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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTCAACGTGCTTGGTAACGAGAAAGCCAGCAGAGAGATATTCAACATCTCGGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAGgtacattcttttctattggctttattgttgtctcatcaatccaaatcgtttcaagtacatcctggtgtggtccgtttgtaatagatatcatactctgagctttttggatcattgcttgagtaaacttattcatgttttcaactctctctcag

Basic information

species Arabidopsis thaliana
transcript AT1G09340.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G09340.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA19G41540.2 (Glycine max), 5'ss of exon 8
TCTCAACGTGCTTGGTAACGAGAAAGCCAGCAGAGAGATATTCAACATCTCGGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAGgtacattcttttctattggctttattgttgtctcatcaatccaaatcgtttcaagtacatcctggt--gtggtccgtttgtaatagatatcatactctgagctttttggatcattgcttgagtaaacttattcatgttttcaactctctctcag
| || | || |||||||| ||||| |||||||  ||  |||||||||||||||| ||||| ||||| || ||||| || ||||||| ||| || || ||||||  |  || |    | |   |||| |    | | ||||  | | |  |   |  |   | |  |  |||   |  ||  | | || | |||    |    | ||   ||  ||| |||  |   | | |||  |                  
TATCCAAGTTCTTGGTAATGAGAAGGCCAGCAAGGAAGTATTCAACATCTCGGGAGAGAAGTATGTCACGTTTGACGGATTAGCAAGAGCATGTGCTAAGgtaagtcattcttgccttgtcatatt-taaggtgaccaatagagagcagtgggaaaatgccttaataagtgaaacaattaaatttgaga-catgtattttagtattgtaatttttgtttgttttggcattttccag------------------

upper sequence: AT1G09340.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA03G38930.1 (Glycine max), 5'ss of exon 8
TCTCAACGTGCTTGGTAACGAGAAAGCCAGCAGAGAGATATTCAACATCTCGGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAGgtacattcttttctattggctttattgttgtctcatcaatccaaatcgtttcaagtacatcctggtgtggtccgtttgtaatagatatcatactctgagctttttggatcattgcttgagtaaacttattcatgttttcaactctctctcag
| || | || |||||||| ||||| |||||||  ||  |||||||||||||||| || || ||||| || |||||||| ||||||| ||| || || ||||||  |  ||        |   |||| |    | | ||||  ||| |      |  |   | |  | ||    |     | || || | ||||    |  | ||   ||  ||| ||   |   | | |||  |                  
TATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAGGAAGTATTCAACATCTCGGGAGATAAGTATGTCACATTTGATGGATTAGCAAGAGCATGTGCTAAGgtaagtcattcatgccatgtcatatt-taaggtgaccaatagaaagcagaaggaaaatgccttaatatgtcaagca---attaaatttgatac----atgtattgtaatttttgtttattttggcattttccag------------------
















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|125033714|gb|EL105983.1|EL105983
EST:     CGGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAG                         GCCGGTGGGTTTCCGGAGCCAGAG
genomic: CGGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAGgtacattctt ... tctctctcagGCCGGTGGGTTTCCGGAGCCAGAG
EST: gi|124886801|gb|EH965703.1|EH965703
EST:     AGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAG                         GCCGGTGGGTTTCCGGAGCCAGAAAGATTGTTCATTACAACCCGAAAGAGT
genomic: AGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAGgtacattctt ... tctctctcagGCCGGTGGGTTTCCGGAGCCAGA--GATTGTTCATTACAACCCGAAAGAGT
EST: gi|124799009|gb|EH888688.1|EH888688
EST:     AATATGTTACCTTTGATGGGTTAGCAAAAGCTTTGCGCAAAG                         GCCGGTGGGTTTCCGGAGCCAGAGATTGTTCATTACAACCCGAAAGAGTTC
genomic: AATATGTTACCTTTGATGGGTTAGCAAAAGC-TTGCGCAAAGgtacattctt ... tctctctcagGCCGGTGGGTTTCCGGAGCCAGAGATTGTTCATTACAACCCGAAAGAGTTC
EST: gi|124897912|gb|EH974126.1|EH974126
EST:     CGGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAG                         GCCGGTGGGTTTCCGGAGCCAGAGATTGTTCATTACAACCCGAA
genomic: CGGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAGgtacattctt ... tctctctcagGCCGGTGGGTTTCCGGAGCCAGAGATTGTTCATTACAACCCGAA
EST: gi|125208659|gb|EL223613.1|EL223613
EST:     CGGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAG                         GCCGGTGGGTTTCCGGAGCCAG
genomic: CGGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAGgtacattctt ... tctctctcagGCCGGTGGGTTTCCGGAGCCAG
EST: gi|86080119|gb|DR375876.1|DR375876
EST:     CGGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAA-STTGCGCAAAG                         GCCGGTGGGTTTCCGGAGCCAGAGATTGTTCATTACAACCCGAAAGAGTTC
genomic: CGGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAGgtacattctt ... tctctctcagGCCGGTGGGTTTCCGGAGCCAGAGATTGTTCATTACAACCCGAAAGAGTTC
EST: gi|116482238|gb|EG524830.1|EG524830
EST:     CGGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAG                         GCCGGTGGGTTTCCGGAGCCAGAGATTGTTCATTACAACCCGAAAGAGTTC
genomic: CGGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAGgtacattctt ... tctctctcagGCCGGTGGGTTTCCGGAGCCAGAGATTGTTCATTACAACCCGAAAGAGTTC
EST: gi|124757668|gb|EH847798.1|EH847798
EST:     C-GGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAG                         GCCGGTGGGTTTCCGGAGCCAGAGATTGTTCATTACAGCCCGAAAGAGTTC
genomic: CGGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAGgtacattctt ... tctctctcagGCCGGTGGGTTTCCGGAGCCAGAGATTGTTCATTACAACCCGAAAGAGTTC
EST: gi|124868998|gb|EH953435.1|EH953435
EST:     CGGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAG                         GCCGGTGGGTTTCCGGAGCCAGAGATTGTTCATTACAACCCG
genomic: CGGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAGgtacattctt ... tctctctcagGCCGGTGGGTTTCCGGAGCCAGAGATTGTTCATTACAACCCG
EST: gi|125225178|gb|EL239263.1|EL239263
EST:     CGGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAG                         GCCGGTGGGTTTCC
genomic: CGGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAGgtacattctt ... tctctctcagGCCGGTGGGTTTCC
EST: gi|124893349|gb|EH972251.1|EH972251
EST:     CTTGCGCAAAG                         GCCGGTGGGTTTCCGGAGCCAGAGATTGTTCATTACAACCCGAAAGAGTTC
genomic: CTTGCGCAAAGgtacattctt ... tctctctcagGCCGGTGGGTTTCCGGAGCCAGAGATTGTTCATTACAACCCGAAAGAGTTC
EST: gi|125168639|gb|EL193184.1|EL193184
EST:     CTTGCGCAAAG                         GCCGGTGGGTTTCCGGAGCCAGAGATTGTTCATTACAACCCGAAAGAGTTC
genomic: CTTGCGCAAAGgtacattctt ... tctctctcagGCCGGTGGGTTTCCGGAGCCAGAGATTGTTCATTACAACCCGAAAGAGTTC
EST: gi|125090155|gb|EL148256.1|EL148256
EST:     CGGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAG                         GCCGGTGGGTTTCCGGAGCCAGAGATTGTTACATTACAACCCGAAAGAGTT
genomic: CGGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAGgtacattctt ... tctctctcagGCCGGTGGGTTTCCGGAGCCAGAGATTGTT-CATTACAACCCGAAAGAGTT
EST: gi|125227563|gb|EL241648.1|EL241648
EST:     C-GGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAG                         GCCGGTGGGTTTCCGGAG
genomic: CGGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAGgtacattctt ... tctctctcagGCCGGTGGGTTTCCGGAG
EST: gi|125230806|gb|EL244891.1|EL244891
EST:     CGGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAG                         GCCGGTGGGTTTCCGGAGCCAGAGATTGTTCATTACAACCCGAAAGAGTTC
genomic: CGGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAGgtacattctt ... tctctctcagGCCGGTGGGTTTCCGGAGCCAGAGATTGTTCATTACAACCCGAAAGAGTTC
EST: gi|124861629|gb|EH946066.1|EH946066
EST:     GGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAG                         GCCGGTGGGTTTCCGGAGCCAGAGATTGTTCATTACAACCCGAAAGAGTTC
genomic: GGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAGgtacattctt ... tctctctcagGCCGGTGGGTTTCCGGAGCCAGAGATTGTTCATTACAACCCGAAAGAGTTC
EST: gi|124933045|gb|EL010246.1|EL010246
EST:     CGGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAG                         GCCGGTGGGTTTCCGGAGCCAGAGATTGTT
genomic: CGGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAGgtacattctt ... tctctctcagGCCGGTGGGTTTCCGGAGCCAGAGATTGTT
EST: gi|124886268|gb|EH965170.1|EH965170
EST:     CGGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAG                         GCCGGTGGGTTTCCGGAGCCAGAGATTG
genomic: CGGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAGgtacattctt ... tctctctcagGCCGGTGGGTTTCCGGAGCCAGAGATTG
EST: gi|86083439|gb|DR379198.1|DR379198
EST:     CGGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAG                         NCCGGTGGGTTTCCGGAGCCAGAGATTGTTCATTACAACCCGAAAGAGTTC
genomic: CGGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAGgtacattctt ... tctctctcagGCCGGTGGGTTTCCGGAGCCAGAGATTGTTCATTACAACCCGAAAGAGTTC
EST: gi|125096508|gb|EL153286.1|EL153286
EST:     C-GGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAG                         GCCGGTGGGTTTCCGGAGCCAGAGA
genomic: CGGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAGgtacattctt ... tctctctcagGCCGGTGGGTTTCCGGAGCCAGAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTCAACGTGCTTGGTAACGAGAAAGCCAGCAGAGAGATATTCAACATCTCGGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAGgtacattcttttctattggctttattgttgtctcatcaatccaaatcgtttcaagtacatcctggtgtggtccgtttgtaatagatatcatactctgagctttttggatcattgcttgagtaaacttattcatgttttcaactctctctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG