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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atagaatatattattaaagaaaagaacaaacttttgttagtattattcatgtttatcgtgtttcttttgaaactgatacattgtttacaattatctgcagCTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAGACCTGCATTTCTTTGTCACTGGTGGTGAAGATGAAAATGAGCTCATTCT

Basic information

species Glycine max
transcript GLYMA08G20370.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G20370.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g21250.1 (Oryza sativa), 3'ss of exon 3
-atagaatatattattaaagaaaagaacaaacttttgttagtattattcatgtttatcgtgtttcttttgaaactgatacattgtttacaattatctgcagCTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAGACCTGCATTTCTTTGTCACTGGTGGTGAAGATGAAAATGAGCTCATTCT
   |   |||| |  |      |   |   |||||| | |   |||||| |   |    | |    |||     ||||||  |||||    || ||| |||||||| ||||| |  ||||   | ||||  |  |||| || |||||||||||||| ||||| |||||||| | |||||| ||||| |||||||||||| |
tcaatgttataattatgtctcgatatatccacttttctgatctttattctttagttgaatttggaattttcctttgatac-ctgtttttggttctctccagCTGAGATAACATTGTTTGATGGCTATATTGTCGTTTATAAGTTTGTACAAGACCTTCATTTTTTTGTCACCGCTGGTGATGATGAGAATGAGCTCATTAT
















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|21256834|gb|BQ453722.1|BQ453722
EST:     TGAGAAGTTTGTATTTACTAAGACTGTTAAGACAAATGCTCGTACGGAAG                         CTGAGGTAACACTACTTGAGAACAATATCATTATTTATAAATTTGTACAAG
genomic: TGAGAAGTTTGTATTTACTAAGACTGTTAAGACAAATGCTCGTACGGAAGgtaagcagta ... ttatctgcagCTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAG
EST: gi|151407511|gb|EV277326.1|EV277326
EST:     TGAGAAGTTTGTATTTACTAAGACTGTTAAGACAAATGCTCGTACGGAAG                         CTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAG
genomic: TGAGAAGTTTGTATTTACTAAGACTGTTAAGACAAATGCTCGTACGGAAGgtaagcagta ... ttatctgcagCTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAG
EST: gi|192330007|gb|FK020823.1|FK020823
EST:     TGAGAAGTTTGTATTTACTAAGACTGTTAAGACAAATGCTCGTACGGAAG                         CTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAG
genomic: TGAGAAGTTTGTATTTACTAAGACTGTTAAGACAAATGCTCGTACGGAAGgtaagcagta ... ttatctgcagCTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAG
EST: gi|15814159|gb|BI786434.1|BI786434
EST:     TGAGAAGTTTGTATTTACTAAGACTGTTAAGACAAATGCTCGTACGGAAG                         CTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAG
genomic: TGAGAAGTTTGTATTTACTAAGACTGTTAAGACAAATGCTCGTACGGAAGgtaagcagta ... ttatctgcagCTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAG
EST: gi|151400839|gb|EV270653.1|EV270653
EST:     TGAGAAGTTTGTATTTACTAAGACTGTTAAGACAAATGCTCGTACGGAAG                         CTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAG
genomic: TGAGAAGTTTGTATTTACTAAGACTGTTAAGACAAATGCTCGTACGGAAGgtaagcagta ... ttatctgcagCTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAG
EST: gi|22523511|gb|BU082322.1|BU082322
EST:     TGAGAAGTTTGTATTTACTAAGACTGTTAAGACAAATGCTCGTACGGAAG                         CTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAG
genomic: TGAGAAGTTTGTATTTACTAAGACTGTTAAGACAAATGCTCGTACGGAAGgtaagcagta ... ttatctgcagCTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAG
EST: gi|7285995|gb|AW598482.1|AW598482
EST:     TGAGAAGTTTGTATTTACTAAGACTGTTAAGACAAATGCTCGTACGGAAG                         CTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAG
genomic: TGAGAAGTTTGTATTTACTAAGACTGTTAAGACAAATGCTCGTACGGAAGgtaagcagta ... ttatctgcagCTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAG
EST: gi|15814245|gb|BI786520.1|BI786520
EST:     TGAGAAGTTTGTATTTACTAAGACTGTTAAGACAAATGCTCGTACGGAAG                         CTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAG
genomic: TGAGAAGTTTGTATTTACTAAGACTGTTAAGACAAATGCTCGTACGGAAGgtaagcagta ... ttatctgcagCTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAG
EST: gi|151410805|gb|EV280620.1|EV280620
EST:     TGAGAAGTTTGTATTTACTAAGACTGTTAAGACAAATGCTCGTACGGAAG                         CTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAG
genomic: TGAGAAGTTTGTATTTACTAAGACTGTTAAGACAAATGCTCGTACGGAAGgtaagcagta ... ttatctgcagCTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAG
EST: gi|19053250|gb|BM731917.1|BM731917
EST:     TGAGAAGTTTGTATTTACTAAGACTGTTAAGACAAATGCTCGTACGGAAG                         CTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAG
genomic: TGAGAAGTTTGTATTTACTAAGACTGTTAAGACAAATGCTCGTACGGAAGgtaagcagta ... ttatctgcagCTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAG
EST: gi|22523391|gb|BU082202.1|BU082202
EST:     TGAGAAGTTTGTATTTACTAAGACTGTTAAGACAAATGCTCGTACGGAAG                         CTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAG
genomic: TGAGAAGTTTGTATTTACTAAGACTGTTAAGACAAATGCTCGTACGGAAGgtaagcagta ... ttatctgcagCTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAG
EST: gi|31560978|gb|CD486816.1|CD486816
EST:     TGAGAAGTTTGTATTTACTAAGACTGTTAAGACAAATGCTCGTACGGAAG                         CTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAG
genomic: TGAGAAGTTTGTATTTACTAAGACTGTTAAGACAAATGCTCGTACGGAAGgtaagcagta ... ttatctgcagCTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAG
EST: gi|192294008|gb|FG987177.1|FG987177
EST:     TGAGAAGTTTGTATTTACTAAGACTGTTAAGACAAATGCTCGTACGGAAG                         CTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAG
genomic: TGAGAAGTTTGTATTTACTAAGACTGTTAAGACAAATGCTCGTACGGAAGgtaagcagta ... ttatctgcagCTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAG
EST: gi|193376778|gb|FK340973.1|FK340973
EST:     GTTAAGACAAATGCTCGTACGGAAG                         CTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAG
genomic: GTTAAGACAAATGCTCGTACGGAAGgtaagcagta ... ttatctgcagCTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAG
EST: gi|10843110|gb|BF066429.1|BF066429
EST:     TGAGAAGTTTGTATTTACTAAGACTGTTAAGACAAATGCTCGTACGGAAG                         CTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAG
genomic: TGAGAAGTTTGTATTTACTAAGACTGTTAAGACAAATGCTCGTACGGAAGgtaagcagta ... ttatctgcagCTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAG
EST: gi|13252293|gb|BG363196.1|BG363196
EST:     TGAGAAGTTTGTATTTACTAAGACTGTTAAGACAAATGCTCGTACGGAAG                         CTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAG
genomic: TGAGAAGTTTGTATTTACTAAGACTGTTAAGACAAATGCTCGTACGGAAGgtaagcagta ... ttatctgcagCTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAG
EST: gi|13480157|gb|BG509500.1|BG509500
EST:     TGAGAAGTTTGTATTTACTAAGACTGTTAAGACAAATGCTCGTACGGAAG                         CTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAG
genomic: TGAGAAGTTTGTATTTACTAAGACTGTTAAGACAAATGCTCGTACGGAAGgtaagcagta ... ttatctgcagCTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatgtttatcgtgtttcttttgaaactgatacattgtttacaattatctgcagCTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAGACCTGCATTTCTTTGTCACTGGTGGTGAAGATGAAAATGAGCTCATTCT
                         aactgat  putative branch site (score: 3)
                                  attgtttacaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atagaatatattattaaagaaaagaacaaacttttgttagtattattcatgtttatcgtgtttcttttgaaactgatacattgtttacaattatctgcagCTGAGGTAACACTACTTGAGAACAATATCATTATTTACAAATTTGTACAAGACCTGCATTTCTTTGTCACTGGTGGTGAAGATGAAAATGAGCTCATTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA