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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttcgctacatgaactatttaaaggctcattctctctagtaactgattacaaattgatcatctagagtcgtgccttccccttatgaacttgggaatcctttaatttatgttaattgttttctcccccctaattgcagCTTTTGGAAGAGGAAGAAGTTGAAGTTCCGGTCACAAAAGAACATTCAGAGGAAACTACTAAGATGGACTCTGACAAAGCTTCTGCTGAGGCAGCTCCTG

Basic information

species Arabidopsis thaliana
transcript AT1G79930.1
intron # 4
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|86087898|gb|DR383657.1|DR383657
EST:     TGAAAGTGAGATTGAACCTTCATGGAATCGTCTCAGTTGAATCTGCAACT                         CTTTTGGAAGAGGAAGAAGTTGAAGTTCCGGTCACAAAAGAACATTCAGAG
genomic: TGAAAGTGAGATTGAACCTTCATGGAATCGTCTCAGTTGAATCTGCAACTgtaagtttcg ... ctaattgcagCTTTTGGAAGAGGAAGAAGTTGAAGTTCCGGTCACAAAAGAACATTCAGAG
EST: gi|86087379|gb|DR383138.1|DR383138
EST:     TGAAAGTGAGATTGAACCTTCATGGAATCGTCTCAGTTGAATCTGCAACT                         CTTTTGGAAGAGGAAGAAGTTGAAGTTCCGGTCACAAAAGAACATTCAGAG
genomic: TGAAAGTGAGATTGAACCTTCATGGAATCGTCTCAGTTGAATCTGCAACTgtaagtttcg ... ctaattgcagCTTTTGGAAGAGGAAGAAGTTGAAGTTCCGGTCACAAAAGAACATTCAGAG
EST: gi|47829158|gb|CK118842.1|CK118842
EST:     TGAAAGTGAGATTGAACCTTCATGGAATCGTCTCAGTTGAATCTGCAACT                         CTTTTGGAAGAGGAAGA-GTTGAAGTTCCG
genomic: TGAAAGTGAGATTGAACCTTCATGGAATCGTCTCAGTTGAATCTGCAACTgtaagtttcg ... ctaattgcagCTTTTGGAAGAGGAAGAAGTTGAAGTTCCG
EST: gi|86087897|gb|DR383656.1|DR383656
EST:     TGAAAGTGAGATTGAACCTTCATGGAATCGTCTCAGTTGAATCTGCAACT                         CTTTTGGAAGAGGAAGAAGTTGAAGTTCCGGTCACAAAAGAACATTCAGAG
genomic: TGAAAGTGAGATTGAACCTTCATGGAATCGTCTCAGTTGAATCTGCAACTgtaagtttcg ... ctaattgcagCTTTTGGAAGAGGAAGAAGTTGAAGTTCCGGTCACAAAAGAACATTCAGAG
EST: gi|86087380|gb|DR383139.1|DR383139
EST:     TGAAAGTGAGATTGAACCTTCATGGAATCGTCTCAGTTGAATCTGCAACT                         CTTTTGGAAGAGGAAGAAGTTGAAGTTCCGGTCACAAAAGAACATTCAGAG
genomic: TGAAAGTGAGATTGAACCTTCATGGAATCGTCTCAGTTGAATCTGCAACTgtaagtttcg ... ctaattgcagCTTTTGGAAGAGGAAGAAGTTGAAGTTCCGGTCACAAAAGAACATTCAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaacttgggaatcctttaatttatgttaattgttttctcccccctaattgcagCTTTTGGAAGAGGAAGAAGTTGAAGTTCCGGTCACAAAAGAACATTCAGAGGAAACTACTAAGATGGACTCTGACAAAGCTTCTGCTGAGGCAGCTCCTG
                                           ccctaat  putative branch site (score: 3)
                               ttgttttctcccccct  CT-rich tract
           aatcctttaatttatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttcgctacatgaactatttaaaggctcattctctctagtaactgattacaaattgatcatctagagtcgtgccttccccttatgaacttgggaatcctttaatttatgttaattgttttctcccccctaattgcagCTTTTGGAAGAGGAAGAAGTTGAAGTTCCGGTCACAAAAGAACATTCAGAGGAAACTACTAAGATGGACTCTGACAAAGCTTCTGCTGAGGCAGCTCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC