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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaccttaaagagtattacttaaaagctaaaacgtttttgatttcttcaggacataagcggtagtaaaagtttatggctttttctttgttagCGGCTGAAGCGATTTGGGCGTGTTCGATTGAAGAACTAGGGCTGGAGAATGAGGCCGAGAAACCGAGCAATGCGTTGTTAACTAGAGCTTGGTCTCCAGG

Basic information

species Arabidopsis thaliana
transcript AT1G04400.1
intron # 3
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|116403790|gb|EG446382.1|EG446382
EST:     TGAATCCGTTATGCTTCCTCCTCCTTGGCGGTTGATGCCAATAACTGCAG                         CGGCTGAAGCGATTTGGGCGTGTTCGATTGAAGAACTAGGGCTGGAGAATG
genomic: TGAATCCGTTATGCTTCCTCCTCCTTGGCGGTTGATGCCAATAACTGCAGgtaaaacctt ... tctttgttagCGGCTGAAGCGATTTGGGCGTGTTCGATTGAAGAACTAGGGCTGGAGAATG
EST: gi|116478059|gb|EG520651.1|EG520651
EST:     TGAATCCGTTATGCTTCCTCCTCCTTGGCGGTTGATGCCAATAACTGCAG                         CGGCTGAAGCGATTTGGGCGTGTTCGATTGAAGAACTAGGGCTGGAGAATG
genomic: TGAATCCGTTATGCTTCCTCCTCCTTGGCGGTTGATGCCAATAACTGCAGgtaaaacctt ... tctttgttagCGGCTGAAGCGATTTGGGCGTGTTCGATTGAAGAACTAGGGCTGGAGAATG
EST: gi|125068262|gb|EL134468.1|EL134468
EST:     TGCCAATAACTGCAG                         CGGCTGAAGCGATTTGGGCGTGTTCGATTGAAGAACTAGGGCTGGAGAATG
genomic: TGCCAATAACTGCAGgtaaaacctt ... tctttgttagCGGCTGAAGCGATTTGGGCGTGTTCGATTGAAGAACTAGGGCTGGAGAATG
EST: gi|116478058|gb|EG520650.1|EG520650
EST:     TGAATCCGTTATGCTTCCTCCTCCTTGGCGGTTGATGCCAATAACTGCAG                         CGGCTGAAGCGATTTGGGCGTGTTCGATTGAAGAACTAGGGCTGGAGAATG
genomic: TGAATCCGTTATGCTTCCTCCTCCTTGGCGGTTGATGCCAATAACTGCAGgtaaaacctt ... tctttgttagCGGCTGAAGCGATTTGGGCGTGTTCGATTGAAGAACTAGGGCTGGAGAATG
EST: gi|116478073|gb|EG520665.1|EG520665
EST:     TGAATCCGTTATGCTTCCTCCTCCTTGGCGGTTGATGCCAATAACTGCAG                         CGGCTGAAGCGATTTGGGCGTGTTCGATTGAAGAACTAGGGCTGGAGAATG
genomic: TGAATCCGTTATGCTTCCTCCTCCTTGGCGGTTGATGCCAATAACTGCAGgtaaaacctt ... tctttgttagCGGCTGAAGCGATTTGGGCGTGTTCGATTGAAGAACTAGGGCTGGAGAATG
EST: gi|116456640|gb|EG499232.1|EG499232
EST:     TGAATCCGTTATGCTTCCTCCTCCTTGGCGGTTGATGCCAATAACTGCAG                         CGGCTGAAGCGATTTGGGCGTGTTCGATTGAAGAACTAGGGCTGGAGAATG
genomic: TGAATCCGTTATGCTTCCTCCTCCTTGGCGGTTGATGCCAATAACTGCAGgtaaaacctt ... tctttgttagCGGCTGAAGCGATTTGGGCGTGTTCGATTGAAGAACTAGGGCTGGAGAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatttcttcaggacataagcggtagtaaaagtttatggctttttctttgttagCGGCTGAAGCGATTTGGGCGTGTTCGATTGAAGAACTAGGGCTGGAGAATGAGGCCGAGAAACCGAGCAATGCGTTGTTAACTAGAGCTTGGTCTCCAGG
 ttttgat  putative branch site (score: 4)
                                        ctttttctttgtt  putative PPT
                        tagtaaaagtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaccttaaagagtattacttaaaagctaaaacgtttttgatttcttcaggacataagcggtagtaaaagtttatggctttttctttgttagCGGCTGAAGCGATTTGGGCGTGTTCGATTGAAGAACTAGGGCTGGAGAATGAGGCCGAGAAACCGAGCAATGCGTTGTTAACTAGAGCTTGGTCTCCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT