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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataagcaaccaacagtactctatctaactatttgcattcccatttagagattagtctaaattcatgtcacactaattaaatattaaaatgatagAGCGAATTCGAGGAGATAAACAGGGTTTTGTTGGGAGAGGAAGAGGAGCAGAGGCAGCAAGAGGGAGTGATCGTGGAACTCTCAAAGGAACAAATTCGGC

Basic information

species Glycine max
transcript GLYMA20G28640.1
intron # 3
splice site 3'
intron type U2

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|213598564|gb|DB958148.1|DB958148
EST:     AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCAT                         AGCGAATTCGAGGAGATAAACAGGGTTTTGTTTGGAGAGGAAGAGGAGCAG
genomic: AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCATgtaataagca ... aaaatgatagAGCGAATTCGAGGAGATAAACAGGGTTTTGTTGGGAGAGGAAGAGGAGCAG
EST: gi|209721098|gb|BW666359.1|BW666359
EST:     AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCAT                         AGCGAATTCGAGGAGATAAACAGGNTTTTGTTTGGAGAGGAAGAAGAGCAG
genomic: AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCATgtaataagca ... aaaatgatagAGCGAATTCGAGGAGATAAACAGGGTTTTGTTGGGAGAGGAAGAGGAGCAG
EST: gi|42723198|gb|CK769097.1|CK769097
EST:     AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCAT                         AGCGAATTCGAGGAGATAAACAGGGTTTTGTTTGGAGAGGAAGAGGAGCAG
genomic: AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCATgtaataagca ... aaaatgatagAGCGAATTCGAGGAGATAAACAGGGTTTTGTTGGGAGAGGAAGAGGAGCAG
EST: gi|213597016|gb|DB966339.1|DB966339
EST:     AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCAT                         AGCGAATTCGAGGAGATAAACAGGGTTTTGTTTGGAGAGGAAGAGGAGCAG
genomic: AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCATgtaataagca ... aaaatgatagAGCGAATTCGAGGAGATAAACAGGGTTTTGTTGGGAGAGGAAGAGGAGCAG
EST: gi|7146240|gb|AW508094.1|AW508094
EST:     AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCAT                         AGCGAATTCGAGGAGATAAACAGGGGTTTGTTTGGAGAGGAAGAATGAGCA
genomic: AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCATgtaataagca ... aaaatgatagAGCGAATTCGAGGAGATAAACAGGGTTTTGTTGGGAGAGGAAGAG-GAGCA
EST: gi|5342773|gb|AI795057.1|AI795057
EST:     AGTCCTACTTGCAAGGGTTCAGCCATAATATTCTAGAGACCTCCTTCCAT                         AGCGAATTCGAGGAGATAAACAGGGTTTTGTTTGGAGAGGAAGAGGAGCAG
genomic: AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCATgtaataagca ... aaaatgatagAGCGAATTCGAGGAGATAAACAGGGTTTTGTTGGGAGAGGAAGAGGAGCAG
EST: gi|6915510|gb|AW397040.1|AW397040
EST:     AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCAT                         AGCGAATTCGAAGAGATAAACAGGGTTTTGTTTGGAGAGGAAGA
genomic: AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCATgtaataagca ... aaaatgatagAGCGAATTCGAGGAGATAAACAGGGTTTTGTTGGGAGAGGAAGA
EST: gi|7145659|gb|AW507581.1|AW507581
EST:     AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCAT                         AGCGAATTCGAGGAGATAAACAGGGTTTTGTTTGGAGAGGAAGAGGAGCAG
genomic: AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCATgtaataagca ... aaaatgatagAGCGAATTCGAGGAGATAAACAGGGTTTTGTTGGGAGAGGAAGAGGAGCAG
EST: gi|298164587|gb|HO014232.1|HO014232
EST:     AGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCAT                         AGCGAATTCGAGGAGATAAACAGGGTTTTGTTTGGAGAGGAAGAGGAGCAG
genomic: AGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCATgtaataagca ... aaaatgatagAGCGAATTCGAGGAGATAAACAGGGTTTTGTTGGGAGAGGAAGAGGAGCAG
EST: gi|5126381|gb|AI748117.1|AI748117
EST:     AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCAT                         AGCGAATTCGAGGAGATAAACAGGGTTTTGTTGGGAGAGGAAGAGGAGCAG
genomic: AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCATgtaataagca ... aaaatgatagAGCGAATTCGAGGAGATAAACAGGGTTTTGTTGGGAGAGGAAGAGGAGCAG
EST: gi|6915643|gb|AW397173.1|AW397173
EST:     AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCAT                         AGCGAATTCGAGGAGATAAACAGGGTTGTGTTTGGAGAAGAAGAAGAGCAG
genomic: AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCATgtaataagca ... aaaatgatagAGCGAATTCGAGGAGATAAACAGGGTTTTGTTGGGAGAGGAAGAGGAGCAG
EST: gi|209724177|gb|BW659711.1|BW659711
EST:     AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCAT                         AGCGAATTCGAGGAGATAAACAGGGTTTTGTTTGGAGAGGAAGAGGAGCAG
genomic: AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCATgtaataagca ... aaaatgatagAGCGAATTCGAGGAGATAAACAGGGTTTTGTTGGGAGAGGAAGAGGAGCAG
EST: gi|209714460|gb|BW684849.1|BW684849
EST:     AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCAT                         AGCGAATTCGAGGAGATAAACAGGGTTTTGTTTGGAGAGGAAGAGGAGCAG
genomic: AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCATgtaataagca ... aaaatgatagAGCGAATTCGAGGAGATAAACAGGGTTTTGTTGGGAGAGGAAGAGGAGCAG
EST: gi|61241574|gb|DN590967.1|DN590967
EST:     AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCAT                         AGCGAATTCGAGGAGATAAACAGGGTTTTGTTTGGAGAGGAAGAGGAGCAG
genomic: AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCATgtaataagca ... aaaatgatagAGCGAATTCGAGGAGATAAACAGGGTTTTGTTGGGAGAGGAAGAGGAGCAG
EST: gi|213594890|gb|DB971777.1|DB971777
EST:     AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCAT                         AGCGAATTCGAGGAGATNAACAGGGTTTTGTTTGGAGAGGAAGAGGAGCAG
genomic: AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCATgtaataagca ... aaaatgatagAGCGAATTCGAGGAGATAAACAGGGTTTTGTTGGGAGAGGAAGAGGAGCAG
EST: gi|6916308|gb|AW397838.1|AW397838
EST:     AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCAT                         AGCGAATTCGAGGAGATAAACCAGG-TTTTGNTGGAAGAGGA-GAAGAGCA
genomic: AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCATgtaataagca ... aaaatgatagAGCGAATTCGAGGAGATAAAC-AGGGTTTTGTTGGGAGAGGAAGAGGAGCA
EST: gi|5057596|gb|AI736072.1|AI736072
EST:     AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCAT                         AGCGAATTCGACGAGATAAACCAGG-TTTTGTTTGGAGAGGAAGAGGAGCA
genomic: AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCATgtaataagca ... aaaatgatagAGCGAATTCGAGGAGATAAAC-AGGGTTTTGTTGGGAGAGGAAGAGGAGCA
EST: gi|7232890|gb|AW568242.1|AW568242
EST:     AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCAT                         AGCGAATTCGAGGAGATAAACAGGGTTTTGTTTGGAGAGGAAGAGGAGCAG
genomic: AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCATgtaataagca ... aaaatgatagAGCGAATTCGAGGAGATAAACAGGGTTTTGTTGGGAGAGGAAGAGGAGCAG
EST: gi|7147552|gb|AW509474.1|AW509474
EST:     AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCAT                         AGCGAATTCGAGGAGATAAACAGGGTTTTGTTTGGAGAGGAAGAAGAGCAG
genomic: AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCATgtaataagca ... aaaatgatagAGCGAATTCGAGGAGATAAACAGGGTTTTGTTGGGAGAGGAAGAGGAGCAG
EST: gi|7042725|gb|AW472619.1|AW472619
EST:     AGTCCTACTTGCTAGGCTTCAGCCATAATATTCTATAGACCTTCTTGCAT                         AGCGAATTCGATGAGATAAACATGGTTTTGTTTGGAGATGAAGAGGAGCAG
genomic: AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCATgtaataagca ... aaaatgatagAGCGAATTCGAGGAGATAAACAGGGTTTTGTTGGGAGAGGAAGAGGAGCAG
EST: gi|192298683|gb|FG988579.1|FG988579
EST:     AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCTAT                         AGCGAATTCGAGGAGATAAACAGGGTTTTGTTTGGAGAGGAAGAGGAGCAG
genomic: AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCATgtaataagca ... aaaatgatagAGCGAATTCGAGGAGATAAACAGGGTTTTGTTGGGAGAGGAAGAGGAGCAG
EST: gi|6915594|gb|AW397124.1|AW397124
EST:     AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTNCAT                         AGCGAATTCGAGGAGATANACAGGGTTNTGTTTGGAGAGGAAGAGGAGCAG
genomic: AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCATgtaataagca ... aaaatgatagAGCGAATTCGAGGAGATAAACAGGGTTTTGTTGGGAGAGGAAGAGGAGCAG
EST: gi|209709049|gb|BW658765.1|BW658765
EST:     AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCAT                         AGCGAATTCGAGGAGATAAACAGGGTTTTGTTTGGAGAGGAAGAGGAGCAG
genomic: AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCATgtaataagca ... aaaatgatagAGCGAATTCGAGGAGATAAACAGGGTTTTGTTGGGAGAGGAAGAGGAGCAG
EST: gi|192297000|gb|FG990301.1|FG990301
EST:     AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCAT                         AGCGAATTCGAGGAGATAAACAGGGTTTTGTTTGGAGAGGAAGAGGAGCAG
genomic: AGTCCTACTTGCAAGGCTTCAGCCATAATATTCTAGAGACCTCCTTCCATgtaataagca ... aaaatgatagAGCGAATTCGAGGAGATAAACAGGGTTTTGTTGGGAGAGGAAGAGGAGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatttagagattagtctaaattcatgtcacactaattaaatattaaaatgatagAGCGAATTCGAGGAGATAAACAGGGTTTTGTTGGGAGAGGAAGAGGAGCAGAGGCAGCAAGAGGGAGTGATCGTGGAACTCTCAAAGGAACAAATTCGGC
                              cactaat  putative branch site (score: 2)
                           tcacactaattaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaataagcaaccaacagtactctatctaactatttgcattcccatttagagattagtctaaattcatgtcacactaattaaatattaaaatgatagAGCGAATTCGAGGAGATAAACAGGGTTTTGTTGGGAGAGGAAGAGGAGCAGAGGCAGCAAGAGGGAGTGATCGTGGAACTCTCAAAGGAACAAATTCGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA