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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttctctttttctgaacagtttgaccagaatttagttatgatttagaatgccacgtttctttatgtaactatgaatttcctgatgatgtgtggggttttacaacatttcagGAGAAAGCTCCTTATGTTGCTAAGGCTGAGAAACGCAAGGTTGAATATGAGAAGAACATTAAAGCTTACAACAAGAAACTG

Basic information

species Arabidopsis thaliana
transcript AT1G20693.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G20693.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA04G01840.1 (Glycine max), 3'ss of exon 5
gtacgttctctttttctgaacagtttgaccagaatttagttatgatttagaatgccacgtt-tctttatgtaactatgaatttcctga----tgatgtgtggggttttacaacatttcagGAGAAAGCTCCTTATGTTGCTAAGGCTGAGAAACGCAAGGTTGAATATGAGAAGAACATTAAAGCTTACAACAAGAAACTG
                                        |||| | |  ||||     || | | ||  || |  | |  ||  |      || | |      |||   ||   || |||| ||||| |||||||| || ||| |||||||| | || || || || ||||||||||| | |||||| |||||||||| |
---------------------------------------gtatgttgttcaatgtttttttgtttataaatagcgtttagatttttagcatttgttattcaaattttatgaattgtttagGAAAAAGCACCTTATGTGGCAAAGTCTGAGAAAAGGAAAGTGGAGTACGAGAAGAACATGAGAGCTTATAACAAGAAACAG

upper sequence: AT1G20693.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA04G01840.5 (Glycine max), 3'ss of exon 5
gtacgttctctttttctgaacagtttgaccagaatttagttatgatttagaatgccacgtt-tctttatgtaactatgaatttcctga----tgatgtgtggggttttacaacatttcagGAGAAAGCTCCTTATGTTGCTAAGGCTGAGAAACGCAAGGTTGAATATGAGAAGAACATTAAAGCTTACAACAAGAAACTG----
                                        |||| | |  ||||     || | | ||  || |  | |  ||  |      || | |      |||   ||   || |||| ||||| |||||||| || ||| |||||||| | || || || || ||||||||||| | |||||| |||||||||| |    
---------------------------------------gtatgttgttcaatgtttttttgtttataaatagcgtttagatttttagcatttgttattcaaattttatgaattgtttagGAAAAAGCACCTTATGTGGCAAAGTCTGAGAAAAGGAAAGTGGAGTACGAGAAGAACATGAGAGCTTATAACAAGAAACAGGTTG
















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|164234508|gb|ES101559.1|ES101559
EST:     GTTGGAAAAGCTGCTGGAGACAAGTGGAAGTCCTTATCTGATTCT                         GAGAAAGCTCCTTATGTTGCTAAGG
genomic: GTTGGAAAAGCTGCTGGAGACAAGTGGAAGTCCTTGTCTGATTCTgtacgttctc ... aacatttcagGAGAAAGCTCCTTATGTTGCTAAGG
EST: gi|164010533|gb|ES061091.1|ES061091
EST:     GTTGGAAAAGCTGCTGGAGACAAGTGGAAGTCCTTATCTGATTCT                         GAGAAAGCTCCTTA
genomic: GTTGGAAAAGCTGCTGGAGACAAGTGGAAGTCCTTGTCTGATTCTgtacgttctc ... aacatttcagGAGAAAGCTCCTTA
EST: gi|125150390|gb|EL183061.1|EL183061
EST:     GCTGGAGACAAGTGGAAGTCCTTGTCTGTATTCT                         GAGAAAGCTCCTTATGTTGCTAAGGCTGAGAAACGCAAGGTTGAATATGA
genomic: GCTGGAGACAAGTGGAAGTCCTTGTCTG-ATTCTgtacgttctc ... aacatttcagGAGAAAGCTCCTTATGTTGCTAAGGCTGAGAAACGCAAGGTTGAATATGA
EST: gi|163969828|gb|ES148976.1|ES148976
EST:     GTTGGAAAAGCTGCTGGAGACAAGTGGAAGTCCTTATCTGATTCT                         GAGAAAGCTCCTTATGTTGCTAAG
genomic: GTTGGAAAAGCTGCTGGAGACAAGTGGAAGTCCTTGTCTGATTCTgtacgttctc ... aacatttcagGAGAAAGCTCCTTATGTTGCTAAG
EST: gi|164237972|gb|ES129256.1|ES129256
EST:     GTTGGAAAAGCTGCTGGAGACAAGTGGAAGTCCTTATCTGATTCT                         GAGAAAGCTCCTTATGTTGCTAAGGCTGAGAAACGCAAGGTTGA
genomic: GTTGGAAAAGCTGCTGGAGACAAGTGGAAGTCCTTGTCTGATTCTgtacgttctc ... aacatttcagGAGAAAGCTCCTTATGTTGCTAAGGCTGAGAAACGCAAGGTTGA
EST: gi|116400368|gb|EG442960.1|EG442960
EST:     GTTGGAAAAGCTGCTGGAGACAAGTGGAAGTCCTTGTCTGATTCT                         GAGAAAGCTCCTTATGTTGCTAAGGCTGAGAAACGCAAGGTTGAATATGAG
genomic: GTTGGAAAAGCTGCTGGAGACAAGTGGAAGTCCTTGTCTGATTCTgtacgttctc ... aacatttcagGAGAAAGCTCCTTATGTTGCTAAGGCTGAGAAACGCAAGGTTGAATATGAG
EST: gi|125299616|gb|EL313701.1|EL313701
EST:     TTGTCTGATTCT                         GAGAAAGCTCCTTATGTTGCTAAGGCTGAGAAACGCAAGGTTGAATATGAG
genomic: TTGTCTGATTCTgtacgttctc ... aacatttcagGAGAAAGCTCCTTATGTTGCTAAGGCTGAGAAACGCAAGGTTGAATATGAG
EST: gi|164194508|gb|ES167794.1|ES167794
EST:     TGCTGGAGACAAGTGGAAGTCCTTATCTGATTCT                         GAGAAAGCTCCTTATGTTGCTAAGGCTGAGAAACGCAAGGTTGAAATATGA
genomic: TGCTGGAGACAAGTGGAAGTCCTTGTCTGATTCTgtacgttctc ... aacatttcagGAGAAAGCTCCTTATGTTGCTAAGGCTGAGAAACGCAAGGTTGAA-TATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttatgtaactatgaatttcctgatgatgtgtggggttttacaacatttcagGAGAAAGCTCCTTATGTTGCTAAGGCTGAGAAACGCAAGGTTGAATATGAGAAGAACATTAAAGCTTACAACAAGAAACTG
                     tcctgat  putative branch site (score: 3)
             tatgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgttctctttttctgaacagtttgaccagaatttagttatgatttagaatgccacgtttctttatgtaactatgaatttcctgatgatgtgtggggttttacaacatttcagGAGAAAGCTCCTTATGTTGCTAAGGCTGAGAAACGCAAGGTTGAATATGAGAAGAACATTAAAGCTTACAACAAGAAACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA