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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgactcttttgattatatctaaatggaattcttttgcttggtgtgctatgtatggaatatgtcaagttttttgttttgttttatcttttcttggccttctttgatcctttcttctccatcatatgaggattttacaattatgttctgtggcagGCACACTACATGCTAGGACTTGCATTATTGCAGAAGAAAGAATTTACTAATGGAGTCAAAGAATTGCAAAGG

Basic information

species Arabidopsis thaliana
transcript AT3G07370.1
intron # 3
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|86048653|gb|DR344408.1|DR344408
EST:     TTGAAGAGGATTGTCGCAAAGCTATTCAGCTTGTCCACAATTCCGTCAAG                         GCACACTACATGCTAGGACTTGCATTATTGCAGAAGAAAGAATTTACTAAT
genomic: TTGAAGAGGATTGTCGCAAAGCTATTCAGCTTGTCCACAATTCCGTCAAGgtttgactct ... tctgtggcagGCACACTACATGCTAGGACTTGCATTATTGCAGAAGAAAGAATTTACTAAT
EST: gi|86048650|gb|DR344405.1|DR344405
EST:     TTGAAGAGGATTGTCGCAAAGCTATTCAGCTTGTCCACAATTCCGTCAAG                         GCACACTACATGCTAGGACTTGCATTATTGCAGAAGAAAGAATTTACTAAT
genomic: TTGAAGAGGATTGTCGCAAAGCTATTCAGCTTGTCCACAATTCCGTCAAGgtttgactct ... tctgtggcagGCACACTACATGCTAGGACTTGCATTATTGCAGAAGAAAGAATTTACTAAT
EST: gi|86048663|gb|DR344418.1|DR344418
EST:     TTGAAGAGGATTGTCGCAAAGCTATTCAGCTTGTCCACAATTCCGTCAAG                         GCACACTACATGCTAGGACTTGCATTATTGCAGAAGAAAGAATTTACTAAT
genomic: TTGAAGAGGATTGTCGCAAAGCTATTCAGCTTGTCCACAATTCCGTCAAGgtttgactct ... tctgtggcagGCACACTACATGCTAGGACTTGCATTATTGCAGAAGAAAGAATTTACTAAT
EST: gi|86048652|gb|DR344407.1|DR344407
EST:     TTGAAGAGGATTGTCGCAAAGCTATTCAGCTTGTCCACAATTCCGTCAAG                         GCACACTACATGCTAGGACTTGCATTATTGCAGAAGAAAGAATTTACTAAT
genomic: TTGAAGAGGATTGTCGCAAAGCTATTCAGCTTGTCCACAATTCCGTCAAGgtttgactct ... tctgtggcagGCACACTACATGCTAGGACTTGCATTATTGCAGAAGAAAGAATTTACTAAT
EST: gi|86048662|gb|DR344417.1|DR344417
EST:     TTGAAGAGGATTGTCGCAAAGCTATTCAGCTTGTCCACAATTCCGTCAAG                         GCACACTACATGCTAGGACTTGCATTATTGCAGAAGAAAG
genomic: TTGAAGAGGATTGTCGCAAAGCTATTCAGCTTGTCCACAATTCCGTCAAGgtttgactct ... tctgtggcagGCACACTACATGCTAGGACTTGCATTATTGCAGAAGAAAG
EST: gi|86048659|gb|DR344414.1|DR344414
EST:     TTGAAGAGGATTGTCGCAAAGCTATTCAGCTTGTCCACAATTCCGTCAAG                         GCACACTACATGCTAGGACTTGCATTATTGCAGAAGAAAGAATTTACTAAT
genomic: TTGAAGAGGATTGTCGCAAAGCTATTCAGCTTGTCCACAATTCCGTCAAGgtttgactct ... tctgtggcagGCACACTACATGCTAGGACTTGCATTATTGCAGAAGAAAGAATTTACTAAT
EST: gi|86048665|gb|DR344420.1|DR344420
EST:     TTGAAGAGGATTGTCGCAAAGCTATTCAGCTTGTCCACAATTCCGTCAAG                         GCACACTACATGCTAGGAACTTGCATTATTGCAGAAGAAAGAATTTACTAA
genomic: TTGAAGAGGATTGTCGCAAAGCTATTCAGCTTGTCCACAATTCCGTCAAGgtttgactct ... tctgtggcagGCACACTACATGCTAGGA-CTTGCATTATTGCAGAAGAAAGAATTTACTAA
EST: gi|86048657|gb|DR344412.1|DR344412
EST:     TTGAAGAGGATTGTCGCAAAGCTATTCAGCTTGTCCACAATTCCGTCAAG                         GCACACTACATGCTAGGACTTGCATTATTGCAGAAGAAAGAATTTACTAAT
genomic: TTGAAGAGGATTGTCGCAAAGCTATTCAGCTTGTCCACAATTCCGTCAAGgtttgactct ... tctgtggcagGCACACTACATGCTAGGACTTGCATTATTGCAGAAGAAAGAATTTACTAAT
EST: gi|86048661|gb|DR344416.1|DR344416
EST:     TTGAAGAGGATTGTCGCAAAGCTATTCAGCTTGTCCACAATTCCGTCAAG                         GCACACTACATGCTAGGACTTGCATTATTGCAGAAGAAAGAATTTACTAAT
genomic: TTGAAGAGGATTGTCGCAAAGCTATTCAGCTTGTCCACAATTCCGTCAAGgtttgactct ... tctgtggcagGCACACTACATGCTAGGACTTGCATTATTGCAGAAGAAAGAATTTACTAAT
EST: gi|86048658|gb|DR344413.1|DR344413
EST:     TTGAAGAGGATTGTCGCAAAGCTATTCAGCTTGTCCACAATTCCGTCAAG                         GCACACTACATGCTAGGACTTGCATTATTGCAGAAGAAAGAATTTACTAAT
genomic: TTGAAGAGGATTGTCGCAAAGCTATTCAGCTTGTCCACAATTCCGTCAAGgtttgactct ... tctgtggcagGCACACTACATGCTAGGACTTGCATTATTGCAGAAGAAAGAATTTACTAAT
EST: gi|86048660|gb|DR344415.1|DR344415
EST:     TTGAAGAGGATTGTCGCAAAGCTATTCAGCTTGTCCACAATTCCGTCAAG                         GCACACTACATGCTAGGACTTGCATTATTGCAGAAGAAAGAATTTACTAAT
genomic: TTGAAGAGGATTGTCGCAAAGCTATTCAGCTTGTCCACAATTCCGTCAAGgtttgactct ... tctgtggcagGCACACTACATGCTAGGACTTGCATTATTGCAGAAGAAAGAATTTACTAAT
EST: gi|86048664|gb|DR344419.1|DR344419
EST:     TTGAAGAGGATTGTCGCAAAGCTATTCAGCTTGTCCACAATTCCGTCAAG                         GCACACTACATGCTAGGACTTGCATTATTGCAGAAGAAAGAATTTACTAAT
genomic: TTGAAGAGGATTGTCGCAAAGCTATTCAGCTTGTCCACAATTCCGTCAAGgtttgactct ... tctgtggcagGCACACTACATGCTAGGACTTGCATTATTGCAGAAGAAAGAATTTACTAAT
EST: gi|86048648|gb|DR344403.1|DR344403
EST:     TTGAAGAGRATTGTCGCAAAGCTATTCAGCTTGTCCACAATTCCGTCAAG                         GCACACTACATGCTAGGACTTGCATTATTGCAGA
genomic: TTGAAGAGGATTGTCGCAAAGCTATTCAGCTTGTCCACAATTCCGTCAAGgtttgactct ... tctgtggcagGCACACTACATGCTAGGACTTGCATTATTGCAGA
EST: gi|86048654|gb|DR344409.1|DR344409
EST:     TTGAAGAGGATTGTCGCAAAGCTATTCAGCTTGTCCACAATTCCGTCAAG                         GCACACTACATGCTAGGACTTGCATTATTGCAGAAGAAAGAATTTACTAAT
genomic: TTGAAGAGGATTGTCGCAAAGCTATTCAGCTTGTCCACAATTCCGTCAAGgtttgactct ... tctgtggcagGCACACTACATGCTAGGACTTGCATTATTGCAGAAGAAAGAATTTACTAAT
EST: gi|86048656|gb|DR344411.1|DR344411
EST:     TTGAAGAGGATTGTCGCAAAGCTATTCAGCTTGTCCACAATTCCGTCAAG                         GCACACTACATGCTAGGACTTGCATTATTGCAGAAGAAAGAATTTACTAAT
genomic: TTGAAGAGGATTGTCGCAAAGCTATTCAGCTTGTCCACAATTCCGTCAAGgtttgactct ... tctgtggcagGCACACTACATGCTAGGACTTGCATTATTGCAGAAGAAAGAATTTACTAAT
EST: gi|86048655|gb|DR344410.1|DR344410
EST:     TTGAAGAGGATTGTCGCAAAGCTATTCAGCTTGTCCACAATTCCGTCAAG                         GCACACTACATGCWAGGACTTGCATTATTGCAGAAG
genomic: TTGAAGAGGATTGTCGCAAAGCTATTCAGCTTGTCCACAATTCCGTCAAGgtttgactct ... tctgtggcagGCACACTACATGCTAGGACTTGCATTATTGCAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgatcctttcttctccatcatatgaggattttacaattatgttctgtggcagGCACACTACATGCTAGGACTTGCATTATTGCAGAAGAAAGAATTTACTAATGGAGTCAAAGAATTGCAAAGG
 ctttgat  putative branch site (score: 5)
                              attttacaattatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgactcttttgattatatctaaatggaattcttttgcttggtgtgctatgtatggaatatgtcaagttttttgttttgttttatcttttcttggccttctttgatcctttcttctccatcatatgaggattttacaattatgttctgtggcagGCACACTACATGCTAGGACTTGCATTATTGCAGAAGAAAGAATTTACTAATGGAGTCAAAGAATTGCAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG