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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaagtctcaacctttatggatgaatcaacctggtatccatttcttgagcttctctaaagaaccatctttttcatgaaattcttgaacctcaacattttgccctcaatgatgttatctttatggatatgtgagtgtgtctgattaataaaaactgataactcggggacattgttcttgtagGATCCAAAAGAAGGGCACTGGTGGATGCAGTTTGGAGACGGGTATGTGTTGGGATACTGGCCAAGCTTTCTATTCTCTTACTTAGCAGATAGTGCATCAA

Basic information

species Arabidopsis thaliana
transcript AT5G56530.2
intron # 7
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|163993793|gb|ES095791.1|ES095791
EST:     TCCATAACCCGCAATACGATATAAGTATTACCATTTGGAAG                         GATCCAAAAGAAGGGCACTGGTGGATGCAGTTTGGAGACGGGTATGTGTTG
genomic: TCCATAACCCGCAATACGATATAAGTATTACCATTTGGAAGgtaaaaagtc ... gttcttgtagGATCCAAAAGAAGGGCACTGGTGGATGCAGTTTGGAGACGGGTATGTGTTG
EST: gi|116442545|gb|EG485137.1|EG485137
EST:     TATCTGGCTTCCATAACCCGCAATACGATATAAGTATTACCATTTGGAAG                         GATCCAAAAGAAGGGCACTGGTGGATGCAGTTTGGAGACGGGTATGTGTTG
genomic: TATCTGGCTTCCATAACCCGCAATACGATATAAGTATTACCATTTGGAAGgtaaaaagtc ... gttcttgtagGATCCAAAAGAAGGGCACTGGTGGATGCAGTTTGGAGACGGGTATGTGTTG
EST: gi|116431119|gb|EG473711.1|EG473711
EST:     TATCTGGCTTCCATAACCCGCAATACGATATAAGTATTACCATTTGGAAG                         GATCCAAAAGAAGGGCACTGGTGGATGCAGTTTGGAGACGGGTATGTGTTG
genomic: TATCTGGCTTCCATAACCCGCAATACGATATAAGTATTACCATTTGGAAGgtaaaaagtc ... gttcttgtagGATCCAAAAGAAGGGCACTGGTGGATGCAGTTTGGAGACGGGTATGTGTTG
EST: gi|164022472|gb|ES017985.1|ES017985
EST:     TATCTGGCTTCCATAACCCGCAATACGATATAAGTATTACCATTTGGAAG                         GATCCAAAAGAAGGGCAC
genomic: TATCTGGCTTCCATAACCCGCAATACGATATAAGTATTACCATTTGGAAGgtaaaaagtc ... gttcttgtagGATCCAAAAGAAGGGCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtgagtgtgtctgattaataaaaactgataactcggggacattgttcttgtagGATCCAAAAGAAGGGCACTGGTGGATGCAGTTTGGAGACGGGTATGTGTTGGGATACTGGCCAAGCTTTCTATTCTCTTACTTAGCAGATAGTGCATCAA
                           tgataac  putative branch site (score: 2)
                                           ttgttctt  putative PPT
               attaataaaaactgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaagtctcaacctttatggatgaatcaacctggtatccatttcttgagcttctctaaagaaccatctttttcatgaaattcttgaacctcaacattttgccctcaatgatgttatctttatggatatgtgagtgtgtctgattaataaaaactgataactcggggacattgttcttgtagGATCCAAAAGAAGGGCACTGGTGGATGCAGTTTGGAGACGGGTATGTGTTGGGATACTGGCCAAGCTTTCTATTCTCTTACTTAGCAGATAGTGCATCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT