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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcgagtttcttcaataactttgatacttggtatattatatggtcatcatttagtttcgttttcaagctctatgtctgaggtttctacttgtttgattgatgaacagGAAAGTTCCCAACACTTGTGAGTCACCAAGAGTCATTGGAAGCAAAGGTGAATGAGACCAAAGCAACAGTGAAGTTCCAGTTGAAGAAAGTTCTGTGTAT

Basic information

species Arabidopsis thaliana
transcript AT2G27530.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G27530.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G39270.2 (Glycine max), 3'ss of exon 3
gcgagtttcttcaataactttgatact-tggtatattatatggtcatcatttag--tttcgttttcaagctctatgtctgaggtttctacttg-tttgattga-tgaacagGAAAGTTCCCAACACTTGTGAGTCACCAAGAGTCATTGGAAGCAAAGGTGAATGAGACCAAAGCAACAGTGAAGTTCCAGTTGAAGAAAGTTCTGTGTAT
           ||   | |  ||| || || | ||   | | || ||  | | |  |||   ||||||  |   | |    | ||| |  ||| |||| |||| |   |||| |||||||| |||||||||| ||||||||| ||  | ||  ||||||| ||||||||||| || |  || ||||||||| | ||||| ||||| || ||
-----------catctagtaagatgctctgttttaaagttttgttattttctgggttttaaatttcaatgttgctttagctgatttatgattgatttggttgactttgcagGGAAGTTCCCTACACTTGTGACTCACCAAGAATCTCTCGAGTCAAAGGTTAATGAGACCAAGGCCATGGTCAAGTTCCAGCTTAAGAAGGTTCTCTGCAT
















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|164108280|gb|ES164768.1|ES164768
EST:     CTTCTTGGTCCTGGTCTTAACAAGGCAG                         GAAAGTTCCCAACACTTGTGAGTCACCAAGAGTCATTGGAAGCAAAGGTGA
genomic: CTTCTTGGTCCTGGTCTTAACAAGGCAGgcgagtttct ... tgatgaacagGAAAGTTCCCAACACTTGTGAGTCACCAAGAGTCATTGGAAGCAAAGGTGA
EST: gi|164202428|gb|ES139390.1|ES139390
EST:     CTGGTCTTAACAAGGCAG                         GAAAGTTCCCAACACTTGTGAGTCACCAAGAGTCATTGGAAGCAAAGGTGA
genomic: CTGGTCTTAACAAGGCAGgcgagtttct ... tgatgaacagGAAAGTTCCCAACACTTGTGAGTCACCAAGAGTCATTGGAAGCAAAGGTGA
EST: gi|125222155|gb|EL236240.1|EL236240
EST:     GTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTTAACAAGGCAG                         GAAAGTTCCCAACACTTGTGAGTCACCAAGAGTCA
genomic: GTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTTAACAAGGCAGgcgagtttct ... tgatgaacagGAAAGTTCCCAACACTTGTGAGTCACCAAGAGTCA
EST: gi|86077209|gb|DR372966.1|DR372966
EST:     TGTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTTAACAAGGCAG                         GAAAGTTCCCAACACTTGTGAGTCACCAAGAGTCATTGGAAGCAAAGGTGA
genomic: TGTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTTAACAAGGCAGgcgagtttct ... tgatgaacagGAAAGTTCCCAACACTTGTGAGTCACCAAGAGTCATTGGAAGCAAAGGTGA
EST: gi|125082027|gb|EL143040.1|EL143040
EST:     GATTCCTCGTCTTCTTGGTCCTGGTCTTAACAAGGCAG                         GAAAGTTCCCAACACTTGTGAGTCACCAAGAGTCATTGGAAGCAAAGGTGA
genomic: GATTCCTCGTCTTCTTGGTCCTGGTCTTAACAAGGCAGgcgagtttct ... tgatgaacagGAAAGTTCCCAACACTTGTGAGTCACCAAGAGTCATTGGAAGCAAAGGTGA
EST: gi|164217427|gb|ES162849.1|ES162849
EST:     TGTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTTAACAAGGCAG                         GAAAGTTCCCAACA
genomic: TGTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTTAACAAGGCAGgcgagtttct ... tgatgaacagGAAAGTTCCCAACA
EST: gi|125269802|gb|EL283887.1|EL283887
EST:     AGATTCCTCGTCTTCTTGGTCCTGGTCTTAACAAGGCAG                         GAAAGTTCCCAACACTTGTGAGTCACCAAGAGTCATTGGAAGCAAAGGTGA
genomic: AGATTCCTCGTCTTCTTGGTCCTGGTCTTAACAAGGCAGgcgagtttct ... tgatgaacagGAAAGTTCCCAACACTTGTGAGTCACCAAGAGTCATTGGAAGCAAAGGTGA
EST: gi|164170431|gb|ES062520.1|ES062520
EST:     CGTCTTCTTGGTCCTGGTCTTAACAAGGCAG                         GAAAGTTCCCAACACTTGTGAGTCACCAAGAGTCATTGGAAGCAAAGGTGA
genomic: CGTCTTCTTGGTCCTGGTCTTAACAAGGCAGgcgagtttct ... tgatgaacagGAAAGTTCCCAACACTTGTGAGTCACCAAGAGTCATTGGAAGCAAAGGTGA
EST: gi|124938402|gb|EL015033.1|EL015033
EST:     GTCTTAACAAGGCAG                         GAAAGTTCCCAACACTTGTGAGTCACCAAGAGTCATTGGAAGCAAAGGTGA
genomic: GTCTTAACAAGGCAGgcgagtttct ... tgatgaacagGAAAGTTCCCAACACTTGTGAGTCACCAAGAGTCATTGGAAGCAAAGGTGA
EST: gi|125065602|gb|EL132773.1|EL132773
EST:     CCTGGTCTTAACAAGGCAG                         GAAAGTTCCCAACACTTGTGAGTCACCAAGAGTCATTGGAAGCAAAGGTGA
genomic: CCTGGTCTTAACAAGGCAGgcgagtttct ... tgatgaacagGAAAGTTCCCAACACTTGTGAGTCACCAAGAGTCATTGGAAGCAAAGGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttcgttttcaagctctatgtctgaggtttctacttgtttgattgatgaacagGAAAGTTCCCAACACTTGTGAGTCACCAAGAGTCATTGGAAGCAAAGGTGAATGAGACCAAAGCAACAGTGAAGTTCCAGTTGAAGAAAGTTCTGTGTAT
                                          gattgat  putative branch site (score: 4)
       ttttcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcgagtttcttcaataactttgatacttggtatattatatggtcatcatttagtttcgttttcaagctctatgtctgaggtttctacttgtttgattgatgaacagGAAAGTTCCCAACACTTGTGAGTCACCAAGAGTCATTGGAAGCAAAGGTGAATGAGACCAAAGCAACAGTGAAGTTCCAGTTGAAGAAAGTTCTGTGTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA