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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcttacctgcattacttttttaatctcttaacacaattgttaatccccccccttttttatcaaattcttatatatcctttgaaactttcctccctcaatttcagGGGTGGTCATGGCATTGGTGGAAGCATGCTTGTAG

Basic information

species Glycine max
transcript GLYMA09G06650.1
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|192322515|gb|FK014636.1|FK014636
EST:     TCTGGTAGTGATCTTGTTCCTGGGCCTGCTGCTGGAGTGTTTCCTTCAAA                         GGGTGGTCATGGCATTGGTGGAAGCATGCTTG
genomic: TCTGGTAGTGATCTTGTTCCTGGGCCTGCTGCTGGAGTGTTTCCTTCAAGgtattcttac ... tcaatttcagGGGTGGTCATGGCATTGGTGGAAGCATGCTTG
EST: gi|26057707|gb|CA800621.1|CA800621
EST:     TCTGGTAGTGATCTTGTTCCTGGGCCTGCTGCTGGAGTGTTTCCTTCAAG                         GGGTGGTCATGGCATTGGTGGAAGCATGCTTGTAG
genomic: TCTGGTAGTGATCTTGTTCCTGGGCCTGCTGCTGGAGTGTTTCCTTCAAGgtattcttac ... tcaatttcagGGGTGGTCATGGCATTGGTGGAAGCATGCTTGTAG
EST: gi|7795266|gb|AW780663.1|AW780663
EST:     TCTGGTAGTGATCTTGTTCCTGGGCCTGCTGCTGGAGTGTTTCCTTCAAG                         GGGTGGTCATGGCATTGGTGGAAGCATGCTTGTAG
genomic: TCTGGTAGTGATCTTGTTCCTGGGCCTGCTGCTGGAGTGTTTCCTTCAAGgtattcttac ... tcaatttcagGGGTGGTCATGGCATTGGTGGAAGCATGCTTGTAG
EST: gi|22929152|gb|BU546291.1|BU546291
EST:     TCTGGTAGTGATCTTGTTCCTGGGCCTGCTGCTGGAGTGTTTCCTTCAAG                         GGGTGGTCATGGCATTGGTGGAAGCATGCTTGTAG
genomic: TCTGGTAGTGATCTTGTTCCTGGGCCTGCTGCTGGAGTGTTTCCTTCAAGgtattcttac ... tcaatttcagGGGTGGTCATGGCATTGGTGGAAGCATGCTTGTAG
EST: gi|209726446|gb|BW662811.1|BW662811
EST:     TCTGGTAGTGATCTTGTTCCTGGGCCTGCTGCTGGAGTGTTTCCTTCAAG                         GGGTGGTCATGGCATTGGTGGAAGCATGCTTGTAG
genomic: TCTGGTAGTGATCTTGTTCCTGGGCCTGCTGCTGGAGTGTTTCCTTCAAGgtattcttac ... tcaatttcagGGGTGGTCATGGCATTGGTGGAAGCATGCTTGTAG
EST: gi|254325977|gb|GR838858.1|GR838858
EST:     TCTGGTAGTGATCTTGTTCCTGGGCCTGCTGCTGGAGTGTTTCCTTCAAG                         GGGTGGTCATGGCATTGGTGGAAGCATGCTTGTAG
genomic: TCTGGTAGTGATCTTGTTCCTGGGCCTGCTGCTGGAGTGTTTCCTTCAAGgtattcttac ... tcaatttcagGGGTGGTCATGGCATTGGTGGAAGCATGCTTGTAG
EST: gi|22928233|gb|BU545372.1|BU545372
EST:     GAGTGTTTCCTTCAAG                         GGGTGGTCATGGCATTGGTGGAAGCATGCTCGTAG
genomic: GAGTGTTTCCTTCAAGgtattcttac ... tcaatttcagGGGTGGTCATGGCATTGGTGGAAGCATGCTTGTAG
EST: gi|192296179|gb|FG991549.1|FG991549
EST:     TCTGGTAGTGATCTTGTTCCTGGGCCTGCTGCTGGAGTGTTTCCTTCAAG                         GGGTGGTCATGGGCATTGGTGGAAGCATGCTTGTAG
genomic: TCTGGTAGTGATCTTGTTCCTGGGCCTGCTGCTGGAGTGTTTCCTTCAAGgtattcttac ... tcaatttcagGGGTGGTCATGG-CATTGGTGGAAGCATGCTTGTAG
EST: gi|192327541|gb|FK020616.1|FK020616
EST:     TCTGGTAGTGATCTTGTTCCTGGGCCTGCTGCTGGAGTGTT-CCTTCAAG                         GG-TGGTCATGGCATTGGTGGAAGCATGCTT
genomic: TCTGGTAGTGATCTTGTTCCTGGGCCTGCTGCTGGAGTGTTTCCTTCAAGgtattcttac ... tcaatttcagGGGTGGTCATGGCATTGGTGGAAGCATGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccttttttatcaaattcttatatatcctttgaaactttcctccctcaatttcagGGGTGGTCATGGCATTGGTGGAAGCATGCTTGTAG
                                   ctttcctccctcaatt  CT-rich tract
     ttttatcaaattctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattcttacctgcattacttttttaatctcttaacacaattgttaatccccccccttttttatcaaattcttatatatcctttgaaactttcctccctcaatttcagGGGTGGTCATGGCATTGGTGGAAGCATGCTTGTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG