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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggtttgtctctaggggtttggtttgtattctaaatttattcaccttagtaaagtgtatttgttgtattaattatcccagAGACCGAAACTTTTGAGGCCAAATGGAAAGATCTATCAGGCAATTAATGTGGATACCTTAAGAGCTCAAAATATAGAAACTTGGCCCTTCTACAACCAG

Basic information

species Glycine max
transcript GLYMA08G19730.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G19730.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv12s0034g01180.t01 (Vitis vinifera), 3'ss of exon 2
---------gtttggtttgtctctaggggtttggtttgtattctaaatttattcacc--ttagtaaagtgtatttgttgtattaattatccc------agAGACCGAAACTTTTGAGGCCAAATGGAAAGATCTATCAGGCAATTAATGTGGATACCTTAAGAGCTCAAAATATAGAAACTTGGCCCTTCTACAACCAG
          | |  ||  | || | |  ||      | || ||   ||  | ||    | || |||    | |   ||| ||   |||  |      |||| || ||| | || || ||||||||||| ||||| ||||| |||||||||||||| || || |||||||| || ||||||||||| |||| |||||||
tatcaattcatgttattcatttccaagtattaatcagggatccttctttcttccagagatcagaaaatataagtaactgtctttgatatttctatggcagAGGCCCAAATTCTTAAGACCAAATGGAAAAATCTACCAGGCCATTAATGTGGATACTTTGAGGGCTCAAAACATGGAAACTTGGCCATTCTTCAACCAG
















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|7639799|gb|AW734114.1|AW734114
EST:     GGAAATGGGAGCTTTTCTATACAACATCTCAATCAATTCTGCAAACACAG                         AGACCGAAACTTTTGAGGCCAAATGGAAAGATCTATCAG
genomic: GGAAATGGGAGCTTTTCTATACAACATCTCAATCAATTCTGCAAACACAGgtttggtttg ... attatcccagAGACCGAAACTTTTGAGGCCAAATGGAAAGATCTATCAG
EST: gi|209698250|gb|BW678021.1|BW678021
EST:     GGAAATGGGAGCTTTTCTATACAACATCTCAATCAATTCTGCAAACACAG                         AGACCGAAACTTTTGAGGCCAAATGGAAAGATCTATCAGGCAATTAATGTG
genomic: GGAAATGGGAGCTTTTCTATACAACATCTCAATCAATTCTGCAAACACAGgtttggtttg ... attatcccagAGACCGAAACTTTTGAGGCCAAATGGAAAGATCTATCAGGCAATTAATGTG
EST: gi|31463706|gb|CD405734.1|CD405734
EST:     TCTATACAACATCTCAATCAATTCTGCAAACACAG                         AGACCGAAACTTTTGAGGCCAAATGGAAAGATCTATCAGGCAATTAATGTG
genomic: TCTATACAACATCTCAATCAATTCTGCAAACACAGgtttggtttg ... attatcccagAGACCGAAACTTTTGAGGCCAAATGGAAAGATCTATCAGGCAATTAATGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtattctaaatttattcaccttagtaaagtgtatttgttgtattaattatcccagAGACCGAAACTTTTGAGGCCAAATGGAAAGATCTATCAGGCAATTAATGTGGATACCTTAAGAGCTCAAAATATAGAAACTTGGCCCTTCTACAACCAG
                                        tattaat  putative branch site (score: 2)
                                              ttatccc  CT-rich tract
                             tgtatttgttgtatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttggtttgtctctaggggtttggtttgtattctaaatttattcaccttagtaaagtgtatttgttgtattaattatcccagAGACCGAAACTTTTGAGGCCAAATGGAAAGATCTATCAGGCAATTAATGTGGATACCTTAAGAGCTCAAAATATAGAAACTTGGCCCTTCTACAACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA