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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacgcggttcacatcactgtatctgcatatgcaaaaatctcacaaaccccatttgtataactggtcgttgctattgtatttacgcttgtgtatttatattgcagCAACTTGTTGTGAAGGCGGTTTCACTAGCCATCGCCCGTGATGGAGCCAGTGGTGGTGTCGTACGGACTGTCATA

Basic information

species Arabidopsis thaliana
transcript AT4G31300.1
intron # 6
splice site 3'
intron type U2

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|116424148|gb|EG466740.1|EG466740
EST:     GGTTCTTCGACCAGGCTTGGAAAGATAACATGACCAAAGAAGAAGCAGAG                         CAACTTGTTGTGAAGGCGGTTTCACTAGCCATCGCCCGTGATGGAGCCAGT
genomic: GGTTCTTCGACCAGGCTTGGAAAGATAACATGACCAAAGAAGAAGCAGAGgtaacgcggt ... tatattgcagCAACTTGTTGTGAAGGCGGTTTCACTAGCCATCGCCCGTGATGGAGCCAGT
EST: gi|124841654|gb|EH926091.1|EH926091
EST:     GGTTCTTCGACCAGGCTTGGAAAGATAACATGACCAAAGAAGAAGCAGAG                         CAACTTGTTGTGAAGGCGGTTTCACTAGCCATCG
genomic: GGTTCTTCGACCAGGCTTGGAAAGATAACATGACCAAAGAAGAAGCAGAGgtaacgcggt ... tatattgcagCAACTTGTTGTGAAGGCGGTTTCACTAGCCATCG
EST: gi|86074232|gb|DR369989.1|DR369989
EST:     GGTTCTTCGACCAGGCTTGGAAAGATAACATGACCAAAGAAGAAGCAGAG                         CAACTTGTTGTGAAGGCGGTTTCACTAGCCATCGCCCGTGATGGAGCCAGT
genomic: GGTTCTTCGACCAGGCTTGGAAAGATAACATGACCAAAGAAGAAGCAGAGgtaacgcggt ... tatattgcagCAACTTGTTGTGAAGGCGGTTTCACTAGCCATCGCCCGTGATGGAGCCAGT
EST: gi|164165644|gb|ES199899.1|ES199899
EST:     GGTTCTTCGACCAGGCTTGGAAAGATAACATGACCAAAGAAGAAGCAGAG                         CAACTTTGTTGTG
genomic: GGTTCTTCGACCAGGCTTGGAAAGATAACATGACCAAAGAAGAAGCAGAGgtaacgcggt ... tatattgcagCAACTT-GTTGTG
EST: gi|124943001|gb|EL019217.1|EL019217
EST:     GGTTCTTCGACCAGGCTTGGAAAGATAACATGACCAAAGAAGAAGCAGAG                         CAACTTGTTGTGAAGGCGGTTTCACTAGCCATCG
genomic: GGTTCTTCGACCAGGCTTGGAAAGATAACATGACCAAAGAAGAAGCAGAGgtaacgcggt ... tatattgcagCAACTTGTTGTGAAGGCGGTTTCACTAGCCATCG
EST: gi|116444628|gb|EG487220.1|EG487220
EST:     GGTTCTTCGACCAGGCTTGGGAAGATAACATGACCAAAGAAGAAGCAGAG                         CAACTTGTTGTGAAGGCGGTTTCACTAGCCATCGCC
genomic: GGTTCTTCGACCAGGCTTGGAAAGATAACATGACCAAAGAAGAAGCAGAGgtaacgcggt ... tatattgcagCAACTTGTTGTGAAGGCGGTTTCACTAGCCATCGCC
EST: gi|125009695|gb|EL081964.1|EL081964
EST:     TTCTTCGACCAGGCTTGGAAAGATAACATGACCAAAGAAGAAGCAGAG                         CAACTTGTTGTGAAGGCGGTTTCACTAGCCATCGCCCGTGATGGAGCCAGT
genomic: TTCTTCGACCAGGCTTGGAAAGATAACATGACCAAAGAAGAAGCAGAGgtaacgcggt ... tatattgcagCAACTTGTTGTGAAGGCGGTTTCACTAGCCATCGCCCGTGATGGAGCCAGT
EST: gi|47831542|gb|CK121226.1|CK121226
EST:     GGTTCTTCGACCAGGCTTGGAAAGATAACATGACCAAAGAAGAAGCAGAG                         CAACTTGTTGTGAAGGCGGTTTCACTAGCCATCGCCCGTGATGGAGCCAGT
genomic: GGTTCTTCGACCAGGCTTGGAAAGATAACATGACCAAAGAAGAAGCAGAGgtaacgcggt ... tatattgcagCAACTTGTTGTGAAGGCGGTTTCACTAGCCATCGCCCGTGATGGAGCCAGT
EST: gi|124999955|gb|EL072224.1|EL072224
EST:     AAGAAGCAGAG                         CAACTTGTTGTGAAGGCGGTTTCACTAGCCATCGCCCGTGATGGAGCCAGT
genomic: AAGAAGCAGAGgtaacgcggt ... tatattgcagCAACTTGTTGTGAAGGCGGTTTCACTAGCCATCGCCCGTGATGGAGCCAGT
EST: gi|164215621|gb|ES204376.1|ES204376
EST:     CATGACCAAAGAAGAAGCAGAG                         CAACTTGTTGTGAAGGCGGTTTCACTAGCCATCGCCCGTGATGGAGCCAGT
genomic: CATGACCAAAGAAGAAGCAGAGgtaacgcggt ... tatattgcagCAACTTGTTGTGAAGGCGGTTTCACTAGCCATCGCCCGTGATGGAGCCAGT
EST: gi|116444625|gb|EG487217.1|EG487217
EST:     GGTTCTTCGACCAGGCTTGGAAAGATAACATGACCAAAGAAGAAGCAGAG                         CAACTTGTTGTGAAGGCGGTTTCACTAGCCATCGCCCGTGATGGAGCCAGT
genomic: GGTTCTTCGACCAGGCTTGGAAAGATAACATGACCAAAGAAGAAGCAGAGgtaacgcggt ... tatattgcagCAACTTGTTGTGAAGGCGGTTTCACTAGCCATCGCCCGTGATGGAGCCAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttgtataactggtcgttgctattgtatttacgcttgtgtatttatattgcagCAACTTGTTGTGAAGGCGGTTTCACTAGCCATCGCCCGTGATGGAGCCAGTGGTGGTGTCGTACGGACTGTCATA
     gtataac  putative branch site (score: 3)
                                    ttgtgtatttatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacgcggttcacatcactgtatctgcatatgcaaaaatctcacaaaccccatttgtataactggtcgttgctattgtatttacgcttgtgtatttatattgcagCAACTTGTTGTGAAGGCGGTTTCACTAGCCATCGCCCGTGATGGAGCCAGTGGTGGTGTCGTACGGACTGTCATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG