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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtcgatatgaatcaactattactattcatagcgtcctggaccttttattgagctttaatcctttattgcttgtttccattcttcagGCGAGGCGCTTCTGAGCTTCAGAAATGCAGTTACTAGATCAGATAGTTTCATCCATCAGTGGAGACCGGAAGATCCAGATCCATGTAACTGGAACGGAGT

Basic information

species Arabidopsis thaliana
transcript AT1G31420.2
intron # 2
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|116452754|gb|EG495346.1|EG495346
EST:     CTCGTTGCTTTGCTCACTATCTAATGAAAGTCAAGCGATTAGTCCTGACG                         GCGAGGCGCTTCTGAGCTTCAGAAATGCAGTTACTAGATCAGATAGTTTCA
genomic: CTCGTTGCTTTGCTCACTATCTAATGAAAGTCAAGCGATTAGTCCTGACGgtacgtcgat ... cattcttcagGCGAGGCGCTTCTGAGCTTCAGAAATGCAGTTACTAGATCAGATAGTTTCA
EST: gi|125223249|gb|EL237334.1|EL237334
EST:     AGTCAAGCGATTAGTCCTGACG                         GCGAGGCGCTTCTGAGCTTCAGAAATGCAGTTA
genomic: AGTCAAGCGATTAGTCCTGACGgtacgtcgat ... cattcttcagGCGAGGCGCTTCTGAGCTTCAGAAATGCAGTTA
EST: gi|125231644|gb|EL245729.1|EL245729
EST:     CTCGTTGCTTTGCTCACTATCTAATGAAAGTCAAGCGATTAGTCCTGACG                         GCGAGGCGCTTCT
genomic: CTCGTTGCTTTGCTCACTATCTAATGAAAGTCAAGCGATTAGTCCTGACGgtacgtcgat ... cattcttcagGCGAGGCGCTTCT
EST: gi|116419338|gb|EG461930.1|EG461930
EST:     CTCGTTGCTTTGCTCACTATCTAATGAAAGTCAAGCGATTAGTCCTGACG                         GCGAGGCGCTTCTGAGCTTCAGAAATGCAGTTACTAGATCAGATAGTTTCA
genomic: CTCGTTGCTTTGCTCACTATCTAATGAAAGTCAAGCGATTAGTCCTGACGgtacgtcgat ... cattcttcagGCGAGGCGCTTCTGAGCTTCAGAAATGCAGTTACTAGATCAGATAGTTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtcctggaccttttattgagctttaatcctttattgcttgtttccattcttcagGCGAGGCGCTTCTGAGCTTCAGAAATGCAGTTACTAGATCAGATAGTTTCATCCATCAGTGGAGACCGGAAGATCCAGATCCATGTAACTGGAACGGAGT
                     ctttaat  putative branch site (score: 4)
                                     cttgtttccattcttc  putative PPT
                      tttaatcctttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtcgatatgaatcaactattactattcatagcgtcctggaccttttattgagctttaatcctttattgcttgtttccattcttcagGCGAGGCGCTTCTGAGCTTCAGAAATGCAGTTACTAGATCAGATAGTTTCATCCATCAGTGGAGACCGGAAGATCCAGATCCATGTAACTGGAACGGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA