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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcacaactttcttcaatatttccacttatttacctttttgttacttttgttaatttttgttgtgaacttgtattataacagGTTAACATACATACTGACACCTTAAACGAATCTGGATTTGTTGAACATACAATTGCTGCATTTAAAGGAAGAACTATTCATACTTACCACAG

Basic information

species Glycine max
transcript GLYMA11G37250.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G37250.1 (Glycine max), 3'ss of exon 12
lower sequence: AT1G67550.1 (Arabidopsis thaliana), 3'ss of exon 11
gcacaactttcttcaatatttccacttatttacctttttgttactt----ttgttaatttttgttgtgaact----tgtatta---taacagGTTAACATACATACTGACACCTTAAACGAATCTGGATTTGTTGAACATACAATTGCTGCATTTAAAGGAAGAACTATTCATACTTACCACAG
        |  ||   | |  |   | |  | |  ||||   |       ||| || |||    | || |||    ||| ||    | |||||| ||||| ||||||||||||||||| ||||| || |||||||| || || ||   |||||||   || ||||| || ||||| || |||||
-------gtcttttcttttccctgatgacatcctcttttaagaaacaggattgatagtttcccatatgtactcaattgttttgatttgacagGTGAACATTCATACTGACACCTTAAATGAATCCGGTTTTGTTGAGCACACTATCAATGCATTTCGTGGGAGAACAATACATACATATCACAG

upper sequence: GLYMA11G37250.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv01s0010g02760.t01 (Vitis vinifera), 3'ss of exon 11
gcacaactttcttcaatatttccacttattta--cctttttgttacttttgttaatttttgttgtgaacttgtattataacagGTTAACATACATACTGACACCTTAAACGAATCTGGATTTGTTGAACATACAATTGCTGCATTTAAAGGAAGAACTATTCATACTTACCACAG
       ||  || | | | |  | |||||||  | ||| ||||||||    |  |   |  | |       |  | | ||||||||| || || ||||||||||| ||||| ||||| ||||| ||||||||||||||||| |||||||  |||||||||||||||||||||||
------gttattttattttatttatttatttaaacttttatgttacttgcagttgtagctagttttcttactttctgttacagGTTAATATCCACACTGACACCTTGAACGAGTCTGGCTTTGTGGAACATACAATTGCTGCGTTTAAAGATAGAACTATTCATACTTACCACAG
















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|151405862|gb|EV275677.1|EV275677
EST:     CGGCTGCAATAGACAGTTGTTTGACAGTTGCAGACCAATATGATATCCAG                         GTTAACATACATACTGACACCTTAAACGAATCTGGATTTGTTGAACATACA
genomic: CGGCTGCAATAGACAGTTGTTTGACAGTTGCAGACCAATATGATATCCAGgcacaacttt ... attataacagGTTAACATACATACTGACACCTTAAACGAATCTGGATTTGTTGAACATACA
EST: gi|16278014|gb|BI942681.1|BI942681
EST:     CGGCTGCAATAGACAGTTGTTTGACAGTTGCAGACCAATATGATATCCAG                         GTTAACATACATACTGACACCTTAAACGAATCTGGATTTGTTGAACATACA
genomic: CGGCTGCAATAGACAGTTGTTTGACAGTTGCAGACCAATATGATATCCAGgcacaacttt ... attataacagGTTAACATACATACTGACACCTTAAACGAATCTGGATTTGTTGAACATACA
EST: gi|151402941|gb|EV272754.1|EV272754
EST:     CGGCTGCAATAGACAGTTGTTTGACAGTTGCAGACCAATATGATATCCAG                         GTTAACATACATACTGACACCTTAAACGAATCTGGATTTGTTGAACATACA
genomic: CGGCTGCAATAGACAGTTGTTTGACAGTTGCAGACCAATATGATATCCAGgcacaacttt ... attataacagGTTAACATACATACTGACACCTTAAACGAATCTGGATTTGTTGAACATACA
EST: gi|208294142|gb|GE092631.1|GE092631
EST:     GACCAATATGATTATCCAG                         GTTAACATACATACTGACACCTTAAACGAATCTGGATTTGTTGAACATAC
genomic: GACCAATATGA-TATCCAGgcacaacttt ... attataacagGTTAACATACATACTGACACCTTAAACGAATCTGGATTTGTTGAACATAC
EST: gi|151394452|gb|EV264323.1|EV264323
EST:     CGGCTGCAATAGACAGTTGTTTGACAGTTGCAGACCAATATGATATCCAG                         GTTAACATACATACTGACACCTTAAACGAATCTGGATTTGTTGAACATACA
genomic: CGGCTGCAATAGACAGTTGTTTGACAGTTGCAGACCAATATGATATCCAGgcacaacttt ... attataacagGTTAACATACATACTGACACCTTAAACGAATCTGGATTTGTTGAACATACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttacctttttgttacttttgttaatttttgttgtgaacttgtattataacagGTTAACATACATACTGACACCTTAAACGAATCTGGATTTGTTGAACATACAATTGCTGCATTTAAAGGAAGAACTATTCATACTTACCACAG
                     tgttaat  putative branch site (score: 3)
        tttttgttacttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcacaactttcttcaatatttccacttatttacctttttgttacttttgttaatttttgttgtgaacttgtattataacagGTTAACATACATACTGACACCTTAAACGAATCTGGATTTGTTGAACATACAATTGCTGCATTTAAAGGAAGAACTATTCATACTTACCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC