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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggttagaatcgctgataacttttaatttggtttattatgatttaattattgtttatatgaaatagaatggtgtgtgcttcaactgattgtgatatgttttgttgtgttgtggaacagCCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCTTTGACGGCTGTTGGGTCTGGACAAACGTCTTTGGGAATTAAAG

Basic information

species Glycine max
transcript GLYMA15G41330.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G41330.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0011g01960.t01 (Vitis vinifera), 3'ss of exon 1
gtatggttagaatcgctgataacttttaatttggtttattatgatttaattattgtttatatgaa-atagaatggtgtgtgcttcaactgattgtgatatgttttgttgtgttgtggaacagCCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCTTTGACGGCTGTTGGGTCTGGACAAACGTCTTTGGGAATTAAAG
                                         | | | | |||||   || ||  | ||  |  |     |  ||    |  || | | || | |   |||||   |  |||| ||||| ||||||||||||||||| |||||||| ||||| || ||||| || || ||||| ||| | || || ||||
----------------------------------------gtaagtaatttattcactagattcacatgcagagactcatattttcgatc-ttctcacatctctatgtgtgtcacgagacagTCCTTCGGGAAAGCTTGTTCAGATCGAGCATGCATTGACCGCCGTTGGCTCAGGCCAAACATCTCTAGGGATCAAAG
















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|38192386|gb|CF921592.1|CF921592
EST:     CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG                         CCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCTTTGACGGCTGTTGGGTC
genomic: CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAGgtatggttag ... tgtggaacagCCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCTTTGACGGCTGTTGGGTC
EST: gi|209699717|gb|BW652089.1|BW652089
EST:     CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG                         CCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCTTTGACGGCTGTTGGGTC
genomic: CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAGgtatggttag ... tgtggaacagCCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCTTTGACGGCTGTTGGGTC
EST: gi|4295815|gb|AI442386.1|AI442386
EST:     CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG                         CCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCTTTGACGGCTGTTGGGTC
genomic: CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAGgtatggttag ... tgtggaacagCCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCTTTGACGGCTGTTGGGTC
EST: gi|38192385|gb|CF921591.1|CF921591
EST:     CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG                         CCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCTTTGACGGCTGTTGGGTC
genomic: CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAGgtatggttag ... tgtggaacagCCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCTTTGACGGCTGTTGGGTC
EST: gi|151401084|gb|EV270898.1|EV270898
EST:     CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG                         CCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCTTTGACGGCTGTTGGGTC
genomic: CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAGgtatggttag ... tgtggaacagCCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCTTTGACGGCTGTTGGGTC
EST: gi|19345956|gb|BM890836.1|BM890836
EST:     CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG                         CCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCTTTGACGGCTGTTGGGTC
genomic: CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAGgtatggttag ... tgtggaacagCCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCTTTGACGGCTGTTGGGTC
EST: gi|38193672|gb|CF922878.1|CF922878
EST:     CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG                         CCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCTTTGACGGCTGTTGGGTC
genomic: CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAGgtatggttag ... tgtggaacagCCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCTTTGACGGCTGTTGGGTC
EST: gi|192305316|gb|FG994012.1|FG994012
EST:     CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG                         CCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCTTTGACGGCTGTTGGGTC
genomic: CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAGgtatggttag ... tgtggaacagCCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCTTTGACGGCTGTTGGGTC
EST: gi|13562525|gb|BG550745.1|BG550745
EST:     CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG                         CCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCTTTGACGGCTGTTGGGTC
genomic: CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAGgtatggttag ... tgtggaacagCCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCTTTGACGGCTGTTGGGTC
EST: gi|213617097|gb|DB963570.1|DB963570
EST:     CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG                         CCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCTTTGACGGCTGTTGGGTC
genomic: CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAGgtatggttag ... tgtggaacagCCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCTTTGACGGCTGTTGGGTC
EST: gi|12688265|gb|BG154601.1|BG154601
EST:     CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG                         CNCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCTTTGACGGCTGTTGGGT
genomic: CGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAGgtatggttag ... tgtggaacagC-CCTTCTGGAAAGCTTGTTCAGATTGAGCATGCTTTGACGGCTGTTGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagaatggtgtgtgcttcaactgattgtgatatgttttgttgtgttgtggaacagCCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCTTTGACGGCTGTTGGGTCTGGACAAACGTCTTTGGGAATTAAAG
                  aactgat  putative branch site (score: 3)
                             atatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggttagaatcgctgataacttttaatttggtttattatgatttaattattgtttatatgaaatagaatggtgtgtgcttcaactgattgtgatatgttttgttgtgttgtggaacagCCCTTCTGGAAAGCTTGTTCAGATTGAGCATGCTTTGACGGCTGTTGGGTCTGGACAAACGTCTTTGGGAATTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT