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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agacttgtgcaaccagtgcaagtttatttatttcctcttatattttgtatatttgacattttgacctggaagttttattctcttttgaatatggatatagGAGGATCAAAGAAATTATTGTTCAGTTCAAAGGGAGCTTTGTGCTAGAATTGCAGCAGAGAGCTATTGAATTCAATTCGATTATTGCAAAGCATCAAAAT

Basic information

species Glycine max
transcript GLYMA01G03890.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G03890.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G017421_T01 (Zea mays), 3'ss of exon 12
agacttgtgcaaccagtg-caagtttatttatttcctcttatattttgtatatttgacattttgacctggaagttttattctcttt-tgaatatggatatagGAGGATCAAAGAAATTATTGTTCAGTTCAAAGGGAGCTTTGTGCTAGAATTGCAGCAGAGAGCTATTGAATTCAATTCGATTATTGCAAAGCATCAAAAT
     |||      |||  ||||| ||  | ||   |    |  | || |||| |   |   || | ||  | ||||||  | ||| |   | ||     ||||| || ||||||||  |||  ||    |||||||    |||||| ||||||||||| ||| |||||||||||| ||| |||||   ||  |||||    
tacagtgtcagcttagtttcaagtctacgtgttcattagattgatgtg-atatattgtaaagtggc-tgataattttatcatttttattcttgtgttgtcagGAGAATAAAAGAAATAGTTGCGCAAAATAAAGGGAATACTGTGCTTGAATTGCAGCAAAGATCTATTGAATTCAGTTCCATTATACAAAGACATCAGTCG

upper sequence: GLYMA01G03890.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G030144_T03 (Zea mays), 3'ss of exon 11
------agacttgtgcaaccagtgcaagtttatttatttcctcttatattttgtatatttgacattttgacctggaagttttattctcttttgaatatggatatagGAGGATCAAAGAAATTATTGTTCAGTTCAAAGGGAGCTTTGTGCTAGAATTGCAGCAGAGAGCTATTGAATTCAATTCGATTATTGCAAAGCATCAAAAT
      |    | ||   ||  |   | |  ||   ||    |   |    |||| | | | ||   |||  |     |||| || |  ||    | |      |||||||| ||||||||  |||  ||    |||||||    |||||| ||||||||||| ||| |||||||||||| ||| |||||   ||  ||||||   
agtttcaagtctatgtgcccccttgtaatgcatgccttgaaacaagttcactgtaaagt-ggcagcatgatttcatcatttttttattcttgtgttgt-----cagGAGGATAAAAGAAATAGTTGCGCAAAATAAAGGGAATACTGTGCTTGAATTGCAGCAAAGATCTATTGAATTCAGTTCCATTATACAAAGACATCAATCG

upper sequence: GLYMA01G03890.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 12
agacttgtgcaaccagtgcaagtttatttatttcctcttatattttgtatatttgacattttgacctggaagtttt-----attctcttttgaatatggat-atagGAGGATCAAAGAAATTATTGTTCAGTTCAAAGGGAGCTTTGTGCTAGAATTGCAGCAGAGAGCTATTGAATTCAATTCGATTATTGCAAAGCATCAAAAT
    | ||      |  |   |   || |  ||   || ||| ||| |  |  | || |||| |  ||||| ||||     ||| |  ||| ||| |  || |||||||||| |  || || ||||| ||||  ||||| ||| ||||||| ||||||||||||||| | |||||||| ||||| |||||||  ||||||||||||
--cttagttgggttaaaggccgaacatatgattttact-ataatttcttcagct-actttttaa--tggaatttttttttaattgttctttaaatgttaattatagGAGGATAAGGGATATAATTGTCCAGTGTAAAGGAAGCCTTGTGCTTGAATTGCAGCAGAGATCCATTGAATTTAATTCCATTATTGGGAAGCATCAAAAT

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|209707485|gb|BW664944.1|BW664944
EST:     GCTTTGGTTGCACTATTAAAGCTCTCTTCACGTTTCCCTTCATGTTCAGA                         GAGGATCAAAGAAATTATTGTTCAGTTCAAAGGGAGCTTTGTGCTAGAATT
genomic: GCTTTGGTTGCACTATTAAAGCTCTCTTCACGTTTCCCTTCATGTTCAGAgtatgatctg ... atggatatagGAGGATCAAAGAAATTATTGTTCAGTTCAAAGGGAGCTTTGTGCTAGAATT
EST: gi|208139507|gb|GD934269.1|GD934269
EST:     GCTTTGGTTGCACTATTAAAGCTCTCTTCACGTTTCCCTTCATGTTCAGA                         GAGGATCAAAGAAATTATTGTTCAGTTCAAAGGGAGCTTTGTGCTAGAATT
genomic: GCTTTGGTTGCACTATTAAAGCTCTCTTCACGTTTCCCTTCATGTTCAGAgtatgatctg ... atggatatagGAGGATCAAAGAAATTATTGTTCAGTTCAAAGGGAGCTTTGTGCTAGAATT
EST: gi|213606433|gb|DB962998.1|DB962998
EST:     GCTTTGGTTGCACTATTAAAGCTCTCTTCACGTTTCCCTTCATGTTCAGA                         GAGGATCAAAGAAATTATTGTTCAGT
genomic: GCTTTGGTTGCACTATTAAAGCTCTCTTCACGTTTCCCTTCATGTTCAGAgtatgatctg ... atggatatagGAGGATCAAAGAAATTATTGTTCAGT
EST: gi|17518713|gb|BM187755.1|BM187755
EST:     GCTTTGGTTGCACTATTAAAGCTCTCTTCACGTTTCCCTTCATGTTCAGA                         GAGGATCAAAGAAATTATTGTTCAGTTCAAAGGGAGCTTTGTGCTAGAATT
genomic: GCTTTGGTTGCACTATTAAAGCTCTCTTCACGTTTCCCTTCATGTTCAGAgtatgatctg ... atggatatagGAGGATCAAAGAAATTATTGTTCAGTTCAAAGGGAGCTTTGTGCTAGAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtatatttgacattttgacctggaagttttattctcttttgaatatggatatagGAGGATCAAAGAAATTATTGTTCAGTTCAAAGGGAGCTTTGTGCTAGAATTGCAGCAGAGAGCTATTGAATTCAATTCGATTATTGCAAAGCATCAAAAT
             ttttgac  putative branch site (score: 3)
                           ttttattctctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agacttgtgcaaccagtgcaagtttatttatttcctcttatattttgtatatttgacattttgacctggaagttttattctcttttgaatatggatatagGAGGATCAAAGAAATTATTGTTCAGTTCAAAGGGAGCTTTGTGCTAGAATTGCAGCAGAGAGCTATTGAATTCAATTCGATTATTGCAAAGCATCAAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - -tgcaacc
- - - - - - - - tgcaagt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacctg