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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatcatagaccactgattttgatattctgataatggtttctgtagcttggaagagtctaatcagtattcttatgtttagTGGGAGGATAGGTTCCAAAGAGGACTTTTTCGCTATGATGTCACTGCCTGCGAAACCAAA

Basic information

species Arabidopsis thaliana
transcript AT4G26850.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G26850.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G46230.1 (Glycine max), 3'ss of exon 2
gtaaatcatagaccactgat-tttgatat--tctgataatggtttctgtagcttggaagagtctaatcagtattcttatgtt-tagTGGGAGGATAGGTTCCAAAGAGGACTTTTTCGCTATGATGTCACTGCCTGCGAAACCAAA
|||  |   | |      |   || | ||  |||  |  || |  |  | | ||  |||  |||||    ||  |||   |   ||||||| ||| |  | || ||||||||||||||||||||||| || ||||| |||||||| 
gtattttgcacatggaaaacgcttaacatcctcttttcttgttaccctttgtttcaaagtttctaaattttaccctttcatggcagTGGGAAGATCGCATGCAGAGAGGACTTTTTCGCTATGATGTTACCGCCTGTGAAACCAAG

upper sequence: AT4G26850.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA14G02500.1 (Glycine max), 3'ss of exon 2
-------------gtaaatcatagaccactgattttgatattctgataatggtttctgtagcttggaagagtctaatcagtattcttatgtt-tagTGGGAGGATAGGTTCCAAAGAGGACTTTTTCGCTATGATGTCACTGCCTGCGAAACCAAA
              |   |||| ||  || | ||   |   |||  |  || |  |  | || |  |||  |||||    ||  |||   |   ||||||| ||| |  | || ||||||||||||||||||||||| || ||||| |||||||| 
gtaaatatggaattttgctcatggagaac-ggttaacaccatcttttcttgttaccctttgcgttaaagtttctaaattttaccctttcatggcagTGGGAAGATCGCATGCAGAGAGGACTTTTTCGCTATGATGTTACCGCCTGTGAAACCAAG
















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|125064177|gb|EL131893.1|EL131893
EST:     AGGCTATAGAGCCTCCTGTAGCTTTTCTCGAGTCCCTTGTTCTCGGAGAG                         TGGGAGGATAGGTTCCAAAGAGGACTTTTTCGCTATGATGTCACTGCCTGC
genomic: AGGCTATAGAGCCTCCTGTAGCTTTTCTCGAGTCCCTTGTTCTCGGAGAGgtaaatcata ... ttatgtttagTGGGAGGATAGGTTCCAAAGAGGACTTTTTCGCTATGATGTCACTGCCTGC
EST: gi|124768830|gb|EH858960.1|EH858960
EST:     AGGCTATAGAGCCTCCTGTAGCTTTTCTCGAGTCCCTTGTTCTCGGAGAG                         TGGGAGGATAGGTTCCAAAGAGGACT
genomic: AGGCTATAGAGCCTCCTGTAGCTTTTCTCGAGTCCCTTGTTCTCGGAGAGgtaaatcata ... ttatgtttagTGGGAGGATAGGTTCCAAAGAGGACT
EST: gi|124764982|gb|EH855112.1|EH855112
EST:     GGCTATAGAGCCTCCTGTAGCTTTTCTCGAGTCCCTTGTTCTCGGAAGAG                         TGGGAGGATAGGTTCCAAAGAGGACTTTT
genomic: GGCTATAGAGCCTCCTGTAGCTTTTCTCGAGTCCCTTGTTCTCGGA-GAGgtaaatcata ... ttatgtttagTGGGAGGATAGGTTCCAAAGAGGACTTTT
EST: gi|125247894|gb|EL261979.1|EL261979
EST:     TAGAGCCTCCTGTAGCTTTTCTCGAGTCCCTTGTTCTCGGAGAG                         TGGGAGGATAGGTTCCAAAGAGGACTTTTTCGCTATGATGTCACTGCCTGC
genomic: TAGAGCCTCCTGTAGCTTTTCTCGAGTCCCTTGTTCTCGGAGAGgtaaatcata ... ttatgtttagTGGGAGGATAGGTTCCAAAGAGGACTTTTTCGCTATGATGTCACTGCCTGC
EST: gi|124896657|gb|EH972871.1|EH972871
EST:     AGGCTATAGAGCCTCCTGTAGCTTTTCTCGAGTCCCTTGTTCTCGGAGAG                         TGGGAGGATAGGTTCCAAAG
genomic: AGGCTATAGAGCCTCCTGTAGCTTTTCTCGAGTCCCTTGTTCTCGGAGAGgtaaatcata ... ttatgtttagTGGGAGGATAGGTTCCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgataatggtttctgtagcttggaagagtctaatcagtattcttatgtttagTGGGAGGATAGGTTCCAAAGAGGACTTTTTCGCTATGATGTCACTGCCTGCGAAACCAAA
                              gtctaat  putative branch site (score: 3)
                                        tattctt  putative PPT
                                        tattcttatgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatcatagaccactgattttgatattctgataatggtttctgtagcttggaagagtctaatcagtattcttatgtttagTGGGAGGATAGGTTCCAAAGAGGACTTTTTCGCTATGATGTCACTGCCTGCGAAACCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA