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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttaaagctccttctgttaccttaccaccactttcatcggtaagaaatatgattttaatgttctgtatttatgaattatataatgtttctttaatcatagGTTGATCCCAATACCGGAGTGTCCATGTATGAATCAGATGGAATCATCAAATATCTATCCGAGAAATATG

Basic information

species Arabidopsis thaliana
transcript AT5G03880.1
intron # 5
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|116475228|gb|EG517820.1|EG517820
EST:     TCCGCCCGAAGGTTAAACAGATGGGCGGGAAACAACAGTTTCCGTACATG                         GTTGATCCCAATACCGGAGTGTCCATGTATGAATCAGATGGAATCATCAAA
genomic: TCCGCCCGAAGGTTAAACAGATGGGCGGGAAACAACAGTTTCCGTACATGgtttggcatt ... ttaatcatagGTTGATCCCAATACCGGAGTGTCCATGTATGAATCAGATGGAATCATCAAA
EST: gi|116475229|gb|EG517821.1|EG517821
EST:     TCCGCCCGAAGGTTAAACAGATGGGCGGGAAACAACAGTTTCCGTACATG                         GTTGATCCCAATACCGGAGTGTCCATGTATGAATCAGATGGAATCATCAAA
genomic: TCCGCCCGAAGGTTAAACAGATGGGCGGGAAACAACAGTTTCCGTACATGgtttggcatt ... ttaatcatagGTTGATCCCAATACCGGAGTGTCCATGTATGAATCAGATGGAATCATCAAA
EST: gi|124934765|gb|EL011809.1|EL011809
EST:     TCCGCCCGAAGGTTAAACAGATGGGCGGGAAACAACAGTTTCCGTACATG                         GTTGATCCCAATACCGGAGTGTCCATGTA
genomic: TCCGCCCGAAGGTTAAACAGATGGGCGGGAAACAACAGTTTCCGTACATGgtttggcatt ... ttaatcatagGTTGATCCCAATACCGGAGTGTCCATGTA
EST: gi|164122647|gb|ES041966.1|ES041966
EST:     TCCGCCCGAAGGTTAAACAGATGGGCGGGAAACAACAGTTTCCGTACATG                         GTTGATCCCAATACCGG
genomic: TCCGCCCGAAGGTTAAACAGATGGGCGGGAAACAACAGTTTCCGTACATGgtttggcatt ... ttaatcatagGTTGATCCCAATACCGG
EST: gi|86080278|gb|DR376035.1|DR376035
EST:     GCCCGAAGGTTAAAACAAGATGGSCGGGAAACNAACAGTTTCCGTACATG                         G-TGATCCCAATACCGGAGTGTCCATGTATGAATCAGATGGAATCATCAAA
genomic: GCCCGAAGGTT-AAAC-AGATGGGCGGGAAAC-AACAGTTTCCGTACATGgtttggcatt ... ttaatcatagGTTGATCCCAATACCGGAGTGTCCATGTATGAATCAGATGGAATCATCAAA
EST: gi|125280992|gb|EL295077.1|EL295077
EST:     TCCGCCCGAAGGTTAAACAGATGGGCGGGAAACAACAGTTTCCGTACATG                         GTTGATCCCAATACCGGAGTGTCCATGTATGAAT
genomic: TCCGCCCGAAGGTTAAACAGATGGGCGGGAAACAACAGTTTCCGTACATGgtttggcatt ... ttaatcatagGTTGATCCCAATACCGGAGTGTCCATGTATGAAT
EST: gi|116483992|gb|EG526584.1|EG526584
EST:     TCCGCCCGAAGGTTAAACAGATGGGCGGGAAACAACAGTTTCCGTACATG                         GTTGATCCCAATACCGGAGTGTCCATGTATGAATCAGATGGAATCATCAAA
genomic: TCCGCCCGAAGGTTAAACAGATGGGCGGGAAACAACAGTTTCCGTACATGgtttggcatt ... ttaatcatagGTTGATCCCAATACCGGAGTGTCCATGTATGAATCAGATGGAATCATCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatatgattttaatgttctgtatttatgaattatataatgtttctttaatcatagGTTGATCCCAATACCGGAGTGTCCATGTATGAATCAGATGGAATCATCAAATATCTATCCGAGAAATATG
                                      tgtttcttt  CT-rich tract
      attttaatgttctgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaaagctccttctgttaccttaccaccactttcatcggtaagaaatatgattttaatgttctgtatttatgaattatataatgtttctttaatcatagGTTGATCCCAATACCGGAGTGTCCATGTATGAATCAGATGGAATCATCAAATATCTATCCGAGAAATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
-ttaaagc
- - - - - - -ctgttac
- - - - - - - - - - - - -caccact
- - - - - - - - - - - - - - - - - - - - taagaaa