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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagggaaacagaatcaatctagtctatctatattcttgtcttgttggtgtattggtgtctcatttggtcttccatttaacaaaacagGTACAACTTGAAGAAACTTACTTACGAGGAGAGGAAGAACAAGTTGATCGAGAGAGTCAAGGCATTGAATGGAGCAGGTGGTGATGATGATGATGAGGAC

Basic information

species Arabidopsis thaliana
transcript AT3G25520.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G25520.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G06580.1 (Glycine max), 3'ss of exon 8
-------------------------------------------------------------------------------------------------------------gtagggaaacagaatcaatctagtctatctatattcttgtcttgttggtgtattggtgtctcatttggtcttccatttaacaaaacagGTACAACTTGAAGAAACTTACTTACGAGGAGAGGAAGAACAAGTTGATCGAGAGAGTCAAGGCATTGAATGGAGCAGGTGGTGATGATGATGATGAGGAC
                                                                                                              |||  |    | ||   |  | | |   ||| ||  ||  | |    |||    | |  | || || ||| ||  ||       |||||||||||||||||| || ||||| ||||||||||||   |||||||| |   | ||   | |  | ||    || | || | | ||||| ||||| || 
gtaaaaatgagttttgacttgaactagaataatactagattcttgatttccagcagtgattttcagctatttatgtgctatattgggcgtgaccgtttttgtttgacttttagaaattttggattggta-acttttggtat-ttactgattggagaatgttcctgagagt-atctgctctgcctctttctg---cagGTACAACTTGAAGAAGCTGACTTATGAGGAGAGGAAGGCTAAGTTGATTGCACGTGTGGCGTCTCTCAACTCTGCTGCTGATAACGATGAAGATGATGAG
















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|125297327|gb|EL311412.1|EL311412
EST:     GACCCCAACCCAAAGAAAACCGTGAAACCTGCTCCCAAGCAACACAAGAG                         GTACAACTTGAAGAAACTTACTTACGAGGAGAGGAAGAACAAGTTGA
genomic: GACCCCAACCCAAAGAAAACCGTGAAACCTGCTCCCAAGCAACACAAGAGgtagggaaac ... aacaaaacagGTACAACTTGAAGAAACTTACTTACGAGGAGAGGAAGAACAAGTTGA
EST: gi|125245370|gb|EL259455.1|EL259455
EST:     GACCCCAACCCAAAGAAAACCGTGAAACCTGCTCCCAAGCAACACAAGAG                         GTACAACTTGAAGAAAC
genomic: GACCCCAACCCAAAGAAAACCGTGAAACCTGCTCCCAAGCAACACAAGAGgtagggaaac ... aacaaaacagGTACAACTTGAAGAAAC
EST: gi|125270021|gb|EL284106.1|EL284106
EST:     GACCCCAACCCAAAGAAAACCGTGAAACCTGCTCCCAAGCAACACAAGAG                         GTACAACTTGAAGAAACTTACTTACGAGGAGAGGAAGAACAAG
genomic: GACCCCAACCCAAAGAAAACCGTGAAACCTGCTCCCAAGCAACACAAGAGgtagggaaac ... aacaaaacagGTACAACTTGAAGAAACTTACTTACGAGGAGAGGAAGAACAAG
EST: gi|164051725|gb|ES188117.1|ES188117
EST:     GACCCCAACCCAAAGAAAACCGTGAAACCTGCTCCCAAGCAACACAAGAG                         GTACAACTTGAAGAAACTTACTTACGAGGAGAGGAAGAACAAGTTGA
genomic: GACCCCAACCCAAAGAAAACCGTGAAACCTGCTCCCAAGCAACACAAGAGgtagggaaac ... aacaaaacagGTACAACTTGAAGAAACTTACTTACGAGGAGAGGAAGAACAAGTTGA
EST: gi|124757980|gb|EH848110.1|EH848110
EST:     AAACCGTGAAACCTGCTCCCAAGCAACACAAGTAG                         GTACAACTTGAAGAAACTTACTTACGAGGAGAGGAAGAACAAGTTGATCG
genomic: AAACCGTGAAACCTGCTCCCAAGCAACACAAG-AGgtagggaaac ... aacaaaacagGTACAACTTGAAGAAACTTACTTACGAGGAGAGGAAGAACAAGTTGATCG
EST: gi|124855213|gb|EH939650.1|EH939650
EST:     GACCCCAACCCAAAGAAAACCGTGAAACCTGCTCCCAAGCAACACAAGAG                         GTACAACTTGAA
genomic: GACCCCAACCCAAAGAAAACCGTGAAACCTGCTCCCAAGCAACACAAGAGgtagggaaac ... aacaaaacagGTACAACTTGAA
EST: gi|164142881|gb|ES054519.1|ES054519
EST:     GACCCCAACCCAAAGAAAACCGTGAAACCTGCTCCCAAGCAACACAAGAG                         GTACAACTTGAAG
genomic: GACCCCAACCCAAAGAAAACCGTGAAACCTGCTCCCAAGCAACACAAGAGgtagggaaac ... aacaaaacagGTACAACTTGAAG
EST: gi|116467789|gb|EG510381.1|EG510381
EST:     GACCCCAACCCAAAGAAAACCGTGAAACCTGCTCCCAAGCAACACAAGAG                         GTACAACTTGAAGAAACTTACTTACGAGGAGAGGAAGAACAAGTTGATCGA
genomic: GACCCCAACCCAAAGAAAACCGTGAAACCTGCTCCCAAGCAACACAAGAGgtagggaaac ... aacaaaacagGTACAACTTGAAGAAACTTACTTACGAGGAGAGGAAGAACAAGTTGATCGA
EST: gi|164062292|gb|ES179954.1|ES179954
EST:     CAACCCAAAGAAAACCGTGAAACCTGCTCCCAAGCAACACAAGA-                         GTACAACTTGAAGAAACTTACTTACGAGGAGAGGAAGAACAAGTTGATCGA
genomic: CAACCCAAAGAAAACCGTGAAACCTGCTCCCAAGCAACACAAGAGgtagggaaac ... aacaaaacagGTACAACTTGAAGAAACTTACTTACGAGGAGAGGAAGAACAAGTTGATCGA
EST: gi|164203042|gb|ES090293.1|ES090293
EST:     CAAAGAAAACCGTGAAACCTGCTCCCAAGCAACACAAGAG                         GTACAACTTGAAGAAACTTACTTACGAGGAGAGGAAGAACAAGTTG
genomic: CAAAGAAAACCGTGAAACCTGCTCCCAAGCAACACAAGAGgtagggaaac ... aacaaaacagGTACAACTTGAAGAAACTTACTTACGAGGAGAGGAAGAACAAGTTG
EST: gi|164128106|gb|ES181933.1|ES181933
EST:     GACCCCAACCCAAAGAAAACCGTGAAACCTGCTCCCAAGCAACACAAGAG                         GTACAACTTGAAGAAACTTACTTACGAGGAGAGGAAGAACAAGT
genomic: GACCCCAACCCAAAGAAAACCGTGAAACCTGCTCCCAAGCAACACAAGAGgtagggaaac ... aacaaaacagGTACAACTTGAAGAAACTTACTTACGAGGAGAGGAAGAACAAGT
EST: gi|164178819|gb|ES210506.1|ES210506
EST:     GACCCCAACCCAAAGAAAACCGTGAAACCTGCTCCCAAGCAACACAAGAG                         GTACAACTTAGAAGAAACTTACTTACGAGGAGAGGAAGAAC
genomic: GACCCCAACCCAAAGAAAACCGTGAAACCTGCTCCCAAGCAACACAAGAGgtagggaaac ... aacaaaacagGTACAACTT-GAAGAAACTTACTTACGAGGAGAGGAAGAAC
EST: gi|125297432|gb|EL311517.1|EL311517
EST:     ACCCCAACCCAAAGAAAACCGTGAAACCTGCTACCCAAGCAACACAAGAG                         GTACAACTTGAAGAA
genomic: ACCCCAACCCAAAGAAAACCGTGAAACCTGCT-CCCAAGCAACACAAGAGgtagggaaac ... aacaaaacagGTACAACTTGAAGAA
EST: gi|125010502|gb|EL082771.1|EL082771
EST:     ACCCCAACCCAAAGAAAACCGTGAAACCTGCTCCCAAGCAACACAAGAG                         GTACAACTTGAAGA
genomic: ACCCCAACCCAAAGAAAACCGTGAAACCTGCTCCCAAGCAACACAAGAGgtagggaaac ... aacaaaacagGTACAACTTGAAGA
EST: gi|124888831|gb|EH967733.1|EH967733
EST:     GACCCCAACCCAAAGAAAACCGTGAAACCTGCTCCCAAGCAACACAAGAG                         GTACAACTTGAAGAAACTTACTTACGAGGAGAGGAAGAACAAGTTGATCGA
genomic: GACCCCAACCCAAAGAAAACCGTGAAACCTGCTCCCAAGCAACACAAGAGgtagggaaac ... aacaaaacagGTACAACTTGAAGAAACTTACTTACGAGGAGAGGAAGAACAAGTTGATCGA
EST: gi|164184962|gb|ES091120.1|ES091120
EST:     CAACACAAGAG                         GTACAACTTGAAGAAACTTACTTACGAGGAGAGGAAGAACAAGTTGATCGA
genomic: CAACACAAGAGgtagggaaac ... aacaaaacagGTACAACTTGAAGAAACTTACTTACGAGGAGAGGAAGAACAAGTTGATCGA
EST: gi|125123555|gb|EL170004.1|EL170004
EST:     GACCCCAACCCAAAGAAAACCGTGAAACCTGCTCCCAAGCAACACAAGAG                         GTACAACTTGAAGAAACTTACTTACGAGGAGAGGAAGAACAAGTTG
genomic: GACCCCAACCCAAAGAAAACCGTGAAACCTGCTCCCAAGCAACACAAGAGgtagggaaac ... aacaaaacagGTACAACTTGAAGAAACTTACTTACGAGGAGAGGAAGAACAAGTTG
EST: gi|164171599|gb|ES083946.1|ES083946
EST:     GACCCCAACCCAAAGAAAACCGTGAAACCTGCTCCCAAGCAACACAAGAG                         GTACAACTTGAAGAAACTTAACTTACGAGGAGAGGAAGAACAAGTTGATCG
genomic: GACCCCAACCCAAAGAAAACCGTGAAACCTGCTCCCAAGCAACACAAGAGgtagggaaac ... aacaaaacagGTACAACTTGAAGAAACTTA-CTTACGAGGAGAGGAAGAACAAGTTGATCG
EST: gi|125023387|gb|EL095656.1|EL095656
EST:     CAAGCAACACAAGAG                         GTACAACTTGAAGAAACTTACTTACGAGGAGAGGAAGAACAAGTTGATCGA
genomic: CAAGCAACACAAGAGgtagggaaac ... aacaaaacagGTACAACTTGAAGAAACTTACTTACGAGGAGAGGAAGAACAAGTTGATCGA
EST: gi|125291064|gb|EL305149.1|EL305149
EST:     CTGCTCCCAAGCAACACAAGAG                         GTACAACTTGAAGAAACTTACTTACGAGGAGAGGAAGAACAAGTTGATCGA
genomic: CTGCTCCCAAGCAACACAAGAGgtagggaaac ... aacaaaacagGTACAACTTGAAGAAACTTACTTACGAGGAGAGGAAGAACAAGTTGATCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttgtcttgttggtgtattggtgtctcatttggtcttccatttaacaaaacagGTACAACTTGAAGAAACTTACTTACGAGGAGAGGAAGAACAAGTTGATCGAGAGAGTCAAGGCATTGAATGGAGCAGGTGGTGATGATGATGATGAGGAC
                                         atttaac  putative branch site (score: 3)
                                         atttaacaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagggaaacagaatcaatctagtctatctatattcttgtcttgttggtgtattggtgtctcatttggtcttccatttaacaaaacagGTACAACTTGAAGAAACTTACTTACGAGGAGAGGAAGAACAAGTTGATCGAGAGAGTCAAGGCATTGAATGGAGCAGGTGGTGATGATGATGATGAGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG