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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaattcagcttaaggattttatcaaatcatttgggattcatgaatacttggatctgctctttttaatctatattctttactaattacagtcaatttatagGTTTACAGTGACCTATCTGTTGATTATTTAAAGATGTTGCTGCTGAACGTCCCGGCTACTGTGATTGCATTAGGATT

Basic information

species Glycine max
transcript GLYMA05G03730.1
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|209698686|gb|BW656511.1|BW656511
EST:     GGAGTGAAATTGTAGCTGAGGGTCCAAGGTGCAGCCTTCGTAGTAGAAAG                         GTTTACAGTGACCTATCTGTTGATTATTTAAAGATGTTGCTGCTGAACGTC
genomic: GGAGTGAAATTGTAGCTGAGGGTCCAAGGTGCAGCCTTCGTAGTAGAAAGgtgagtgtta ... caatttatagGTTTACAGTGACCTATCTGTTGATTATTTAAAGATGTTGCTGCTGAACGTC
EST: gi|31462360|gb|CD404388.1|CD404388
EST:     TCGTAGTAGAAAG                         GTTTACAGTGACCTATCTGTTGATTATTTAAAGATGTTGCTGCTGAACGTC
genomic: TCGTAGTAGAAAGgtgagtgtta ... caatttatagGTTTACAGTGACCTATCTGTTGATTATTTAAAGATGTTGCTGCTGAACGTC
EST: gi|209729083|gb|BW655073.1|BW655073
EST:     GGAGTGAAATTGTAGCTGAGGGTCCAAGGTGCAGCCTTCGTAGTAGAAAG                         GTTTACAGTGACCTATCTGTTGATTATTTAAAGATGTTGCTGCTGAACGTC
genomic: GGAGTGAAATTGTAGCTGAGGGTCCAAGGTGCAGCCTTCGTAGTAGAAAGgtgagtgtta ... caatttatagGTTTACAGTGACCTATCTGTTGATTATTTAAAGATGTTGCTGCTGAACGTC
EST: gi|6455321|gb|AW186004.1|AW186004
EST:     GGAGTGAAATTGTAGCTGAGGGTCCAAGGTGCAGCCTTCGTAGTAGAAAG                         GTTTACAGTGACCTATCTGTTGATTATTTAAAGATGTTGCTGCTGAACGTC
genomic: GGAGTGAAATTGTAGCTGAGGGTCCAAGGTGCAGCCTTCGTAGTAGAAAGgtgagtgtta ... caatttatagGTTTACAGTGACCTATCTGTTGATTATTTAAAGATGTTGCTGCTGAACGTC
EST: gi|120496159|gb|EH224326.1|EH224326
EST:     GGAGTGAAATTGTAGTTGAGGGTCCAAGGTGCAGCCTTCGTAGTAGAAAG                         GTTTACAGTGACCTATCTGTTGATTATTTAAAGATGTTGCTGCTGAACGTC
genomic: GGAGTGAAATTGTAGCTGAGGGTCCAAGGTGCAGCCTTCGTAGTAGAAAGgtgagtgtta ... caatttatagGTTTACAGTGACCTATCTGTTGATTATTTAAAGATGTTGCTGCTGAACGTC
EST: gi|209729478|gb|BW655108.1|BW655108
EST:     GGAGTGAAATTGTAGCTGAGGGTCCAAGGTGCAGCCTTCGTAGTAGAAAG                         GTTTACAGTGACCTATCTGTTGATTATTTAAAGATGTTGCTGCTGAACGTC
genomic: GGAGTGAAATTGTAGCTGAGGGTCCAAGGTGCAGCCTTCGTAGTAGAAAGgtgagtgtta ... caatttatagGTTTACAGTGACCTATCTGTTGATTATTTAAAGATGTTGCTGCTGAACGTC
EST: gi|209698687|gb|BW656512.1|BW656512
EST:     GGAGTGAAATTGTAGCTGAGGGTCCAAGGTGCAGCCTTCGTAGTAGAAAG                         GTTTACAGTGACCTATCTGTTGATTATTTAAAGATGTTGCTGCTGAACGTC
genomic: GGAGTGAAATTGTAGCTGAGGGTCCAAGGTGCAGCCTTCGTAGTAGAAAGgtgagtgtta ... caatttatagGTTTACAGTGACCTATCTGTTGATTATTTAAAGATGTTGCTGCTGAACGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttggatctgctctttttaatctatattctttactaattacagtcaatttatagGTTTACAGTGACCTATCTGTTGATTATTTAAAGATGTTGCTGCTGAACGTCCCGGCTACTGTGATTGCATTAGGATT
                                tactaat  putative branch site (score: 1)
            tctttttaatctatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaattcagcttaaggattttatcaaatcatttgggattcatgaatacttggatctgctctttttaatctatattctttactaattacagtcaatttatagGTTTACAGTGACCTATCTGTTGATTATTTAAAGATGTTGCTGCTGAACGTCCCGGCTACTGTGATTGCATTAGGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - catgaat