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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtctctgcctgcaacttctcagttataataaactaattgtttgttccaagatttttctttcctgtctgcatgttaaaattaactttttgtgtataccagGTTAGAGAAGGTTTGTGCAAATGTGAATTTCCTCAGTATTGCGATTCTCGAAGATAAGGTTTCACCGAGGTGGCAAGAAGGTTTACAATGTAATGCATCA

Basic information

species Glycine max
transcript GLYMA09G35080.2
intron # 6
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|16344369|gb|BI969964.1|BI969964
EST:     GCAAAGTCATCAGAAGGGCTTCAAGAAGGGTATCTTTTACATTTCGAAAG                         GTTAGAGAAGGTTTGTGCAAATGTGAATTTCCTCAGTATTGCGATTCTCGA
genomic: GCAAAGTCATCAGAAGGGCTTCAAGAAGGGTATCTTTTACATTTCGAAAGgtgtgtggat ... tgtataccagGTTAGAGAAGGTTTGTGCAAATGTGAATTTCCTCAGTATTGCGATTCTCGA
EST: gi|16344442|gb|BI970037.1|BI970037
EST:     GCAAAGTCATCAGAAGGGCTTCAAGAAGGGTATCTTTTACATTTCGAAAG                         GTTAGAGAAGGTTTGTGCAAATGTGAATTTCCTCAGTATTGCGATTCTCGA
genomic: GCAAAGTCATCAGAAGGGCTTCAAGAAGGGTATCTTTTACATTTCGAAAGgtgtgtggat ... tgtataccagGTTAGAGAAGGTTTGTGCAAATGTGAATTTCCTCAGTATTGCGATTCTCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccaagatttttctttcctgtctgcatgttaaaattaactttttgtgtataccagGTTAGAGAAGGTTTGTGCAAATGTGAATTTCCTCAGTATTGCGATTCTCGAAGATAAGGTTTCACCGAGGTGGCAAGAAGGTTTACAATGTAATGCATCA
                                aattaac  putative branch site (score: 2)
                                      ctttttgt  CT-rich tract
                            ttaaaattaacttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtctctgcctgcaacttctcagttataataaactaattgtttgttccaagatttttctttcctgtctgcatgttaaaattaactttttgtgtataccagGTTAGAGAAGGTTTGTGCAAATGTGAATTTCCTCAGTATTGCGATTCTCGAAGATAAGGTTTCACCGAGGTGGCAAGAAGGTTTACAATGTAATGCATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- -ctctgcc
- - - - - tgcaact
- - - - - - - - - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaattaa