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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttttcctttttgtgttaaccctcttaaaattcccattctaaatgtttgattaataagttggctatttttcagCTTATGTTTAGCAAATTTGAGTATGATGGTAAGCTTAACCCTACATTCAAAGAAGGACCTTTCGAGCTTCCTTTATCTAGCATTCGAGCTTATATCCAAG

Basic information

species Arabidopsis thaliana
transcript AT4G18810.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G18810.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os02g13970.2 (Oryza sativa), 3'ss of exon 11
-----gtttgttttcctttttgtgttaaccctcttaaaattcccattctaaatgtttgattaataagttggctatttttcagCTTATGTTTAGCAAATTTGAGTATGATGGTAAGCTTAACCCTACATTCAAAGAAGGACCTTTCGAGCTTCCTTTATCTAGCATTCGAGCTTATATCCAAG
      | ||||    | || || | ||   | |   |||  |     | ||  |   |||  |    ||   ||| |  |||| ||||||||||| ||||||||||| || ||||| ||||| ||||| | ||||||  | || ||||| || || || || ||| |||| || ||  | |
gtacaatgtgttcatgtgttggtat-aattttttaggaataac-----tgaacctgaaattgctg---tgataattctgtagCTCATGTTTAGCAAGTTTGAGTATGACGGAAAGCTGAACCCAACATTTACAGAAGGTTCATTTGAGCTCCCCTTTTCAAGTATTAGAGCATACATAAACG
















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|116396418|gb|EG439010.1|EG439010
EST:     ATGCACCACCTTTTAATGCAAGCAGTATCATTTCACTACAG                         CTTATGTTTAGCAAATTTGAGTATGATGGTAAGCTTAACCCTACATTCAAA
genomic: ATGCACCACCTTTTAATGCAAGCAGTATCATTTCACTACAGgtttgttttc ... tatttttcagCTTATGTTTAGCAAATTTGAGTATGATGGTAAGCTTAACCCTACATTCAAA
EST: gi|125147738|gb|EL181799.1|EL181799
EST:     TGCAAGCAGTATCATTTCACTACAG                         CTTATGTTTAGCAAATTTGAGTATGATGGTAAGCTTAACCCTACATTCAAA
genomic: TGCAAGCAGTATCATTTCACTACAGgtttgttttc ... tatttttcagCTTATGTTTAGCAAATTTGAGTATGATGGTAAGCTTAACCCTACATTCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accctcttaaaattcccattctaaatgtttgattaataagttggctatttttcagCTTATGTTTAGCAAATTTGAGTATGATGGTAAGCTTAACCCTACATTCAAAGAAGGACCTTTCGAGCTTCCTTTATCTAGCATTCGAGCTTATATCCAAG
                                            ctatttttc  CT-rich tract
                 attctaaatgtttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttttcctttttgtgttaaccctcttaaaattcccattctaaatgtttgattaataagttggctatttttcagCTTATGTTTAGCAAATTTGAGTATGATGGTAAGCTTAACCCTACATTCAAAGAAGGACCTTTCGAGCTTCCTTTATCTAGCATTCGAGCTTATATCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT