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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctcgtgtagtttgagaatggatgctcttatagatctgtggtttatagattatttagaagagttttggagaatttagtgttttggtttatgtggttgtagATGAGATAGCGAAGTTGTTTCCGGGTCTATATGGCCAGCCATCAGTAGCAGTGGTTCCAGATCAGGATGCACCTTCGTCGGCACCGAAATTGAAGATTGG

Basic information

species Arabidopsis thaliana
transcript AT1G12000.1
intron # 1
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|86069454|gb|DR365211.1|DR365211
EST:     AGCTTTCAAAATCGTCGAAGGTCCCGCTAGTTCCGCCGCCGGGAATCCAG                         ATGAGATAGCGAAGTTGTTTCCGGGTCTATATGGCCAGCCATCAGTAGCAG
genomic: AGCTTTCAAAATCGTCGAAGGTCCCGCTAGTTCCGCCGCCGGGAATCCAGgttagatact ... gtggttgtagATGAGATAGCGAAGTTGTTTCCGGGTCTATATGGCCAGCCATCAGTAGCAG
EST: gi|124967015|gb|EL041079.1|EL041079
EST:     AGTTCCGCCGCCGGGAATCCAG                         ATGAGATAGCGAAGTTGTTTCCGGGTCTATATGGCCAGCCATCAGTAGCAG
genomic: AGTTCCGCCGCCGGGAATCCAGgttagatact ... gtggttgtagATGAGATAGCGAAGTTGTTTCCGGGTCTATATGGCCAGCCATCAGTAGCAG
EST: gi|86069449|gb|DR365206.1|DR365206
EST:     AGTTCCGCCGCCGGGAATCCAG                         ATGAGATAGCGAAGTTGTTTCCGGGTCTATATGGCCAGCCATCAGTAGCAG
genomic: AGTTCCGCCGCCGGGAATCCAGgttagatact ... gtggttgtagATGAGATAGCGAAGTTGTTTCCGGGTCTATATGGCCAGCCATCAGTAGCAG
EST: gi|124727841|gb|EH819243.1|EH819243
EST:     AGCTTTCAAAATCGTCGAAGGTCCCGCTAGTTCCGCCGCCGGGAATCCAG                         ATGAGATAGCGAAGTTGTTTCCGGGTCTATATGGCCAGCCA
genomic: AGCTTTCAAAATCGTCGAAGGTCCCGCTAGTTCCGCCGCCGGGAATCCAGgttagatact ... gtggttgtagATGAGATAGCGAAGTTGTTTCCGGGTCTATATGGCCAGCCA
EST: gi|125257157|gb|EL271242.1|EL271242
EST:     AGCTTTCAAAATCGTCGAAGGTCCCGCTAGTTCCGCCGCCGGGAATCCAG                         ATGAGATAGCGAAGTTG
genomic: AGCTTTCAAAATCGTCGAAGGTCCCGCTAGTTCCGCCGCCGGGAATCCAGgttagatact ... gtggttgtagATGAGATAGCGAAGTTG
EST: gi|86069453|gb|DR365210.1|DR365210
EST:     GCTTTCAAAATCGTCGAAGGTCCCGCTAGTTCCGCCCGCCGGGAATCCAG                         ATGAGATAGCGAAGTTGTTTCCGGGTCTATATGGCCAGCCATCA
genomic: GCTTTCAAAATCGTCGAAGGTCCCGCTAGTTCCGCC-GCCGGGAATCCAGgttagatact ... gtggttgtagATGAGATAGCGAAGTTGTTTCCGGGTCTATATGGCCAGCCATCA
EST: gi|116438055|gb|EG480647.1|EG480647
EST:     AGCTTTCAAAATCGTCGAAGGTCCCGCTAGTTCCGCCGCCGGGAATCCAG                         ATGAGATAGCGAAGTTGTTTCCGGGTCTATATGGCCAGCCATCAGTAGCAG
genomic: AGCTTTCAAAATCGTCGAAGGTCCCGCTAGTTCCGCCGCCGGGAATCCAGgttagatact ... gtggttgtagATGAGATAGCGAAGTTGTTTCCGGGTCTATATGGCCAGCCATCAGTAGCAG
EST: gi|125301347|gb|EL315432.1|EL315432
EST:     AGCTTTCAAAATCGTCGAAGGTCCCGCTAGTTCCGCCGCCGGGAATCCAG                         ATGAGATAGCGAAGTTGTTTCCGGGTCTATAT
genomic: AGCTTTCAAAATCGTCGAAGGTCCCGCTAGTTCCGCCGCCGGGAATCCAGgttagatact ... gtggttgtagATGAGATAGCGAAGTTGTTTCCGGGTCTATAT
EST: gi|86069448|gb|DR365205.1|DR365205
EST:     AGCTTTCAAAATCGTCGAAGGTCCCGCTAGTTCCGCCGCCGGGAATCCAG                         ATGAGATAGCGAAGTTGTTTCCGGGTCTATATGGCCAGCCATCAGTAGCAG
genomic: AGCTTTCAAAATCGTCGAAGGTCCCGCTAGTTCCGCCGCCGGGAATCCAGgttagatact ... gtggttgtagATGAGATAGCGAAGTTGTTTCCGGGTCTATATGGCCAGCCATCAGTAGCAG
EST: gi|86069455|gb|DR365212.1|DR365212
EST:     AGCTTTCAAAATCGTCGAAGGTCCCGCTAGTTCCGCCGCCGGGAATCCAG                         ATGAGATAGCGAAGTTGTTTCCGGGTCTATATGGCCAGCCATCAGTAGCAG
genomic: AGCTTTCAAAATCGTCGAAGGTCCCGCTAGTTCCGCCGCCGGGAATCCAGgttagatact ... gtggttgtagATGAGATAGCGAAGTTGTTTCCGGGTCTATATGGCCAGCCATCAGTAGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagattatttagaagagttttggagaatttagtgttttggtttatgtggttgtagATGAGATAGCGAAGTTGTTTCCGGGTCTATATGGCCAGCCATCAGTAGCAGTGGTTCCAGATCAGGATGCACCTTCGTCGGCACCGAAATTGAAGATTGG
     tatttagaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctcgtgtagtttgagaatggatgctcttatagatctgtggtttatagattatttagaagagttttggagaatttagtgttttggtttatgtggttgtagATGAGATAGCGAAGTTGTTTCCGGGTCTATATGGCCAGCCATCAGTAGCAGTGGTTCCAGATCAGGATGCACCTTCGTCGGCACCGAAATTGAAGATTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - agtttga
- - - - - - - - - - -atgctct
- - - - - - - - - - - - - - - - - - - -ggtttat
- - - - - - - - - - - - - - - - - - - - - - - - - - - tagaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttttgg