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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtctttctcgtaatcctgtatctttatacaacaatttttggatttgagctagtgagaacttgtgttgtgtgttccagACTGAGTTTATGGTGGATATGACATGTGAGGGTTGTGTTAATGCTGTGAAGAACAAATTAGAAACCATTGAAGGTAGTAGGAGAAACAACTTTATTAATC

Basic information

species Arabidopsis thaliana
transcript AT1G12520.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G12520.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G04170.1 (Glycine max), 3'ss of exon 2
---------gtaagtctttctcgtaatcctgtatctttatacaacaatt---tttggatttgagctagtg-----------agaacttgtgttgtgt-----gttccagACTGAGTTTATGGTGGATATGACATGTGAGGGTTGTGTTAATGCTGTGAAGAACAAATTAGAAACCATTGAAGGTAGTAGGAGAAACAACTTTATTAATC
          ||  |  |     |    || | ||||| |    || ||   | |   | | || ||||              |  || | || | |      || ||||| ||||| |||||||| |||| ||| || ||||||||||||||||| || || || ||  |    ||  | |                           
gtcagttagatagattctctctctccctctctctctttttggctcagttaaatctaattcttagttagttccttgttgtctgaattttattttatttttccgatttcagACGGAGTTCATGGTGGACATGAAATGCGAAGGTTGTGTTAATGCTGTCAAAAATAAGTTGAACGAGATAAATG---------------------------

upper sequence: AT1G12520.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv02s0025g04830.t01 (Vitis vinifera), 3'ss of exon 2
-------------gtaagtctttctcgtaatcctgtatctttatacaacaatttttggatttga-gctagtgagaacttgtgttgtgtgttc-----cagACTGAGTTTATGGTGGATATGACATGTGAGGGTTGTGTTAATGCTGTGAAGAACAAATTAGAAACCATTGAAGGTAGTAGGAGAAACAACTTTATTAATC
               || |  |||| |   |    |    | |   |   |  | ||     || | || |  |||||| || | |  ||       ||||| |||||||||||||||||||  ||||| || ||||||||||| || ||||| || ||  |||||||    |                           
tattgcctaactatcaaattcttcttgagttttaatgatgtaaattaggtacctctgatgaggatgatattctgaacttttggtattggtatgataacagACAGAGTTTATGGTGGATATGAAGTGTGAAGGCTGTGTTAATGCCGTAAAGAATAAGTTGCAAACCATCAGTG---------------------------
















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|125222332|gb|EL236417.1|EL236417
EST:     GAGGATCGAGCCATGCCTCAGCTTCTT                         ACTGAGTTTATGGTGGATATGACATG
genomic: GAGGATCGAGCCATGCCTCAGCTTCTTgtaagtcttt ... tgtgttccagACTGAGTTTATGGTGGATATGACATG
EST: gi|124792753|gb|EH882432.1|EH882432
EST:     CCATGCCTCAGCTTCTT                         ACTGAGTTTATGGTGGATATGACATGTGAGGGTTGTGTTAATGCTGTGAAG
genomic: CCATGCCTCAGCTTCTTgtaagtcttt ... tgtgttccagACTGAGTTTATGGTGGATATGACATGTGAGGGTTGTGTTAATGCTGTGAAG
EST: gi|124812810|gb|EH897676.1|EH897676
EST:     TCAGGAGGATCGAGCCATGCCTCAGCTTCTT                         ACTGAGTTTATGGTGGATATGACATGTGAGGGTTGTGTTAATGCTGTGAAG
genomic: TCAGGAGGATCGAGCCATGCCTCAGCTTCTTgtaagtcttt ... tgtgttccagACTGAGTTTATGGTGGATATGACATGTGAGGGTTGTGTTAATGCTGTGAAG
EST: gi|125206919|gb|EL221873.1|EL221873
EST:     GAGGATCGAGCCATGCCTCAGCTTCTT                         ACTGAGTTTATGGTGGA
genomic: GAGGATCGAGCCATGCCTCAGCTTCTTgtaagtcttt ... tgtgttccagACTGAGTTTATGGTGGA
EST: gi|124711089|gb|EH802491.1|EH802491
EST:     GAGGATCGAGCCATGCCTCAGCTTCTT                         ACTGAGTTTATGGTGGATATGACATG
genomic: GAGGATCGAGCCATGCCTCAGCTTCTTgtaagtcttt ... tgtgttccagACTGAGTTTATGGTGGATATGACATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatacaacaatttttggatttgagctagtgagaacttgtgttgtgtgttccagACTGAGTTTATGGTGGATATGACATGTGAGGGTTGTGTTAATGCTGTGAAGAACAAATTAGAAACCATTGAAGGTAGTAGGAGAAACAACTTTATTAATC
       aacaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtctttctcgtaatcctgtatctttatacaacaatttttggatttgagctagtgagaacttgtgttgtgtgttccagACTGAGTTTATGGTGGATATGACATGTGAGGGTTGTGTTAATGCTGTGAAGAACAAATTAGAAACCATTGAAGGTAGTAGGAGAAACAACTTTATTAATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA