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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattatattatatccctcactttaataccaaaaaagaaaattgagattaaatttttgaggaataactgttttttttctgttgcagACACTAAGTCAAGCATTGGCCACAGCCAGGGAACATCTTGCAAGGTCCCTTCTTAAATGATTCAAATGGCATTTGACAGAGGAGGAAACTTGTCTTTTAG

Basic information

species Glycine max
transcript GLYMA09G02270.3
intron # 5
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|192332965|gb|FK024614.1|FK024614
EST:     GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAG                         ACACTAAGTCAAGCATTGGCCACAGCCAGGGAACATCT
genomic: GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAGgtattatatt ... tctgttgcagACACTAAGTCAAGCATTGGCCACAGCCAGGGAACATCT
EST: gi|120493426|gb|EH221593.1|EH221593
EST:     GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAG                         ACACTAAGTCAAGCATTGGCCACAGCCAGGGAACATCTTGCAAGGTCCCTT
genomic: GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAGgtattatatt ... tctgttgcagACACTAAGTCAAGCATTGGCCACAGCCAGGGAACATCTTGCAAGGTCCCTT
EST: gi|120492487|gb|EH220654.1|EH220654
EST:     GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAG                         ACACTAAGTCAAGCATTGGCCACAGCCAGGGAACATCTTGCAAGGTCCCTT
genomic: GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAGgtattatatt ... tctgttgcagACACTAAGTCAAGCATTGGCCACAGCCAGGGAACATCTTGCAAGGTCCCTT
EST: gi|151410972|gb|EV280787.1|EV280787
EST:     GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAG                         ACACTAAGTCAAGCATTGGCCACAGCCAGGGAACATCTTGCAAGGTCCCTT
genomic: GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAGgtattatatt ... tctgttgcagACACTAAGTCAAGCATTGGCCACAGCCAGGGAACATCTTGCAAGGTCCCTT
EST: gi|151405407|gb|EV275221.1|EV275221
EST:     GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAG                         ACACTAAGTCAAGCATTGGCCACAGCCAGGGAACATCTTGCAAGGTCCCTT
genomic: GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAGgtattatatt ... tctgttgcagACACTAAGTCAAGCATTGGCCACAGCCAGGGAACATCTTGCAAGGTCCCTT
EST: gi|151410188|gb|EV280003.1|EV280003
EST:     GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAG                         ACACTAAGTCAAGCATTGGCCACAGCCAGGGAACATCTTGCAAGGTCCCTT
genomic: GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAGgtattatatt ... tctgttgcagACACTAAGTCAAGCATTGGCCACAGCCAGGGAACATCTTGCAAGGTCCCTT
EST: gi|38192921|gb|CF922127.1|CF922127
EST:     GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAG                         ACACTAAGTCAAGCATTGGCCACAGCCAGGGAACATCTTGCAAGGTCCCTT
genomic: GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAGgtattatatt ... tctgttgcagACACTAAGTCAAGCATTGGCCACAGCCAGGGAACATCTTGCAAGGTCCCTT
EST: gi|213607061|gb|DB965059.1|DB965059
EST:     GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAG                         ACACTAAGTCAAGCATTGGCCAC
genomic: GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAGgtattatatt ... tctgttgcagACACTAAGTCAAGCATTGGCCAC
EST: gi|192332966|gb|FK024615.1|FK024615
EST:     GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAG                         ACACTAAGTCAAGCATTGGCCACAGCCAGGGAACATCTTGCAAGGTCCCTT
genomic: GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAGgtattatatt ... tctgttgcagACACTAAGTCAAGCATTGGCCACAGCCAGGGAACATCTTGCAAGGTCCCTT
EST: gi|8670053|gb|BE191160.1|BE191160
EST:     GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAG                         ACACTAAGTCAAGCATTGGCCACAGCCAGGGAACATCTTGCAAGGTCCCTT
genomic: GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAGgtattatatt ... tctgttgcagACACTAAGTCAAGCATTGGCCACAGCCAGGGAACATCTTGCAAGGTCCCTT
EST: gi|298166245|gb|HO009216.1|HO009216
EST:     GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAG                         ACACTAAGTCAAGCATTGGCCACAGC
genomic: GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAGgtattatatt ... tctgttgcagACACTAAGTCAAGCATTGGCCACAGC
EST: gi|213601798|gb|DB982523.1|DB982523
EST:     GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAG                         ACACTAAGTCAAGCATTGGCCACAGCCAGGGAACATCTTGCAAGGTCCCTT
genomic: GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAGgtattatatt ... tctgttgcagACACTAAGTCAAGCATTGGCCACAGCCAGGGAACATCTTGCAAGGTCCCTT
EST: gi|38192996|gb|CF922202.1|CF922202
EST:     GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAG                         ACACTAAGTCAAGCATTGGCCACAGCCAGGGAACATCTTGCAAGGTCCCTT
genomic: GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAGgtattatatt ... tctgttgcagACACTAAGTCAAGCATTGGCCACAGCCAGGGAACATCTTGCAAGGTCCCTT
EST: gi|298179376|gb|HO027847.1|HO027847
EST:     GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAG                         ACACTAAGTCAAGCATTGGCCACAGC
genomic: GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAGgtattatatt ... tctgttgcagACACTAAGTCAAGCATTGGCCACAGC
EST: gi|298182838|gb|HO031573.1|HO031573
EST:     GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAG                         ACACTAAGTCAAGC
genomic: GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAGgtattatatt ... tctgttgcagACACTAAGTCAAGC
EST: gi|192321195|gb|FK014285.1|FK014285
EST:     GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAG                         ACACTAAGTCAAGCATTGGCCACAGCCAGGGAACATCTTGCAAGGTCCCTT
genomic: GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAGgtattatatt ... tctgttgcagACACTAAGTCAAGCATTGGCCACAGCCAGGGAACATCTTGCAAGGTCCCTT
EST: gi|120532300|gb|EH260433.1|EH260433
EST:     GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAG                         ACACTAAGTCAAGCATTGGCCACAGCCAGGGAACATCTTGCAA
genomic: GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAGgtattatatt ... tctgttgcagACACTAAGTCAAGCATTGGCCACAGCCAGGGAACATCTTGCAA
EST: gi|298166774|gb|HO010213.1|HO010213
EST:     GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAG                         ACACTAAGTCAAGCATTGGCCACAGC
genomic: GGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAGgtattatatt ... tctgttgcagACACTAAGTCAAGCATTGGCCACAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaagaaaattgagattaaatttttgaggaataactgttttttttctgttgcagACACTAAGTCAAGCATTGGCCACAGCCAGGGAACATCTTGCAAGGTCCCTTCTTAAATGATTCAAATGGCATTTGACAGAGGAGGAAACTTGTCTTTTAG
                             gaataac  putative branch site (score: 2)
                                   ctgttttttttctgtt  CT-rich tract
      aaaattgagattaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattatattatatccctcactttaataccaaaaaagaaaattgagattaaatttttgaggaataactgttttttttctgttgcagACACTAAGTCAAGCATTGGCCACAGCCAGGGAACATCTTGCAAGGTCCCTTCTTAAATGATTCAAATGGCATTTGACAGAGGAGGAAACTTGTCTTTTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA