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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttagatacagagtattttcttaggttattttacagctcaaattacaaatctgacatttccaaattccatgcatttggaacttggccttgtttgttgcagGTGTAAAAATATGGTTTCTTGCCATTATCTACTTCATAGCAGGGGTCCCTGGAGCATATGTTCTGTGGTATCGCCCATTATATCGTGCTTTTAG

Basic information

species Glycine max
transcript GLYMA13G25460.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G25460.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0301g00030.t01 (Vitis vinifera), 3'ss of exon 7
gtgagtttagatacagagtattttcttaggtt-attttacagctcaaattacaaatctgacatttccaaattccatgcatttggaacttg-gccttgtttgttgcagGTGTAAAAATATGGTTTCTTGCCATTATCTACTTCATAGCAGGGGTCCCTGGAGCATATGTTCTGTGGTATCGCCCATTATATCGTGCTTTTAG
      | ||   | |  | | |  || | ||   |||| |  |     | || || |||    |   ||  |  | ||  | || |||     || |    |  ||| |||||||| ||||||||||| ||||||||||||||||| |||||||| ||||| |||||  ||||||| || ||| | ||||||||||||||
-----gtcagtatctgcttgtgtctttggatttgctttatatttttgtatgcagatttgatggct---aacacagtacaacttgatcttatattttttccaatttagGGGTAAAAATCTGGTTTCTTGCTATTATCTACTTCATAGCCGGGGTCCCAGGAGCTTATGTGTTGTGGTACCGTCCACTTTATCGTGCTTTTAG
















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|298166217|gb|HO009188.1|HO009188
EST:     CCTTTTTTGGAATGTTATAGCTGTTACTGCAGCTTGGATTAAGGGTGAAG                         GTGTAAAAATATGGTTTCTTGCCATTATCTACTTCATAGCAGGGGTCCCTG
genomic: CCTTTTTTGGAATGTTATAGCTGTTACTGCAGCTTGGATTAAGGGTGAAGgtgagtttag ... tttgttgcagGTGTAAAAATATGGTTTCTTGCCATTATCTACTTCATAGCAGGGGTCCCTG
EST: gi|26049086|gb|CA785539.1|CA785539
EST:     CCTTTTTTGGAATGTTATAGCTGTTACTGCAGCTTGGATTAAGGGTGAAG                         GTGTAAAAATA
genomic: CCTTTTTTGGAATGTTATAGCTGTTACTGCAGCTTGGATTAAGGGTGAAGgtgagtttag ... tttgttgcagGTGTAAAAATA
EST: gi|18725114|gb|BM523597.1|BM523597
EST:     CCTTTTTTGGAATGTTATAGCTGTTACTGCAGCTTGGATTAAGGGTGAAG                         GTGTAAAAATATGGTTTCTTGCCATTATCTACTTCATAGCAGGGGTCCCTG
genomic: CCTTTTTTGGAATGTTATAGCTGTTACTGCAGCTTGGATTAAGGGTGAAGgtgagtttag ... tttgttgcagGTGTAAAAATATGGTTTCTTGCCATTATCTACTTCATAGCAGGGGTCCCTG
EST: gi|213602689|gb|DB968915.1|DB968915
EST:     CTTTTTTGGAAATGT-ATAGCTGTTACTGCAGCTTGGATTAAGGGTGAAG                         GTGTAAAAATATGGTTTCTTGCCATTATCTACT
genomic: CTTTTTTGGAA-TGTTATAGCTGTTACTGCAGCTTGGATTAAGGGTGAAGgtgagtttag ... tttgttgcagGTGTAAAAATATGGTTTCTTGCCATTATCTACT
EST: gi|209729488|gb|BW651841.1|BW651841
EST:     CCTTTTTTGGAATGTTATAGCTGTTACTGCAGCTTGGATTAAGGGTGAAG                         GTGTAAAAATATGGTTTCTTGCCATTATCTACTTCATAGCAGGGGTTCCTG
genomic: CCTTTTTTGGAATGTTATAGCTGTTACTGCAGCTTGGATTAAGGGTGAAGgtgagtttag ... tttgttgcagGTGTAAAAATATGGTTTCTTGCCATTATCTACTTCATAGCAGGGGTCCCTG
EST: gi|192299791|gb|FG990057.1|FG990057
EST:     CCTTTTTTGGAATGTTATAGCTGTTACTGCAGCTTGGATTAAGGGTGAAG                         GTGTAAAAATATGGTTTCTTGCCATTATCTACTTCATAGCAGGGGTCCCTG
genomic: CCTTTTTTGGAATGTTATAGCTGTTACTGCAGCTTGGATTAAGGGTGAAGgtgagtttag ... tttgttgcagGTGTAAAAATATGGTTTCTTGCCATTATCTACTTCATAGCAGGGGTCCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaatctgacatttccaaattccatgcatttggaacttggccttgtttgttgcagGTGTAAAAATATGGTTTCTTGCCATTATCTACTTCATAGCAGGGGTCCCTGGAGCATATGTTCTGTGGTATCGCCCATTATATCGTGCTTTTAG
   atctgac  putative branch site (score: 3)
                                        ccttgttt  putative PPT
                aaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtttagatacagagtattttcttaggttattttacagctcaaattacaaatctgacatttccaaattccatgcatttggaacttggccttgtttgttgcagGTGTAAAAATATGGTTTCTTGCCATTATCTACTTCATAGCAGGGGTCCCTGGAGCATATGTTCTGTGGTATCGCCCATTATATCGTGCTTTTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA