactcagGAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTAGATCGTGATTGTTTAAGTGGCTGGGGTGGACATGTTTATGTTGT
||| |  | | |      |          |  ||  |||  |    || |  |  |  ||     | |      ||  ||   | | |||||| | | ||||||||| || ||||| || ||||  ||||| ||||||||||| ||||| ||||||||||| || || ||||| ||||| |||||||| ||||||||
attgtgctaagatacagcatgctccctttagtcatctttcgttcccatgtcaa--gctaatgggatcagctgcattgactctttattttaactattattcagGAACCTGAGGAATTATTTGAGATCATCTCTCAAGCACTGCTCTCATCAGTAGATCGTGACTGCTTGAGTGGTTGGGGAGGACATGTCTATGTTGT
















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|16343834|gb|BI969429.1|BI969429
EST:     CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATG                         GAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATGgtttgtctcg ... tgtgactcagGAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|16996875|gb|BM086247.1|BM086247
EST:     CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATG                         GAACCAGAAGAATTGTTCGAGA
genomic: CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATGgtttgtctcg ... tgtgactcagGAACCAGAAGAATTGTTCGAGA
EST: gi|214005797|gb|DB985945.1|DB985945
EST:     CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATG                         GAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATGgtttgtctcg ... tgtgactcagGAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|298166167|gb|HO009138.1|HO009138
EST:     CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATG                         GAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATGgtttgtctcg ... tgtgactcagGAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|298176811|gb|HO023284.1|HO023284
EST:     CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATG                         GAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATGgtttgtctcg ... tgtgactcagGAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|16348632|gb|BI974227.1|BI974227
EST:     CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATG                         GAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATGgtttgtctcg ... tgtgactcagGAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|193694360|gb|FK629504.1|FK629504
EST:     CTTGTGAGGCGATGTTTAAGCCTGACATG                         GAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
genomic: CTTGTGAGTCAATGTTTAAGCCTGACATGgtttgtctcg ... tgtgactcagGAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|8401459|gb|BE057093.1|BE057093
EST:     CATCCGAGTCTCTGTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATG                         GAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATGgtttgtctcg ... tgtgactcagGAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|192322314|gb|FK014555.1|FK014555
EST:     CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATG                         GAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATGgtttgtctcg ... tgtgactcagGAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|192325513|gb|FK018424.1|FK018424
EST:     CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATG                         GAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATGgtttgtctcg ... tgtgactcagGAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|151409085|gb|EV278893.1|EV278893
EST:     CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATG                         GAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATGgtttgtctcg ... tgtgactcagGAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|7588098|gb|AW703901.1|AW703901
EST:     CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTGTAAGCCTGACATG                         GAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATGgtttgtctcg ... tgtgactcagGAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|17963651|gb|BM270398.1|BM270398
EST:     CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATG                         GAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATGgtttgtctcg ... tgtgactcagGAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|8283379|gb|BE020940.1|BE020940
EST:     CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATG                         GAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATGgtttgtctcg ... tgtgactcagGAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|298178421|gb|HO024156.1|HO024156
EST:     CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATG                         GAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATGgtttgtctcg ... tgtgactcagGAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|213605503|gb|DB968761.1|DB968761
EST:     CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATG                         GAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATGgtttgtctcg ... tgtgactcagGAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|6567370|gb|AW234981.1|AW234981
EST:     CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATG                         GAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATGgtttgtctcg ... tgtgactcagGAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|151397166|gb|EV267039.1|EV267039
EST:     CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATG                         GAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATGgtttgtctcg ... tgtgactcagGAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|151411912|gb|EV281723.1|EV281723
EST:     CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATG                         GAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATGgtttgtctcg ... tgtgactcagGAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|16343936|gb|BI969531.1|BI969531
EST:     CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATG                         GAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATGgtttgtctcg ... tgtgactcagGAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcatagagaagaaacttattcatgttcccttggtttcttaactgtgactcagGAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTAGATCGTGATTGTTTAAGTGGCTGGGGTGGACATGTTTATGTTGT
                                      tcttaac  putative branch site (score: 2)
              aaacttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attcttgaaacttgatagatatttaaaatccagtttttttcatgatcttcatagagaagaaacttattcatgttcccttggtttcttaactgtgactcagGAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTAGATCGTGATTGTTTAAGTGGCTGGGGTGGACATGTTTATGTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - catgatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gaagaaac