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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcttgtaatgattttatgttttgttttggtttgttaagattgatatactacttctgatatgtaccagaaaatattagcatgtgctgttccttttgagtaaggggaaagttggttaactctatctccgtgtgtattatgatttggtcttgtgcagGCTTCTTTTGTTGGAGCCATGGCTATTGCTGACTTAGTGAAGACAACCTTGGGGCCAAAGGGAATG

Basic information

species Glycine max
transcript GLYMA12G09250.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G09250.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 3
gtgagcttgtaatgattttatgttttgttttggtttgttaagattgatatactacttctgatatgtaccagaaaatattagcatgtgctgttccttttgagtaaggggaaagttggttaactctatctccgtgtgtattatgatttg----gtcttgtgcagGCTTCTTTTGTTGGAGCCATGGCTATTGCTGACTTAGTGAAGACAACCTTGGGGCCAAAGGGAATG
                                                            | |  |    ||||  || | ||  | || || |      || |        ||      |||    ||     | || ||  |||      | |  |  |||| || ||| ||||||| ||||| ||||||||| | || ||||||||||| |||||||||||||||
------------------------------------------------------------aaaatttttggaaagcat-aacacattctatttcacc-atgtgaccttttgtttttgctgctcggattcttgaagaatgattgtttatgttatttgttatagGCGTCCTTTATTGGAGCAATGGCGATTGCTGACCTGGTTAAGACAACCTTAGGGCCAAAGGGAATG
















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|7591500|gb|AW707232.1|AW707232
EST:     ATATTTTTAAAAATGAAGCTAGTGAAGAAAAAGGAGAGCGTGCCAGAATG                         GCTTCTTTTGTTGGAGCCATGGCTATTGCTGACTTAGTGAAGACAACCTTG
genomic: ATATTTTTAAAAATGAAGCTAGTGAAGAAAAAGGAGAGCGTGCCAGAATGgtgagcttgt ... tcttgtgcagGCTTCTTTTGTTGGAGCCATGGCTATTGCTGACTTAGTGAAGACAACCTTG
EST: gi|207783070|gb|GD751071.1|GD751071
EST:     TTTTTAAAAATGAAGCTAGTGAGGAAAAAGGAGAGCGTGCCAGAATG                         GCTTCTTTTGTTGGAGCCATGGCTATTGCTGACTTAGTGAAGACAACCTTG
genomic: TTTTTAAAAATGAAGCTAGTGAAGAAAAAGGAGAGCGTGCCAGAATGgtgagcttgt ... tcttgtgcagGCTTCTTTTGTTGGAGCCATGGCTATTGCTGACTTAGTGAAGACAACCTTG
EST: gi|193729723|gb|FK664669.1|FK664669
EST:     ATTTTTTAAAAAATGAAGCTAGTGAAGAAAAAGGAGAGCGTGCCAGAATG                         GCTTCTTTTGTTGGAGCCATGGCTATTGCTGACTTAGTGAAGACAACCTTG
genomic: A-TTTTT-AAAAATGAAGCTAGTGAAGAAAAAGGAGAGCGTGCCAGAATGgtgagcttgt ... tcttgtgcagGCTTCTTTTGTTGGAGCCATGGCTATTGCTGACTTAGTGAAGACAACCTTG
EST: gi|192302430|gb|FG996684.1|FG996684
EST:     ATATTTTTAAAAATGAAGCTAGTGAAGAAAAAGGAGAGCGTGCCAGAGTG                         GCTTCTTTTGTTGGAGCCATGGCTATTGCTGACTTAGTGAAGACAACCTTG
genomic: ATATTTTTAAAAATGAAGCTAGTGAAGAAAAAGGAGAGCGTGCCAGAATGgtgagcttgt ... tcttgtgcagGCTTCTTTTGTTGGAGCCATGGCTATTGCTGACTTAGTGAAGACAACCTTG
EST: gi|15200734|gb|BI424502.1|BI424502
EST:     ATATTTTTAAAAATGAAGCTAGTGAAGAAAAAGGAGAGCGTGCCAGAATG                         GCTTCTTTTGTTGGAGCCATGGCTATTGCTGACTTAGTGAAGACAACCTTG
genomic: ATATTTTTAAAAATGAAGCTAGTGAAGAAAAAGGAGAGCGTGCCAGAATGgtgagcttgt ... tcttgtgcagGCTTCTTTTGTTGGAGCCATGGCTATTGCTGACTTAGTGAAGACAACCTTG
EST: gi|213601247|gb|DB956527.1|DB956527
EST:     ATATTTTTAAAAATGAAGCTAGTGAAGAAAAAGGAGAGCGTGCCAGAATG                         GCTTCTTTTGTTGGAGCCATGGCTATTGCTGACTTAGTGAAGACAACCTTG
genomic: ATATTTTTAAAAATGAAGCTAGTGAAGAAAAAGGAGAGCGTGCCAGAATGgtgagcttgt ... tcttgtgcagGCTTCTTTTGTTGGAGCCATGGCTATTGCTGACTTAGTGAAGACAACCTTG
EST: gi|261497099|gb|GT185167.1|GT185167
EST:     ATATTTTTAAAAATGAAGCTAGTGAAGAAAAAGGAGAGCGTGCCAGAATG                         GCTTCTTTTGTTGGAGCCATGGCTATTGCTGACTTAGTGAAGACAACCTTG
genomic: ATATTTTTAAAAATGAAGCTAGTGAAGAAAAAGGAGAGCGTGCCAGAATGgtgagcttgt ... tcttgtgcagGCTTCTTTTGTTGGAGCCATGGCTATTGCTGACTTAGTGAAGACAACCTTG
EST: gi|208198857|gb|GD998538.1|GD998538
EST:     ATA-TTTT-AAAATGAAGCTAGTG-AGGAAAAGGAGAGCGTGCCAGAATG                         GCTTCTTTTGTTGGAGCCATGGCTATTGCTGACTTAGTGAAGACAACCTTG
genomic: ATATTTTTAAAAATGAAGCTAGTGAAGAAAAAGGAGAGCGTGCCAGAATGgtgagcttgt ... tcttgtgcagGCTTCTTTTGTTGGAGCCATGGCTATTGCTGACTTAGTGAAGACAACCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggggaaagttggttaactctatctccgtgtgtattatgatttggtcttgtgcagGCTTCTTTTGTTGGAGCCATGGCTATTGCTGACTTAGTGAAGACAACCTTGGGGCCAAAGGGAATG
           ggttaac  putative branch site (score: 3)
                                tattatgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcttgtaatgattttatgttttgttttggtttgttaagattgatatactacttctgatatgtaccagaaaatattagcatgtgctgttccttttgagtaaggggaaagttggttaactctatctccgtgtgtattatgatttggtcttgtgcagGCTTCTTTTGTTGGAGCCATGGCTATTGCTGACTTAGTGAAGACAACCTTGGGGCCAAAGGGAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA