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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaacaagctccaaagtttgttcctttttttcaattttcgccaattctgtaatctcatcattgtccttgtttgtttgtttgattcaacacacaattcttgttttgatttggatgcagAAGTTTTTGGCTTTGAATTGGATTTGGGTTTCGTTCCAAAATCAGCTCTTTTTGTTAATCAG

Basic information

species Arabidopsis thaliana
transcript AT4G20380.1
intron # 1
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|152037987|gb|BP804959.2|BP804959
EST:     GCTCTAGCTTTCGCGGGTTTGGGATTCGATTCCTTACCCTTCTCCAATC-                         --GTTTTTGGCTTTGAATTGGATTTGGGTTTCGTTCCAAAATCAGCTCTTT
genomic: GCTCTAGCTTTCGCGGGTTTTGGATTCGATTCCTTACCCTTCTCCAATCGgtaagaacaa ... ttggatgcagAAGTTTTTGGCTTTGAATTGGATTTGGGTTTCGTTCCAAAATCAGCTCTTT
EST: gi|164077642|gb|ES046682.1|ES046682
EST:     GCTCTAGATTTCGCGGGTTTTGGATTCGATTCCTTACCCTTCTCCAATCG                         AAGTTTTTGGCTTTGAATTGGATTTGGGTTTCGTTCCAAAATCAGCTCTTT
genomic: GCTCTAGCTTTCGCGGGTTTTGGATTCGATTCCTTACCCTTCTCCAATCGgtaagaacaa ... ttggatgcagAAGTTTTTGGCTTTGAATTGGATTTGGGTTTCGTTCCAAAATCAGCTCTTT
EST: gi|301502089|gb|HO207629.1|HO207629
EST:     GCTCTAGCTTTCGCGGGTTTTGGATTCGATTCCTTACCCTTCTCCAATCG                         AAGTTTTTGGCTTTGAATTGGATTTGGGTTTCGTTCCAAAATCAGCTCTTT
genomic: GCTCTAGCTTTCGCGGGTTTTGGATTCGATTCCTTACCCTTCTCCAATCGgtaagaacaa ... ttggatgcagAAGTTTTTGGCTTTGAATTGGATTTGGGTTTCGTTCCAAAATCAGCTCTTT
EST: gi|47830281|gb|CK119965.1|CK119965
EST:     GCTCTAGATTTCGCGGGTTTTGGATTCGATTCCTTACCCTTCTCCAATCG                         AAGTTTTTGGCTTTGAATTGGATTTGGGTTTCGTTCCAAAATCAGCTCTTT
genomic: GCTCTAGCTTTCGCGGGTTTTGGATTCGATTCCTTACCCTTCTCCAATCGgtaagaacaa ... ttggatgcagAAGTTTTTGGCTTTGAATTGGATTTGGGTTTCGTTCCAAAATCAGCTCTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtccttgtttgtttgtttgattcaacacacaattcttgttttgatttggatgcagAAGTTTTTGGCTTTGAATTGGATTTGGGTTTCGTTCCAAAATCAGCTCTTTTTGTTAATCAG
                                      ttttgat  putative branch site (score: 4)
                                      ttttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaacaagctccaaagtttgttcctttttttcaattttcgccaattctgtaatctcatcattgtccttgtttgtttgtttgattcaacacacaattcttgttttgatttggatgcagAAGTTTTTGGCTTTGAATTGGATTTGGGTTTCGTTCCAAAATCAGCTCTTTTTGTTAATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC