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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacttggcattgttttttctttcttttgatttcatcttgtgttcatcgaaattgatgttcattgcgtttacagtacattaactggtttttgtgattgaagGAGATGTTCATTGAGCGGTTTTCTGAAGAAGCTTATGATAGTTCCGTCAAGGACAAAAAGAAATTCATCCACTACAAACACCTCT

Basic information

species Arabidopsis thaliana
transcript AT1G07980.1
intron # 1
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|86078563|gb|DR374320.1|DR374320
EST:     CTGCTCCTCAGATTATGCAGGATGCTGTATTTCTTGTCAACAAAGCCACG                         GAGATGTTCATTGAGCGGTTTTCTGAAGAAGCTTATGATAGTTCCGTCAAG
genomic: CTGCTCCTCAGATTATGCAGGATGCTGTATTTCTTGTCAACAAAGCCACGgtatagtact ... gtgattgaagGAGATGTTCATTGAGCGGTTTTCTGAAGAAGCTTATGATAGTTCCGTCAAG
EST: gi|86019064|gb|DR314810.1|DR314810
EST:     CTGCTCCTCAGATTATGCAGGATGCTGTATTTCTTGTCAACAAAGCCACG                         GAGATGTTCATTGAGCGGTTTTCTGAAGAAGCTTATGATAGTTCCGTCAA
genomic: CTGCTCCTCAGATTATGCAGGATGCTGTATTTCTTGTCAACAAAGCCACGgtatagtact ... gtgattgaagGAGATGTTCATTGAGCGGTTTTCTGAAGAAGCTTATGATAGTTCCGTCAA
EST: gi|19876673|gb|AU237504.1|AU237504
EST:     CTGCTCCTCAGATTATGCAGGATGCTGTATTTCTTGTCAACAAAGCCACG                         GAGATGTTCATTGAGCGGTTTTCTGAAGAAGCTTATGATAGTTCCGTCAAG
genomic: CTGCTCCTCAGATTATGCAGGATGCTGTATTTCTTGTCAACAAAGCCACGgtatagtact ... gtgattgaagGAGATGTTCATTGAGCGGTTTTCTGAAGAAGCTTATGATAGTTCCGTCAAG
EST: gi|86019063|gb|DR314809.1|DR314809
EST:     TGCTCCTCAGATTATGCAGGATGCTGTNATTTCTTGTCAACAAAGCCACG                         GAGATGTTCATTGAGCGGTTTTCTGAAGAAGCT
genomic: TGCTCCTCAGATTATGCAGGATGCTGT-ATTTCTTGTCAACAAAGCCACGgtatagtact ... gtgattgaagGAGATGTTCATTGAGCGGTTTTCTGAAGAAGCT
EST: gi|86019065|gb|DR314811.1|DR314811
EST:     CTGCTCCTCAGATTATGCAGGATGCTGTATTTCTTGTCAACAAAGCCACG                         GAGATGTTCATTGAGCGG
genomic: CTGCTCCTCAGATTATGCAGGATGCTGTATTTCTTGTCAACAAAGCCACGgtatagtact ... gtgattgaagGAGATGTTCATTGAGCGG
EST: gi|86019070|gb|DR314816.1|DR314816
EST:     CTGCTCCTCAGATTATGCAGGATGCTGTATTTCTTGTCAACAAAGCCACG                         GAGATGTTCATTGAGCGGTTTTCTGAAGAAGCTTATGATAGTTC
genomic: CTGCTCCTCAGATTATGCAGGATGCTGTATTTCTTGTCAACAAAGCCACGgtatagtact ... gtgattgaagGAGATGTTCATTGAGCGGTTTTCTGAAGAAGCTTATGATAGTTC
EST: gi|86019067|gb|DR314813.1|DR314813
EST:     CTGCTCCTCAGATTATGCAGGATGCTGTATTTCTTGTCAACAAAGCCACG                         GAGATGTTCAT
genomic: CTGCTCCTCAGATTATGCAGGATGCTGTATTTCTTGTCAACAAAGCCACGgtatagtact ... gtgattgaagGAGATGTTCAT
EST: gi|86019066|gb|DR314812.1|DR314812
EST:     CTGCTCCTCAGATTATGCAGGATGCTGTATTTCTTGTCAACAAAGCCACG                         GAGATGTTCATTGAGCGGTTTTCTGAAGAAGCTTATGATAGTTCCGTCAA
genomic: CTGCTCCTCAGATTATGCAGGATGCTGTATTTCTTGTCAACAAAGCCACGgtatagtact ... gtgattgaagGAGATGTTCATTGAGCGGTTTTCTGAAGAAGCTTATGATAGTTCCGTCAA
EST: gi|86019072|gb|DR314818.1|DR314818
EST:     CTGCTCCTCAGATTATGCAGGATGCTGTATTTCTTGTCAACAAAGCCACG                         GAGATGTTCATTGAGCGGTTTTCTGAAGAAGCTTATGATAGTT
genomic: CTGCTCCTCAGATTATGCAGGATGCTGTATTTCTTGTCAACAAAGCCACGgtatagtact ... gtgattgaagGAGATGTTCATTGAGCGGTTTTCTGAAGAAGCTTATGATAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgaaattgatgttcattgcgtttacagtacattaactggtttttgtgattgaagGAGATGTTCATTGAGCGGTTTTCTGAAGAAGCTTATGATAGTTCCGTCAAGGACAAAAAGAAATTCATCCACTACAAACACCTCT
                              cattaac  putative branch site (score: 2)
                                        tttttgt  putative PPT
                            tacattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacttggcattgttttttctttcttttgatttcatcttgtgttcatcgaaattgatgttcattgcgtttacagtacattaactggtttttgtgattgaagGAGATGTTCATTGAGCGGTTTTCTGAAGAAGCTTATGATAGTTCCGTCAAGGACAAAAAGAAATTCATCCACTACAAACACCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - cgaaatt