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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacgtaactttgttgttggtgtctttgtaggagaatgttgtttgatgttaaggagataatggtcttttgattttgtatgcagAATGAATTGTTTTCCACCATTCCTGCAAAGCAGAGAAGACCAGAAGCAACGCAAGCTTACATCACAAGAAACAAATACCAACTTCACGAAGCATTCAATG

Basic information

species Arabidopsis thaliana
transcript AT1G72970.2
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|164222937|gb|ES147398.1|ES147398
EST:     TTCATACTCACTATGGGATTATGTCGAACAAG                         AATGAATTGTTTTCCACCATTCCTGCAAAGCAGAGAAGACCAGAAGCAACG
genomic: TTCATACTCACTATGGGATTATGTCGAACAAGgtaacgtaac ... ttgtatgcagAATGAATTGTTTTCCACCATTCCTGCAAAGCAGAGAAGACCAGAAGCAACG
EST: gi|124961541|gb|EL036060.1|EL036060
EST:     TATTCATACTCACTATGGGATTATG-CGAACAAG                         AATGAATTGTTTTCCACCATTCCTGCAAAGCAGAGAAGACCAGA
genomic: TATTCATACTCACTATGGGATTATGTCGAACAAGgtaacgtaac ... ttgtatgcagAATGAATTGTTTTCCACCATTCCTGCAAAGCAGAGAAGACCAGA
EST: gi|164041248|gb|ES096104.1|ES096104
EST:     GCAATCTCCTGAGAGTATTCATACTCACTATGGGGATTATGTCGAACAAG                         AATGAATTGTTTTC
genomic: GCAATCTCCTGAGAGTATTCATACTCACTATGGG-ATTATGTCGAACAAGgtaacgtaac ... ttgtatgcagAATGAATTGTTTTC
EST: gi|164101017|gb|EL984251.1|EL984251
EST:     GGCAATCTCCTGAGAGTATTCATACTCACTATGGGATTATGTCGAACAAG                         AATGAATTGTTTTCCACCATTCCTGCAAAGCAGAGAAG
genomic: GGCAATCTCCTGAGAGTATTCATACTCACTATGGGATTATGTCGAACAAGgtaacgtaac ... ttgtatgcagAATGAATTGTTTTCCACCATTCCTGCAAAGCAGAGAAG
EST: gi|124756363|gb|EH846493.1|EH846493
EST:     ATCTCCTGAGAGTATTCATACTCACTATGGGATTATGTCGAACAAG                         AATGAATTGTTTTCCACCATTCCTGCAAAGCAGAGAAGA
genomic: ATCTCCTGAGAGTATTCATACTCACTATGGGATTATGTCGAACAAGgtaacgtaac ... ttgtatgcagAATGAATTGTTTTCCACCATTCCTGCAAAGCAGAGAAGA
EST: gi|164231453|gb|ES172334.1|ES172334
EST:     GAGTATTCATACTCACTATGGGATTATGTCGAACAAG                         AATGAATTGTTTTCCACCATTCCTGCAAAGCAGAGAAGACCAGAAGCAACG
genomic: GAGTATTCATACTCACTATGGGATTATGTCGAACAAGgtaacgtaac ... ttgtatgcagAATGAATTGTTTTCCACCATTCCTGCAAAGCAGAGAAGACCAGAAGCAACG
EST: gi|164129510|gb|ES030299.1|ES030299
EST:     GGCAATCTCCTGAGAGTATTCATACTCACTATGGGATTATGTCGAACAAG                         AATGAATTGTTTTC
genomic: GGCAATCTCCTGAGAGTATTCATACTCACTATGGGATTATGTCGAACAAGgtaacgtaac ... ttgtatgcagAATGAATTGTTTTC
EST: gi|125011251|gb|EL083520.1|EL083520
EST:     GGCAATCTCCTGAGAGTATTCATACTCACTATGGGATTATGTCGAACAAG                         AATGAATTGTTTTCCACCATTCCTGCAAAGCAGAGAAGAC
genomic: GGCAATCTCCTGAGAGTATTCATACTCACTATGGGATTATGTCGAACAAGgtaacgtaac ... ttgtatgcagAATGAATTGTTTTCCACCATTCCTGCAAAGCAGAGAAGAC
EST: gi|164064634|gb|ES092582.1|ES092582
EST:     CTATGGGATTATGTCGAACAAG                         AATGAATTGTTTTCCACCATTCCTGCAAAGCAGAGAAGACCAGAAGCAACG
genomic: CTATGGGATTATGTCGAACAAGgtaacgtaac ... ttgtatgcagAATGAATTGTTTTCCACCATTCCTGCAAAGCAGAGAAGACCAGAAGCAACG
EST: gi|86024736|gb|DR320489.1|DR320489
EST:     GGCAATCTCCTGAGAGTATTCATACTCACTATGGGATTATGTCGAACAAG                         AATGAATTGTTTTCCACCATTCCTGCAAAGCAGAGAAGACCAGAAGCAACG
genomic: GGCAATCTCCTGAGAGTATTCATACTCACTATGGGATTATGTCGAACAAGgtaacgtaac ... ttgtatgcagAATGAATTGTTTTCCACCATTCCTGCAAAGCAGAGAAGACCAGAAGCAACG
EST: gi|164221734|gb|ES048526.1|ES048526
EST:     TCATACTCACTATGGGATTATGTCGAACAAG                         AATGAATTGTTTTCCACCATTCCTGCAAAGCAGAGAAGACCAGAAGCAACG
genomic: TCATACTCACTATGGGATTATGTCGAACAAGgtaacgtaac ... ttgtatgcagAATGAATTGTTTTCCACCATTCCTGCAAAGCAGAGAAGACCAGAAGCAACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taggagaatgttgtttgatgttaaggagataatggtcttttgattttgtatgcagAATGAATTGTTTTCCACCATTCCTGCAAAGCAGAGAAGACCAGAAGCAACGCAAGCTTACATCACAAGAAACAAATACCAACTTCACGAAGCATTCAATG
                                     ttttgat  putative branch site (score: 4)
                                     ttttgattttgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacgtaactttgttgttggtgtctttgtaggagaatgttgtttgatgttaaggagataatggtcttttgattttgtatgcagAATGAATTGTTTTCCACCATTCCTGCAAAGCAGAGAAGACCAGAAGCAACGCAAGCTTACATCACAAGAAACAAATACCAACTTCACGAAGCATTCAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA