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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcatcaatattttatatgtgatttgatgtgtcttgaactaagatatagtatatatatatatatatgtgtgtgtgtgtgcgcgcgcttttgttgatggtgtgagatattttcccagTGCATCTTGGTGTCTGAAGAAGATGAGGAAGCAACATTTGTGGAACCTTCTAAGCGTGGAAA

Basic information

species Glycine max
transcript GLYMA20G30620.1
intron # 3
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|120533894|gb|EH262027.1|EH262027
EST:     TCCTATCCAATGATGTCTTCATCAAGGCATTGATCAGCAGTGGACGAACA                         TGCATCTTGGTGTCTGAAGAAGATGAGGAAGCAACATTTGTGGAACCTTCT
genomic: TCCTATCCAATGATGTCTTCATCAAGGCATTGATCAGCAGTGGACGAACAgtaagtcatc ... attttcccagTGCATCTTGGTGTCTGAAGAAGATGAGGAAGCAACATTTGTGGAACCTTCT
EST: gi|120531951|gb|EH260084.1|EH260084
EST:     TCCTATCCAATGATGTCTTCATCAAGGCATTGATCAGCAGTGGACGAACA                         TGCATCTTGGTGTCTGAAGAAGATGAGGAAGCAACATTTGTGGAACCTTCT
genomic: TCCTATCCAATGATGTCTTCATCAAGGCATTGATCAGCAGTGGACGAACAgtaagtcatc ... attttcccagTGCATCTTGGTGTCTGAAGAAGATGAGGAAGCAACATTTGTGGAACCTTCT
EST: gi|120529729|gb|EH257863.1|EH257863
EST:     TCCTATCCAATGATGTCTTCATCAAGGCATTGATCAGCAGTGGACGAACA                         TGCATCTTGGTGTCTGAAGAAGATGAGGAAGCAACATTTGTGGAACCTTCT
genomic: TCCTATCCAATGATGTCTTCATCAAGGCATTGATCAGCAGTGGACGAACAgtaagtcatc ... attttcccagTGCATCTTGGTGTCTGAAGAAGATGAGGAAGCAACATTTGTGGAACCTTCT
EST: gi|192316335|gb|FK011680.1|FK011680
EST:     TCCTATCCAATGATGTCTTCATCAAGGCATTGATCAGCAGTGGACGAACA                         TGCATCTTGGTGTCTGAAGAAGATGAGGAAGCAACATTTGTGGAACCTTCT
genomic: TCCTATCCAATGATGTCTTCATCAAGGCATTGATCAGCAGTGGACGAACAgtaagtcatc ... attttcccagTGCATCTTGGTGTCTGAAGAAGATGAGGAAGCAACATTTGTGGAACCTTCT
EST: gi|20497840|gb|BQ272770.1|BQ272770
EST:     TCCTATCCAATGATGTCTTCATCAAGGCATTGATCAGCACTGGACGAACA                         TGCATCTTGGTGTCTGAAGAAGATGAGGAAGCAACATTTGTGGAACCTTCT
genomic: TCCTATCCAATGATGTCTTCATCAAGGCATTGATCAGCAGTGGACGAACAgtaagtcatc ... attttcccagTGCATCTTGGTGTCTGAAGAAGATGAGGAAGCAACATTTGTGGAACCTTCT
EST: gi|209707338|gb|BW670901.1|BW670901
EST:     TCCTATCCAATGATGTCTTCATCAAGGCATTGATCAGCAGTGGACGAACA                         TGCATCTTGGTGTCTGAAGAAGATGAGGAAGCAACATTTGTGGAACCTTCT
genomic: TCCTATCCAATGATGTCTTCATCAAGGCATTGATCAGCAGTGGACGAACAgtaagtcatc ... attttcccagTGCATCTTGGTGTCTGAAGAAGATGAGGAAGCAACATTTGTGGAACCTTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatgtgtgtgtgtgtgcgcgcgcttttgttgatggtgtgagatattttcccagTGCATCTTGGTGTCTGAAGAAGATGAGGAAGCAACATTTGTGGAACCTTCTAAGCGTGGAAA
                            tgttgat  putative branch site (score: 4)
                                            tattttccc  putative PPT
                                         agatatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcatcaatattttatatgtgatttgatgtgtcttgaactaagatatagtatatatatatatatatgtgtgtgtgtgtgcgcgcgcttttgttgatggtgtgagatattttcccagTGCATCTTGGTGTCTGAAGAAGATGAGGAAGCAACATTTGTGGAACCTTCTAAGCGTGGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA