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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttaaggattttttaaaaagtgcgtaggtcctttctcctagtatatatatgcttctctacttgttacgttttggcttagcaagagctgaatcttatacagGAGTTTGTAACCATGCTTTTCACTTCCATTGCATAAGCCGATGGCTCAAGACCCGTCAAGTATGTCCTCTAG

Basic information

species Glycine max
transcript GLYMA12G32060.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G32060.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g47870.1 (Oryza sativa), 3'ss of exon 3
tttaaggattttttaaaaagtgcgtaggtcctttctcctagtatatat-atgcttc----tctacttgttacgttttggcttagcaagagctgaatcttata-cagGAGTTTGTAACCATGCTTTTCACTTCCATTGCATAAGCCGATGGCTCAAGACCCGTCAAGTATGTCCTCTAG
     |  ||  ||  |  |    | |    ||     |    || ||   |||      || |||    | ||  ||  | | |||    |   | || |  |||||||||| |||||||| || |||||||| ||||| ||||| |||||||||||||||||||| || |||||||
-----gtgttgcttttagtggatattgcattttcgcagtgaattaaatcgagctgtgaagtcaactatccatgtactga-tgaacaatctatctttgttgtgtcagGAGTTTGCAACCATGCATTCCACTTCCACTGCATCAGCCGTTGGCTCAAGACCCGTCAAGTGTGCCCTCTAG

upper sequence: GLYMA12G32060.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G361074_T02 (Zea mays), 3'ss of exon 1
-tttaaggattttttaaaaagtgcgtag-gtcctttctcctagtatatatatgcttctctacttgttacgttttggcttagcaagagctgaatcttatacagGAGTTTGTAACCATGCTTTTCACTTCCATTGCATAAGCCGATGGCTCAAGACCCGTCAAGTATGTCCTCTAG
   |||| ||   ||  |   |||  || |      ||| ||| | |   |  || |   ||| |         |   |  |||    |   | || | ||||| |||| |||||||| || |||||||| || || ||||| ||||| |||||||||||||| || ||||| |
tactaagcatgcattgtattttgcaaagcgctgaaactcttagcagagcca--ctgcctcactggactttgaaagaactgacaatctgtttgtattcttcagGAATTTGCAACCATGCATTCCACTTCCACTGTATCAGCCGTTGGCTAAAGACCCGTCAAGTGTGCCCTCTTG

upper sequence: GLYMA12G32060.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ06425 (Selaginella moellendorffii), 3'ss of exon 2
tttaaggattttttaaaaagtgcgtaggtcctttctcctagtatatatatgcttctctacttgttacgttttggcttagcaagagctgaatctt-atacagGAGTTTGTAACCATGCTTTTCACTTCCATTGCATAAGCCGATGGCTCAAGACCCGTCAAGTATGTCCTCTAG
                                   |   || | ||        ||||| | |||  ||        |  |    ||   | |  || |||| || || |||||||| ||||||||||| ||||| ||||| ||||| ||||| || ||||| || ||||| |
----------------------------------gtaagagaagatgatcatagctctattggttttgtgacaatgcaaaacacactctttgtggatccagGCGTGTGCAACCATGCGTTTCACTTCCACTGCATCAGCCGCTGGCTAAAGACTCGCCAAGTCTGCCCTCTCG

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|6848570|gb|AW350860.1|AW350860
EST:     CCAGGCCAACCAGGCTAGCGCCACTAGCGAGGAATGCACTGTAGCTTGGG                         GAGTTTGTAACCATGCTTTTCACTTCCATTGCATAAGCCGATGGCTCAAGA
genomic: CCAGGCCAACCAGGCTAGCGCCACTAGCGAGGAATGCACTGTAGCTTGGGgtacgctctg ... tcttatacagGAGTTTGTAACCATGCTTTTCACTTCCATTGCATAAGCCGATGGCTCAAGA
EST: gi|4396229|gb|AI495226.1|AI495226
EST:     CAGGCCAACCAGGCTAGCGCCACTAGCGAGGAATGCACTGTAGCTTGGNG                         GAGTT-GTAACCATGCTTTTCACTTCCATTGCATAAGCCGATGGCTCAAG
genomic: CAGGCCAACCAGGCTAGCGCCACTAGCGAGGAATGCACTGTAGCTTGG-Ggtacgctctg ... tcttatacagGAGTTTGTAACCATGCTTTTCACTTCCATTGCATAAGCCGATGGCTCAAG
EST: gi|7590116|gb|AW705876.1|AW705876
EST:     CCAGGCCAACCAAGCTAGCGCCACTAGCGAGGAATGCACTGTAGCTTGGG                         GAGTTTGTAACCATGCTTTTCACTTCCATTGCATAAGCCGATGGCTCAAGA
genomic: CCAGGCCAACCAGGCTAGCGCCACTAGCGAGGAATGCACTGTAGCTTGGGgtacgctctg ... tcttatacagGAGTTTGTAACCATGCTTTTCACTTCCATTGCATAAGCCGATGGCTCAAGA
EST: gi|17023367|gb|BM094401.1|BM094401
EST:     CCAGGCCAACCAGGCTAGCGCCACTAGCGAGGAATGCACTGTAGCTTGGG                         GAGTTTGTAACCATGCTTTTCACTTCCATTGCATAAGCCGATGGCTCAAGA
genomic: CCAGGCCAACCAGGCTAGCGCCACTAGCGAGGAATGCACTGTAGCTTGGGgtacgctctg ... tcttatacagGAGTTTGTAACCATGCTTTTCACTTCCATTGCATAAGCCGATGGCTCAAGA
EST: gi|120532606|gb|EH260739.1|EH260739
EST:     CCAGGCCAACCAGGCTAGCGCCACTAGCGAGGAATGCACTGTAGCTTGGG                         GAGTTTGTAACCATGCTTTTCACTTCCATTGCATAAGCCGATGGCTCAAGA
genomic: CCAGGCCAACCAGGCTAGCGCCACTAGCGAGGAATGCACTGTAGCTTGGGgtacgctctg ... tcttatacagGAGTTTGTAACCATGCTTTTCACTTCCATTGCATAAGCCGATGGCTCAAGA
EST: gi|17152950|gb|BM142883.1|BM142883
EST:     CCAGGCCAACCAGGCTAGCGCCACTAGCGAGGAATGCACTGTAGCTTGGG                         GAGTTTGTAACCATGCTTTTCACTTCCATTGCATAAGCCGATGGCTCAAGA
genomic: CCAGGCCAACCAGGCTAGCGCCACTAGCGAGGAATGCACTGTAGCTTGGGgtacgctctg ... tcttatacagGAGTTTGTAACCATGCTTTTCACTTCCATTGCATAAGCCGATGGCTCAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatgcttctctacttgttacgttttggcttagcaagagctgaatcttatacagGAGTTTGTAACCATGCTTTTCACTTCCATTGCATAAGCCGATGGCTCAAGACCCGTCAAGTATGTCCTCTAG
                                           aatcttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttaaggattttttaaaaagtgcgtaggtcctttctcctagtatatatatgcttctctacttgttacgttttggcttagcaagagctgaatcttatacagGAGTTTGTAACCATGCTTTTCACTTCCATTGCATAAGCCGATGGCTCAAGACCCGTCAAGTATGTCCTCTAG

- - - - - - - - aaagtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agctgaa