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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacatatctagtgttttctctagaactagcattaaaaattatgtgttccaacattcttattgtaatagtattagtattttcttttgtttgttatgttttcagAGAATAGCGATAGCATACTTAGTTGTTGCATTGTGCGAGATTTGGTTAAAGGGAAACCATAATGTTAGCTCAGAGTTATCTATGATCAAGAAATATAGAT

Basic information

species Arabidopsis thaliana
transcript AT5G47900.4
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|116435431|gb|EG478023.1|EG478023
EST:     TAACTTATGGAATAGATGTAGAAAAAATTAGACTCATGGGTATATTACAG                         AGAATAGCGATAGCATACTTAGTTGTTGCATTGTGCGAGATTTGGTTAAAG
genomic: TAACTTATGGAATAGATGTAGAAAAAATTAGACTCATGGGTATATTACAGgtatacatat ... atgttttcagAGAATAGCGATAGCATACTTAGTTGTTGCATTGTGCGAGATTTGGTTAAAG
EST: gi|116435430|gb|EG478022.1|EG478022
EST:     TAACTTATGGAATAGATGTAGAAAAAATTAGACTCATGGGTATATTACAG                         AGAATAGCGATAGCATACTTAGTTGTTGCATTGTGCGAGATTTGGTTAAAG
genomic: TAACTTATGGAATAGATGTAGAAAAAATTAGACTCATGGGTATATTACAGgtatacatat ... atgttttcagAGAATAGCGATAGCATACTTAGTTGTTGCATTGTGCGAGATTTGGTTAAAG
EST: gi|116435445|gb|EG478037.1|EG478037
EST:     TAACTTATGGAATAGATGTAGAAAAAATTAGACTCATGGGTATATTACAG                         AGAATAGCGATAGCATACTTAGTTGTTGCATTGTGCGAGATTTGGTTAAAG
genomic: TAACTTATGGAATAGATGTAGAAAAAATTAGACTCATGGGTATATTACAGgtatacatat ... atgttttcagAGAATAGCGATAGCATACTTAGTTGTTGCATTGTGCGAGATTTGGTTAAAG
EST: gi|116435426|gb|EG478018.1|EG478018
EST:     TAACTTATGGAATAGATGTAGAAAAAATTAGACTCATGGGTATATTACAG                         AGAATAGCGATAGCATACTTAGTTGTTGCATTGTGCGAGATTTGGTTAAAG
genomic: TAACTTATGGAATAGATGTAGAAAAAATTAGACTCATGGGTATATTACAGgtatacatat ... atgttttcagAGAATAGCGATAGCATACTTAGTTGTTGCATTGTGCGAGATTTGGTTAAAG
EST: gi|116435425|gb|EG478017.1|EG478017
EST:     TAACTTATGGAATAGATGTAGAAAAAATTAGACTCATGGGTATATTACAG                         AGAATAGCGATAGCATACTTAGTTGTTGCATTGTGCGAGATTTGGTTAAAG
genomic: TAACTTATGGAATAGATGTAGAAAAAATTAGACTCATGGGTATATTACAGgtatacatat ... atgttttcagAGAATAGCGATAGCATACTTAGTTGTTGCATTGTGCGAGATTTGGTTAAAG
EST: gi|86073277|gb|DR369034.1|DR369034
EST:     TAACTTATGGAATAGATGTAGAAAAAATTAGACTCATGGGTATATTACAG                         AGAATAGCGATAGCATACTTAGTTGTTGCATTGTGCGAGATTTGGTTAAAG
genomic: TAACTTATGGAATAGATGTAGAAAAAATTAGACTCATGGGTATATTACAGgtatacatat ... atgttttcagAGAATAGCGATAGCATACTTAGTTGTTGCATTGTGCGAGATTTGGTTAAAG
EST: gi|116435420|gb|EG478012.1|EG478012
EST:     TAACTTATGGAATAGATGTNNNNNNNNTTAGACTCATGGGTATATTACAG                         AGAATAGCGATAGCATACTTAGTTGTTGCATTGTGCGAGATTTGGTTAAAG
genomic: TAACTTATGGAATAGATGTAGAAAAAATTAGACTCATGGGTATATTACAGgtatacatat ... atgttttcagAGAATAGCGATAGCATACTTAGTTGTTGCATTGTGCGAGATTTGGTTAAAG
EST: gi|116435443|gb|EG478035.1|EG478035
EST:     TAACTTATGGAATAGATGTAGAAAAAATTAGACTCATGGGTATATTACAG                         AGAATAGCGATAGCATACTTAGTTGTTGCATTGTGCGAGATTTGGTTAAAG
genomic: TAACTTATGGAATAGATGTAGAAAAAATTAGACTCATGGGTATATTACAGgtatacatat ... atgttttcagAGAATAGCGATAGCATACTTAGTTGTTGCATTGTGCGAGATTTGGTTAAAG
EST: gi|116435429|gb|EG478021.1|EG478021
EST:     TAACTTATGGAATAGATGTAGAAAAAATTAGACTCATGGGTATATTACAG                         AGAATAGCGATAGCATACTTAGTTGTTGCATTGTGCGAGATTTGGTTAAAG
genomic: TAACTTATGGAATAGATGTAGAAAAAATTAGACTCATGGGTATATTACAGgtatacatat ... atgttttcagAGAATAGCGATAGCATACTTAGTTGTTGCATTGTGCGAGATTTGGTTAAAG
EST: gi|116435479|gb|EG478071.1|EG478071
EST:     TAACTTATGGAATAGATGTAGAAAAAATTAGACTCATGGGTATATTACAG                         AGAATAGCGATAGCATACTTAGTTGTTGCATTGTGCGAGATTTGGTTAAAG
genomic: TAACTTATGGAATAGATGTAGAAAAAATTAGACTCATGGGTATATTACAGgtatacatat ... atgttttcagAGAATAGCGATAGCATACTTAGTTGTTGCATTGTGCGAGATTTGGTTAAAG
EST: gi|116464698|gb|EG507290.1|EG507290
EST:     TAACTTATGGAATAGATGTNNNNNNNNTTAGACTCATGGGTATATTACAG                         AGAATAGCGATAGCATACTTAGTTGTTGCATTGTGCGAGATTTGGTTAAAG
genomic: TAACTTATGGAATAGATGTAGAAAAAATTAGACTCATGGGTATATTACAGgtatacatat ... atgttttcagAGAATAGCGATAGCATACTTAGTTGTTGCATTGTGCGAGATTTGGTTAAAG
EST: gi|116435436|gb|EG478028.1|EG478028
EST:     TAACTTATGGAATAGATGTAGAAAAAATTAGACTCGTGGGTATATTACAG                         AGAATAGCGATAGCATACTTAGTTGTTGCATTGTGCGAGATTTGGTTAAAG
genomic: TAACTTATGGAATAGATGTAGAAAAAATTAGACTCATGGGTATATTACAGgtatacatat ... atgttttcagAGAATAGCGATAGCATACTTAGTTGTTGCATTGTGCGAGATTTGGTTAAAG
EST: gi|116435440|gb|EG478032.1|EG478032
EST:     TAACTTATGGAATAGATGTNNNNNNNNTTAGACTCATGGGTATATTACAG                         AGAATAGCGATAGCATACTTAGTTGTTGCATTGTGCGAGATTTGGTTAAAG
genomic: TAACTTATGGAATAGATGTAGAAAAAATTAGACTCATGGGTATATTACAGgtatacatat ... atgttttcagAGAATAGCGATAGCATACTTAGTTGTTGCATTGTGCGAGATTTGGTTAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaacattcttattgtaatagtattagtattttcttttgtttgttatgttttcagAGAATAGCGATAGCATACTTAGTTGTTGCATTGTGCGAGATTTGGTTAAAGGGAAACCATAATGTTAGCTCAGAGTTATCTATGATCAAGAAATATAGAT
                                              tgttttc  CT-rich tract
         ttattgtaatagtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatacatatctagtgttttctctagaactagcattaaaaattatgtgttccaacattcttattgtaatagtattagtattttcttttgtttgttatgttttcagAGAATAGCGATAGCATACTTAGTTGTTGCATTGTGCGAGATTTGGTTAAAGGGAAACCATAATGTTAGCTCAGAGTTATCTATGATCAAGAAATATAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA