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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttctctagctattttcaagtgttgaggctctttaactcaattaacttcttacaaaacttttttggattagGGTGAAAAGTTGAAACTTTTCTATAATCCAGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACG

Basic information

species Arabidopsis thaliana
transcript AT3G15840.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G15840.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G03360.2 (Glycine max), 3'ss of exon 3
gtaagtttctcta-gctattttcaagtgttgaggctctttaactcaattaacttcttacaaaact-tttttggatt-----agGGTGAAAAGTTGAAACTTTTCTATAATCCAGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACG
|||||| |        |   || |    |||    |  || | ||||||| |||     ||||   |||    |||     |||| |||||| | |||||||||||||||||||||||||   ||||    | ||| ||||| | |||  ||||||| || |
gtaagtataaaagtattgagttaactcattgcttgttattcaatcaattatctttcagtaaaaaaatttacaaattttggcagGGAGAAAAGCTAAAACTTTTCTATAATCCAGCTGCAACTCAACTTGTCCCTAATGAAGAATTTGGAATTGCTTTTAATG

upper sequence: AT3G15840.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G22740.1 (Glycine max), 3'ss of exon 3
------gtaagtttctctagctattttcaagtgttgaggctctttaactcaattaacttcttacaaaact-tttttggatt-----agGGTGAAAAGTTGAAACTTTTCTATAATCCAGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACG
       |||   | |  || ||  | | ||  |    | |  |||| ||||||| ||| |   ||||   |||    |||     |||| |||||| | |||||||||||||||||||||||||   ||||    | ||| ||||| | |||  ||||||| || |
gtaagtataaaagtattgagttaactcctagctt----gttacttaa-tcaattaccttttagtaaaaaaatttacaaattttggcagGGAGAAAAGCTAAAACTTTTCTATAATCCAGCTGCAACTCAACTTGTCCCTAATGAAGAATTTGGAATTGCTTTTAATG
















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|125140334|gb|EL178636.1|EL178636
EST:     ACTGCTCCTGTGTACTGGAAAACCATGTTAATGGTCTTCCACCAACCTCA                         GGTGAAAAGTTGAAACTTTTCTATAATCCAGCTGCAAGCAAACTCACTCTT
genomic: ACTGCTCCTGTGTACTGGAAAACCATG--AATGGTCTTCCACCAACCTCAgtaagtttct ... tttggattagGGTGAAAAGTTGAAACTTTTCTATAATCCAGCTGCAAGCAAACTCACTCTT
EST: gi|47828825|gb|CK118509.1|CK118509
EST:     GTACTGCTCCTGTGTACTGGAAAACCATGAATGGTCTTCCACCAACCTCA                         GGTGAAAAGTTGAAACTTTTCTATAATCCAGCTGCAAGCAAACTCACTCTT
genomic: GTACTGCTCCTGTGTACTGGAAAACCATGAATGGTCTTCCACCAACCTCAgtaagtttct ... tttggattagGGTGAAAAGTTGAAACTTTTCTATAATCCAGCTGCAAGCAAACTCACTCTT
EST: gi|47828827|gb|CK118511.1|CK118511
EST:     GTACTGCTCCTGTGTACTGGAAAACCATGAATGGTCTTCCACCAACCTCA                         GGTGAAAAGTTGAAACTTTTCTATAATCCAGCTGCAAGCAAACTCACTCTT
genomic: GTACTGCTCCTGTGTACTGGAAAACCATGAATGGTCTTCCACCAACCTCAgtaagtttct ... tttggattagGGTGAAAAGTTGAAACTTTTCTATAATCCAGCTGCAAGCAAACTCACTCTT
EST: gi|116420760|gb|EG463352.1|EG463352
EST:     GTACTGCTCCTGTGTACTGGAAAACCATGAATGGTCTTCCACCAACCTCA                         GGTGAAAAGTTGAAACTTTTCTATAATCCAGCTGCAAGCAAACTCACTCTT
genomic: GTACTGCTCCTGTGTACTGGAAAACCATGAATGGTCTTCCACCAACCTCAgtaagtttct ... tttggattagGGTGAAAAGTTGAAACTTTTCTATAATCCAGCTGCAAGCAAACTCACTCTT
EST: gi|47828708|gb|CK118392.1|CK118392
EST:     GTACTGCTCCTGTGTACTGGAAAACCATGAATGGTCTTCCACCAACCTCA                         GGTGAAAAGTTGAAACTTTTCTATAATCCAGCTGCAAGCAAACTCACTCTT
genomic: GTACTGCTCCTGTGTACTGGAAAACCATGAATGGTCTTCCACCAACCTCAgtaagtttct ... tttggattagGGTGAAAAGTTGAAACTTTTCTATAATCCAGCTGCAAGCAAACTCACTCTT
EST: gi|125127295|gb|EL172214.1|EL172214
EST:     GTACTGCTCCTGTGTACTGGAAAACCATGAATGGTCTTCCACCAACCTCA                         GGTGAAAAGTTGAAACTTT
genomic: GTACTGCTCCTGTGTACTGGAAAACCATGAATGGTCTTCCACCAACCTCAgtaagtttct ... tttggattagGGTGAAAAGTTGAAACTTT
EST: gi|124825140|gb|EH910006.1|EH910006
EST:     GTACTGCTCCTGTGTACTGGAAAACCATGAATGGTCTTCCACCAACCTCA                         GGTGAAAAGTTGAAACTTTTCTATAATCCAGCTGCAA
genomic: GTACTGCTCCTGTGTACTGGAAAACCATGAATGGTCTTCCACCAACCTCAgtaagtttct ... tttggattagGGTGAAAAGTTGAAACTTTTCTATAATCCAGCTGCAA
EST: gi|116441102|gb|EG483694.1|EG483694
EST:     GTACTGCTCCTGTGTACTGGAAAACCATGAATGGTCTTCCACCAACCTCA                         GGTGAAAAGTTGAAACTTTTCTATAATCCAGCTGCAAGCAAACTCACTCTT
genomic: GTACTGCTCCTGTGTACTGGAAAACCATGAATGGTCTTCCACCAACCTCAgtaagtttct ... tttggattagGGTGAAAAGTTGAAACTTTTCTATAATCCAGCTGCAAGCAAACTCACTCTT
EST: gi|47831953|gb|CK121637.1|CK121637
EST:     GTACTGCTCCTGTGTACTGGAAAACCATGAATGGTCTTCCACCAACCTC-                         -------A-TTGAAACTTTTCTATAATCCAGCTGCAAGCAAACTCACTCTT
genomic: GTACTGCTCCTGTGTACTGGAAAACCATGAATGGTCTTCCACCAACCTCAgtaagtttct ... tttggattagGGTGAAAAGTTGAAACTTTTCTATAATCCAGCTGCAAGCAAACTCACTCTT
EST: gi|47830759|gb|CK120443.1|CK120443
EST:     GTACTGCTCCTGTGTACTGGAAAACCATGAATGGTCTTCCACCAACCTCA                         GGTGAAAAGTTGAAACTTTTCTATAATCCAGCTGCAAGCAAACTCACTCTT
genomic: GTACTGCTCCTGTGTACTGGAAAACCATGAATGGTCTTCCACCAACCTCAgtaagtttct ... tttggattagGGTGAAAAGTTGAAACTTTTCTATAATCCAGCTGCAAGCAAACTCACTCTT
EST: gi|125321733|gb|EL335818.1|EL335818
EST:     CTGGAAAACCATGAATGGTCTTCCACCAACCTCA                         GGTGAAAAGTTGAAACTTTTCTATAATCCAGCTGCAAACAAACTCACTACT
genomic: CTGGAAAACCATGAATGGTCTTCCACCAACCTCAgtaagtttct ... tttggattagGGTGAAAAGTTGAAACTTTTCTATAATCCAGCTGCAAGCAAACTCACT-CT
EST: gi|47832287|gb|CK121971.1|CK121971
EST:     GTACTGCTCCTGTGTACTGGAAAACCATGAATGGTCTTCCACCAACCTCA                         GGTGAAAAGTTGAAACTTTTCTATAATCCAGCTGCAAGCAAACTCACTCTT
genomic: GTACTGCTCCTGTGTACTGGAAAACCATGAATGGTCTTCCACCAACCTCAgtaagtttct ... tttggattagGGTGAAAAGTTGAAACTTTTCTATAATCCAGCTGCAAGCAAACTCACTCTT
EST: gi|124808956|gb|EH894810.1|EH894810
EST:     GTACTGCTCCTGTGTACTGGAAAACCATGAATGGTCTTCCACCAACCTCA                         GGTGAAAAGTTGAAACTTTTCTATAATACCAGCTGCAAGCAAACTCACTCT
genomic: GTACTGCTCCTGTGTACTGGAAAACCATGAATGGTCTTCCACCAACCTCAgtaagtttct ... tttggattagGGTGAAAAGTTGAAACTTTTCTATAAT-CCAGCTGCAAGCAAACTCACTCT
EST: gi|116479684|gb|EG522276.1|EG522276
EST:     GTACTGCTCCTGTGTACTGGAAAACCATGAATGGTCTTCCACCAACCTCA                         GGTGAAAAGTTGAAACTTTTCTATAATCCAGCTGCAAGCAAACTCACTCTT
genomic: GTACTGCTCCTGTGTACTGGAAAACCATGAATGGTCTTCCACCAACCTCAgtaagtttct ... tttggattagGGTGAAAAGTTGAAACTTTTCTATAATCCAGCTGCAAGCAAACTCACTCTT
EST: gi|125118175|gb|EL167002.1|EL167002
EST:     CTGGAAAACCATGAATGGTCTTCCACCAACCTCA                         GGTGAAAAGTTGAAACTTTTCTATAATCCAGCTGCAAGCAAACTCAACTCT
genomic: CTGGAAAACCATGAATGGTCTTCCACCAACCTCAgtaagtttct ... tttggattagGGTGAAAAGTTGAAACTTTTCTATAATCCAGCTGCAAGCAAACTCA-CTCT
EST: gi|125298219|gb|EL312304.1|EL312304
EST:     GTACTGCTCCTGTGTACTGGAAAACCATGAATGGTCTTCCACCAACCTCA                         GGTGAAAAGTTGAAACTTTT
genomic: GTACTGCTCCTGTGTACTGGAAAACCATGAATGGTCTTCCACCAACCTCAgtaagtttct ... tttggattagGGTGAAAAGTTGAAACTTTT
EST: gi|116428971|gb|EG471563.1|EG471563
EST:     TGCTCCTGTGTACTGGAAAACCATGAATGGTCTTCCACCAACCTCA                         GGTGAAAAGTTGAAACTTTTCTATAATCCAGCTGCAAGCAAACTCACTCTT
genomic: TGCTCCTGTGTACTGGAAAACCATGAATGGTCTTCCACCAACCTCAgtaagtttct ... tttggattagGGTGAAAAGTTGAAACTTTTCTATAATCCAGCTGCAAGCAAACTCACTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagtgttgaggctctttaactcaattaacttcttacaaaacttttttggattagGGTGAAAAGTTGAAACTTTTCTATAATCCAGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACG
                              ttcttac  putative branch site (score: 2)
                                         ctttttt  putative PPT
                                 ttacaaaactttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttctctagctattttcaagtgttgaggctctttaactcaattaacttcttacaaaacttttttggattagGGTGAAAAGTTGAAACTTTTCTATAATCCAGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA