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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacttttaaatttaatatctcagtagataaaaaaagtcactattttacacttgaaatctcaagccactttaattttcaaaactattattatgagaagtgcattatcagtgttattcatatccgaaggaataaattctttgatcatcttccagagatgagtagtaaccaaagatttctgtgattcagGGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGATTGTTAACAATGCTCGAGGGGCAATTGCGGACACCCAAGCAATTGCAGAT

Basic information

species Glycine max
transcript GLYMA13G23790.3
intron # 4
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|11275020|gb|BF325344.1|BF325344
EST:     CCAAAGTGTGATGTAATTGTTATCAACACCCCTCTCACTGAGCAGACAAG                         GGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGAT
genomic: CCAAAGTGTGATGTAATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatactttt ... tgtgattcagGGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGAT
EST: gi|17401257|gb|BM178039.1|BM178039
EST:     CCAAAGTGTGATGTAATTGTTATCAACACCCCTCTCACTGAGCAGACAAG                         GGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGAT
genomic: CCAAAGTGTGATGTAATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatactttt ... tgtgattcagGGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGAT
EST: gi|5688024|gb|AI941039.1|AI941039
EST:     NCAA-GTGTGATGTAATTGTTATCAACACCCCTCTCACTGAGCAGACANG                         GGGATTGTTTGACAAAAATAGAATTGCGAAGTGCANGAAAAGTGTCTTGAT
genomic: -CAAAGTGTGATGTAATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatactttt ... tgtgattcagGGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGAT
EST: gi|42723252|gb|CK769151.1|CK769151
EST:     GTAATTGTTATCAACACCCCTCTCACTGAGCAGACAAG                         GGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGAT
genomic: GTAATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatactttt ... tgtgattcagGGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGAT
EST: gi|214008422|gb|DB989988.1|DB989988
EST:     CCAAAGTGTGATGTTGGCGTTATCAACACCCCTCTCACTGAGCAGACAAG                         GGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGAT
genomic: CCAAAGTGTGATGTAATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatactttt ... tgtgattcagGGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGAT
EST: gi|42723195|gb|CK769094.1|CK769094
EST:     CCAAAGTGTGATGTAATTGTTATCAACACCCCTCTCACTGAGCAGACAAG                         GGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGAT
genomic: CCAAAGTGTGATGTAATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatactttt ... tgtgattcagGGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGAT
EST: gi|4260047|gb|AI416543.1|AI416543
EST:     GTTATCAACACCCCTCTCACTGAGCAGACAAG                         GGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGAT
genomic: GTTATCAACACCCCTCTCACTGAGCAGACAAGgtatactttt ... tgtgattcagGGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGAT
EST: gi|6341426|gb|AW164250.1|AW164250
EST:     CCAAAGTGTGATGTAATTGTTATCAACACCCCTCTCACTGAGCAGACAAG                         GGGATTGTTTGACAAAAATAGAATTGCAAAGTGCAAGAAAGGTGTCTGGAT
genomic: CCAAAGTGTGATGTAATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatactttt ... tgtgattcagGGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGAT
EST: gi|11688868|gb|BF596544.1|BF596544
EST:     CCAAAGTGTGATGTAATTGTTATCAACACCCCTCTCACTGAGCAGACAAG                         GGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGAT
genomic: CCAAAGTGTGATGTAATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatactttt ... tgtgattcagGGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGAT
EST: gi|298164748|gb|HO014393.1|HO014393
EST:     CCAAAGTGTGATGTAACTGTTATCAACACCCCTCTCACTGAGCAGACAAG                         GGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGA
genomic: CCAAAGTGTGATGTAATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatactttt ... tgtgattcagGGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGA
EST: gi|7232927|gb|AW568278.1|AW568278
EST:     CCAAAGTGTGATGTAATTGTTATCAACACCCCTCTCACTGAGCAGACAAG                         GGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGAT
genomic: CCAAAGTGTGATGTAATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatactttt ... tgtgattcagGGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGAT
EST: gi|16995760|gb|BM085132.1|BM085132
EST:     CCAAAGTGTGATGTAATTGTTATCAACACCCCTCTCACTGAGCAGACAAG                         GGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGAT
genomic: CCAAAGTGTGATGTAATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatactttt ... tgtgattcagGGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGAT
EST: gi|209715917|gb|BW650930.1|BW650930
EST:     CCAAAGTGTGATGTAATTGTTATCAACACCCCTCTCACTGAGCAGACAAG                         GGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGAT
genomic: CCAAAGTGTGATGTAATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatactttt ... tgtgattcagGGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGAT
EST: gi|26060128|gb|CA803042.1|CA803042
EST:     CCAAAGTGTGATGTAATTGTTATCAACACCCCTCTCACTGAGCAGACAAG                         GGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGAT
genomic: CCAAAGTGTGATGTAATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatactttt ... tgtgattcagGGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGAT
EST: gi|13790807|gb|BG653398.1|BG653398
EST:     CCAAAGTGTGATGTAATTGTTATCAACACCCCTCTCACTGAGCAGACAAG                         GGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGAT
genomic: CCAAAGTGTGATGTAATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatactttt ... tgtgattcagGGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGAT
EST: gi|7232967|gb|AW568318.1|AW568318
EST:     CCAAAGTGTGATGTAATTGTTATCAACACCCCTCTCACTGAGCAGACAAG                         GGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGAT
genomic: CCAAAGTGTGATGTAATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatactttt ... tgtgattcagGGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGAT
EST: gi|6200999|gb|AW153099.1|AW153099
EST:     CCAAAGTGTGATGTAATTGTTATCAACACCCCTCTCACTGAGCAGACAAG                         GGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGAT
genomic: CCAAAGTGTGATGTAATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatactttt ... tgtgattcagGGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGAT
EST: gi|11687793|gb|BF595469.1|BF595469
EST:     NCAAAGTGTGATGTAATTGTTATCAACACCCCTCTCACTGAGCAGACAAN                         GGGATTGTTTGACAAAAATAGAAATTG-GAAGTGCAAGGAAGGTGTCTTGA
genomic: CCAAAGTGTGATGTAATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatactttt ... tgtgattcagGGGATTGTTTGACAAAAATAGAA-TTGCGAAGTGCAAGAAAGGTGTCTTGA
EST: gi|7029106|gb|AW458880.1|AW458880
EST:     NCAAAGTGTGATGTAATTGTTATCAACACCCCTCTCACTGAGCAGACAAG                         GGGATTGGTTGACAAAAATAGAATTGCGAAGTGCAGGAAAGGTGTCTTGAT
genomic: CCAAAGTGTGATGTAATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatactttt ... tgtgattcagGGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattctttgatcatcttccagagatgagtagtaaccaaagatttctgtgattcagGGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGATTGTTAACAATGCTCGAGGGGCAATTGCGGACACCCAAGCAATTGCAGAT
                            tagtaac  putative branch site (score: 1)
                                         tttctgt  putative PPT
                                    aaagattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatacttttaaatttaatatctcagtagataaaaaaagtcactattttacacttgaaatctcaagccactttaattttcaaaactattattatgagaagtgcattatcagtgttattcatatccgaaggaataaattctttgatcatcttccagagatgagtagtaaccaaagatttctgtgattcagGGGATTGTTTGACAAAAATAGAATTGCGAAGTGCAAGAAAGGTGTCTTGATTGTTAACAATGCTCGAGGGGCAATTGCGGACACCCAAGCAATTGCAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT