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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttcttataatgtcatatggttctgtgggtacattctgatatgttagcatgttagtataggtatatgcgtagttcagagtttctagatatcttcccaagtctttatctttattgacttccagatttaggtcagattgttttacaagatcctaacttttctctttgtttcattgattgatcttcattacttgaagAATTGCATGTCATTGATGGAATCCCGCAGCTAATTTTCGCTCATACAAGCTACACAATCGAG

Basic information

species Arabidopsis thaliana
transcript AT5G56280.1
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|86054010|gb|DR349767.1|DR349767
EST:     TGCTATCAATCACACACAGAAGGATCTTCCAGTGACTATTTATGAAAGTG                         AATTGCATGTCATTGATGGAATCCCGCAGCTAATTTTCGCTCATACAAGCT
genomic: TGCTATCAATCACACACAGAAGGATCTTCCAGTGACTATTTATGAAAGTGgtatgcttct ... ttacttgaagAATTGCATGTCATTGATGGAATCCCGCAGCTAATTTTCGCTCATACAAGCT
EST: gi|86054007|gb|DR349764.1|DR349764
EST:     TGCTATCAATCACACACAGAAGGATCTTCCAGTGACTATTTATGAAAGTG                         AATTGCATGTCATTGATGGAATCCCGCAGCTAATTTTCGCTCATA
genomic: TGCTATCAATCACACACAGAAGGATCTTCCAGTGACTATTTATGAAAGTGgtatgcttct ... ttacttgaagAATTGCATGTCATTGATGGAATCCCGCAGCTAATTTTCGCTCATA
EST: gi|164069766|gb|ES023136.1|ES023136
EST:     TCACACACAGAAGGATCTTCCAGTGACTATTTATGAAAGTG                         AATTGCATGTCATTGATGGAATCCCGCAGCTAATTTTCGCTCATACAAGC
genomic: TCACACACAGAAGGATCTTCCAGTGACTATTTATGAAAGTGgtatgcttct ... ttacttgaagAATTGCATGTCATTGATGGAATCCCGCAGCTAATTTTCGCTCATACAAGC
EST: gi|19876192|gb|AU237023.1|AU237023
EST:     TGCTATCAATCACACACAGAAGGATCTTCCAGTGACTATTTATGAAAGTG                         AATTGCATGTCATTGATGGAATCCCGCAGCTAATTTTCGCTCATACAAGCT
genomic: TGCTATCAATCACACACAGAAGGATCTTCCAGTGACTATTTATGAAAGTGgtatgcttct ... ttacttgaagAATTGCATGTCATTGATGGAATCCCGCAGCTAATTTTCGCTCATACAAGCT
EST: gi|86054006|gb|DR349763.1|DR349763
EST:     TGCTATCAATCACACACAGAAGGATCTTCCAGTGACTATTTATGAAAGTG                         AATTGCATGTCATTGATGGAATCCCGCAGCTAATTTTCGCTCATACAAGCT
genomic: TGCTATCAATCACACACAGAAGGATCTTCCAGTGACTATTTATGAAAGTGgtatgcttct ... ttacttgaagAATTGCATGTCATTGATGGAATCCCGCAGCTAATTTTCGCTCATACAAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacaagatcctaacttttctctttgtttcattgattgatcttcattacttgaagAATTGCATGTCATTGATGGAATCCCGCAGCTAATTTTCGCTCATACAAGCTACACAATCGAG
                                       tcttcatt  CT-rich tract
           taactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcttcttataatgtcatatggttctgtgggtacattctgatatgttagcatgttagtataggtatatgcgtagttcagagtttctagatatcttcccaagtctttatctttattgacttccagatttaggtcagattgttttacaagatcctaacttttctctttgtttcattgattgatcttcattacttgaagAATTGCATGTCATTGATGGAATCCCGCAGCTAATTTTCGCTCATACAAGCTACACAATCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT