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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttcttgcttctgttaacattttgttcctagattagatttatcttcctcaaatatctccttgaaggcacttggagttgcaaatgctttttttttttatgtaaaggattttctctaactcatatcattttttttcggttgcagGCCCTAACCACATGATGTTGGAG

Basic information

species Arabidopsis thaliana
transcript AT1G54100.2
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|116420807|gb|EG463399.1|EG463399
EST:     GCTGTTGGTTTGAGCCGACAACTCAATGGATCGGTTATACCTTCAGAAC                         GCCCTAACCACATGATGTTGGAG
genomic: GCTGTTGGTTTGAGCCGACAACTCAATGGATCGGTTATACCTTCAGAACgtgagttctt ... tcggttgcagGCCCTAACCACATGATGTTGGAG
EST: gi|116486592|gb|EG529184.1|EG529184
EST:     TGCTGTTGGTTTGAGCCGACAACTCAATGGATCGGTTATACCTTCAGAAC                         GCCCTAACCACATGATGTTGGAG
genomic: TGCTGTTGGTTTGAGCCGACAACTCAATGGATCGGTTATACCTTCAGAACgtgagttctt ... tcggttgcagGCCCTAACCACATGATGTTGGAG
EST: gi|301501447|gb|HO206987.1|HO206987
EST:     TGCTGTTGGTTTGAGCCGACAACTCAATGGATCGGTTATACCTTCAGAAC                         GCCCTAACCACATGATGTTGGAG
genomic: TGCTGTTGGTTTGAGCCGACAACTCAATGGATCGGTTATACCTTCAGAACgtgagttctt ... tcggttgcagGCCCTAACCACATGATGTTGGAG
EST: gi|116486594|gb|EG529186.1|EG529186
EST:     TGCTGTTGGTTTGAGCCGACAACTCAATGGATCGGTTATACCTTCAGAAC                         GCCCTAACCACATGATGTTGGAG
genomic: TGCTGTTGGTTTGAGCCGACAACTCAATGGATCGGTTATACCTTCAGAACgtgagttctt ... tcggttgcagGCCCTAACCACATGATGTTGGAG
EST: gi|86061617|gb|DR357374.1|DR357374
EST:     TGCTGTTGGTTTGAGCCGACAACTCAATGGATCGGTTATACCTTCAGAAC                         GCCCTAACCACATGATGTTGGAG
genomic: TGCTGTTGGTTTGAGCCGACAACTCAATGGATCGGTTATACCTTCAGAACgtgagttctt ... tcggttgcagGCCCTAACCACATGATGTTGGAG
EST: gi|301501173|gb|HO206713.1|HO206713
EST:     TGCTGTTGGTTTGAGCCGACAACTCAATGGATCGGTTATACCTTCAGAAC                         GCCCTAACCACATGATGTTGGAG
genomic: TGCTGTTGGTTTGAGCCGACAACTCAATGGATCGGTTATACCTTCAGAACgtgagttctt ... tcggttgcagGCCCTAACCACATGATGTTGGAG
EST: gi|116420806|gb|EG463398.1|EG463398
EST:     TGCTGTTGGTTTGAGCCGACAACTCAATGGATCGGTTATACCTTCAGAAC                         GCCCTAACCACATGATGTTGGAG
genomic: TGCTGTTGGTTTGAGCCGACAACTCAATGGATCGGTTATACCTTCAGAACgtgagttctt ... tcggttgcagGCCCTAACCACATGATGTTGGAG
EST: gi|301502366|gb|HO207906.1|HO207906
EST:     TGCTGTTGGTTTGAGCCGACAACTCAATGGATCGGTTATACCTTCAGAAC                         GCCCTAACCACATGATGTTGGAG
genomic: TGCTGTTGGTTTGAGCCGACAACTCAATGGATCGGTTATACCTTCAGAACgtgagttctt ... tcggttgcagGCCCTAACCACATGATGTTGGAG
EST: gi|116486590|gb|EG529182.1|EG529182
EST:     TGCTGTTGGTTTGAGCCGACAACTCAATGGATCGGTTATACCTTCAGAAC                         GCCCTAACCACATGATGTTGGAG
genomic: TGCTGTTGGTTTGAGCCGACAACTCAATGGATCGGTTATACCTTCAGAACgtgagttctt ... tcggttgcagGCCCTAACCACATGATGTTGGAG
EST: gi|301502094|gb|HO207634.1|HO207634
EST:     TGCTGTTGGTTTGAGCCGACAACTCAATGGATCGGTTATACCTTCAGAAC                         GCCCTAACCACATGATGTTGGAG
genomic: TGCTGTTGGTTTGAGCCGACAACTCAATGGATCGGTTATACCTTCAGAACgtgagttctt ... tcggttgcagGCCCTAACCACATGATGTTGGAG
EST: gi|116486591|gb|EG529183.1|EG529183
EST:     TGCTGTTGGTTTGAGCCGACAACTCAATGGATCGGTTATACCTTCAGAAC                         GCCCTAACCACATGATGTTGGAG
genomic: TGCTGTTGGTTTGAGCCGACAACTCAATGGATCGGTTATACCTTCAGAACgtgagttctt ... tcggttgcagGCCCTAACCACATGATGTTGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttttttatgtaaaggattttctctaactcatatcattttttttcggttgcagGCCCTAACCACATGATGTTGGAG
                       ctctaac  putative branch site (score: 2)
                                 tatcattttttttc  putative PPT
                              tcatatcatttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttcttgcttctgttaacattttgttcctagattagatttatcttcctcaaatatctccttgaaggcacttggagttgcaaatgctttttttttttatgtaaaggattttctctaactcatatcattttttttcggttgcagGCCCTAACCACATGATGTTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG