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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggattttgtggattagcttaaatcggactttgatttggatttcttttgcttagattttgttactgttggcagATTACATCTCGCAAAAGCAGTCGCTTGGTGGATTGTTGATTTTGCTTCCTCAGACGTTTAGGCCTGGGAATGTTGGTGGTGGAAGTTTAAGCTCTGAAAA

Basic information

species Arabidopsis thaliana
transcript AT3G44330.1
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|86067760|gb|DR363517.1|DR363517
EST:     TTCTGTACTTATACTTCCTCTTCGNGAGCTTGACATTGCTTTTGTTCGAG                         ATTACATCTCGCAAAAGCAGTCGCTTGGNGGATTGTTGATTTTGCTTCCTC
genomic: TTCTGTACTTATACTTCCTCTTCGTGAGCTTGACATTGCTTTTGTTCAAGgtttggattt ... ctgttggcagATTACATCTCGCAAAAGCAGTCGCTTGGTGGATTGTTGATTTTGCTTCCTC
EST: gi|86067761|gb|DR363518.1|DR363518
EST:     TTCTGTACTTATACTTCCTCTTCGTGAGCTTGACATTGCTTTTGTTCGAG                         ATTACATCTCGCAAAAGCAGTCGCTTGGTGGATTGTTGATTTTGCTTCCTC
genomic: TTCTGTACTTATACTTCCTCTTCGTGAGCTTGACATTGCTTTTGTTCAAGgtttggattt ... ctgttggcagATTACATCTCGCAAAAGCAGTCGCTTGGTGGATTGTTGATTTTGCTTCCTC
EST: gi|125009718|gb|EL081987.1|EL081987
EST:     TTCTGTACTTATACTTCCTCTTCGTGAGCTTGACATTGCTTTTGTTCAAG                         ATTACATCTCGCAAAAGCAGTCGCTTGGTGGATTGTT
genomic: TTCTGTACTTATACTTCCTCTTCGTGAGCTTGACATTGCTTTTGTTCAAGgtttggattt ... ctgttggcagATTACATCTCGCAAAAGCAGTCGCTTGGTGGATTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaatcggactttgatttggatttcttttgcttagattttgttactgttggcagATTACATCTCGCAAAAGCAGTCGCTTGGTGGATTGTTGATTTTGCTTCCTCAGACGTTTAGGCCTGGGAATGTTGGTGGTGGAAGTTTAAGCTCTGAAAA
          ctttgat  putative branch site (score: 5)
                     atttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttggattttgtggattagcttaaatcggactttgatttggatttcttttgcttagattttgttactgttggcagATTACATCTCGCAAAAGCAGTCGCTTGGTGGATTGTTGATTTTGCTTCCTCAGACGTTTAGGCCTGGGAATGTTGGTGGTGGAAGTTTAAGCTCTGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG