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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtttctcttattttaacaccaaattcatagctaaaacatttgtaacattaagtgacaacttatgtagtacaatattaaaacagGTAGGAGATCTTGGCTTTGCATCTGAGCTTGGAAACTATGCTGAATACAGCGGTGCACCCAAAGAAGAGGAGGTCTTGCAGTATGCCAGAGTTGTAATTG

Basic information

species Glycine max
transcript GLYMA02G04120.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G04120.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv01s0127g00260.t01 (Vitis vinifera), 3'ss of exon 10
gtgtgtttctc-ttattttaacaccaaattcatagctaaaacatttg----taacattaagtgacaacttatgtagtac-----aatattaa-----aacagGTAGGAGATCTTGGCTTTGCATCTGAGCTTGGAAACTATGCTGAATACAGCGGTGCACCCAAAGAAGAGGAGGTCTTGCAGTATGCCAGAGTTGTAATTG
||| | ||||| | |||| ||        | |   ||  ||  |||     ||   | |  | |     | | || |       ||||||       | ||||| || ||||| || | ||| ||||||||||| |||||||| || || || || ||||| || |||||||| || ||||||||||| |||||||||||||
gtgcggttctcatcatttaaatttagggattaggacttcaaggttttaatttactttcagctcatgctatttttactgttaataaatatttcgtcttatcagGTTGGTGATCTCGGTTATGCTTCTGAGCTTGGGAACTATGCAGAGTATAGTGGAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTG
















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|18735196|gb|BM528624.1|BM528624
EST:     TTTGGACAATGGTAGCTGGGGGAGGTGCTAGTGTCATTTATGCTGATACG                         GTAGGAGATCTTGGCTTTGCATCTGAGCTTGGAAACTATGCTGAATACAGT
genomic: TTTGGACAATGGTAGCTGGGGGAGGTGCTAGTGTTATCTATGCTGATACGgtgtgtttct ... attaaaacagGTAGGAGATCTTGGCTTTGCATCTGAGCTTGGAAACTATGCTGAATACAGC
EST: gi|57575455|gb|CX548430.1|CX548430
EST:     TTTGGACAATGGTAGCTGGGGGAGGTGCTAGTGTTATCTATGCTGATACG                         GTAGGAGATCTTGGCTTTGCATCTGAGCTTGGAAACTATGCTGAATACAGC
genomic: TTTGGACAATGGTAGCTGGGGGAGGTGCTAGTGTTATCTATGCTGATACGgtgtgtttct ... attaaaacagGTAGGAGATCTTGGCTTTGCATCTGAGCTTGGAAACTATGCTGAATACAGC
EST: gi|6134722|gb|AW133115.1|AW133115
EST:     TTTGGACAATGGTAGCTGGGGGAGGTGCTAGTGTTATCTATGCTGATACG                         GTANGAGATCTTGG
genomic: TTTGGACAATGGTAGCTGGGGGAGGTGCTAGTGTTATCTATGCTGATACGgtgtgtttct ... attaaaacagGTAGGAGATCTTGG
EST: gi|4397575|gb|AI496572.1|AI496572
EST:     TTTGGACAATGGTAGCTGGGGGAGGTGCTAGTGTTATCTATGCTGATACG                         GTAGGAGATCTTGGCTTTGCATCTGAGCTTGGAAACTATGCTGAATACAGC
genomic: TTTGGACAATGGTAGCTGGGGGAGGTGCTAGTGTTATCTATGCTGATACGgtgtgtttct ... attaaaacagGTAGGAGATCTTGGCTTTGCATCTGAGCTTGGAAACTATGCTGAATACAGC
EST: gi|6725270|gb|AW309669.1|AW309669
EST:     TTTGGACAATGGTAGCTGGGCGAGGTGCTAGTGTTATCTATGCTGATACG                         GTAGAAGATCTTGGCTNTGCATCTGAGCTTGGAAACTATGCTGAATACAGC
genomic: TTTGGACAATGGTAGCTGGGGGAGGTGCTAGTGTTATCTATGCTGATACGgtgtgtttct ... attaaaacagGTAGGAGATCTTGGCTTTGCATCTGAGCTTGGAAACTATGCTGAATACAGC
EST: gi|58016426|gb|CX703168.1|CX703168
EST:     TTTGGACAATGGTAGCTGGGGGAGGTGCTAGTGTTATCTATGCTGATACG                         GTAGGAGATCTTGGCTTTGCATCTGAGCTTGGAAACTATGCTGAATACAGC
genomic: TTTGGACAATGGTAGCTGGGGGAGGTGCTAGTGTTATCTATGCTGATACGgtgtgtttct ... attaaaacagGTAGGAGATCTTGGCTTTGCATCTGAGCTTGGAAACTATGCTGAATACAGC
EST: gi|19453151|gb|BM954561.1|BM954561
EST:     TTTGGACAATGGTAGCTGGGGGAGGTGCTAGTGTTATCTATGCTGATACG                         GTAGGAGATCTTGGCTTTGCATCTGAGCTTGGAAACTATGCTGAATACAGC
genomic: TTTGGACAATGGTAGCTGGGGGAGGTGCTAGTGTTATCTATGCTGATACGgtgtgtttct ... attaaaacagGTAGGAGATCTTGGCTTTGCATCTGAGCTTGGAAACTATGCTGAATACAGC
EST: gi|6134504|gb|AW132897.1|AW132897
EST:     TTTGGACAATGGTAGCTGGGGGAGGTGCTAGTGTTATCTATGCTGATACG                         GTAGGAGATCTTGGCTTTGCATCTGAGCTTGGAAACTATGCTGAATACAGC
genomic: TTTGGACAATGGTAGCTGGGGGAGGTGCTAGTGTTATCTATGCTGATACGgtgtgtttct ... attaaaacagGTAGGAGATCTTGGCTTTGCATCTGAGCTTGGAAACTATGCTGAATACAGC
EST: gi|193357790|gb|FK318914.1|FK318914
EST:     TGCTAGTGTTATCTATGCTGATACG                         GTAGGAGATCTTGGCTTTGCATCTAGAGCTTGGAA
genomic: TGCTAGTGTTATCTATGCTGATACGgtgtgtttct ... attaaaacagGTAGGAGATCTTGGCTTTGCATCT-GAGCTTGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctaaaacatttgtaacattaagtgacaacttatgtagtacaatattaaaacagGTAGGAGATCTTGGCTTTGCATCTGAGCTTGGAAACTATGCTGAATACAGCGGTGCACCCAAAGAAGAGGAGGTCTTGCAGTATGCCAGAGTTGTAATTG
           ttgtaac  putative branch site (score: 2)
                               ttatgtagtacaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtttctcttattttaacaccaaattcatagctaaaacatttgtaacattaagtgacaacttatgtagtacaatattaaaacagGTAGGAGATCTTGGCTTTGCATCTGAGCTTGGAAACTATGCTGAATACAGCGGTGCACCCAAAGAAGAGGAGGTCTTGCAGTATGCCAGAGTTGTAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG