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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaacgaaactattttccttaactgatcaaaagtcttaatactttccaatgaaaaaagacttataccatagcttgaatccaatctgatatagaaaacgttaaactgaattagagcttgaaatgtttttccttcagattgttttcttgtttctgattagacattgaagcatgacgtgttataatattgcagGATAGTAGCTGTGAGTTTGGTTACCGTCTTGTCGGGGATGTATGTTACGAGGAAGCGTTAGGTGTTGCCTCGGCTATCACTCCCGTACCGGGAGGAGTTG

Basic information

species Arabidopsis thaliana
transcript AT2G38660.3
intron # 5
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|19742513|gb|AU227866.1|AU227866
EST:     GCTTAAGCCTGGAGCAGTTGTCAGTTGATGTTGGAACAACTCCAGTCGAG                         GATAGTAGCTGTGAGTTTGGTTACCGTCTTGTCGGGGATGTATGTTACGAG
genomic: GCTTAAGCCTGGAGCAGTTGTCA-TTGATGTTGGAACAACTCCAGTCGAGgtaaaaacga ... aatattgcagGATAGTAGCTGTGAGTTTGGTTACCGTCTTGTCGGGGATGTATGTTACGAG
EST: gi|124908961|gb|EH983041.1|EH983041
EST:     GGCTTAAGCCTGGAGCAGTTGTCATTGATGTTGGAACAACTCCAGTCGAG                         GATAGTAGCTGTGAGTTTGGTTACCGT
genomic: GGCTTAAGCCTGGAGCAGTTGTCATTGATGTTGGAACAACTCCAGTCGAGgtaaaaacga ... aatattgcagGATAGTAGCTGTGAGTTTGGTTACCGT
EST: gi|125294762|gb|EL308847.1|EL308847
EST:     AGCCTGGAGCAGTTGTCATTGATGTTGGAACAACTCCAGTCGAG                         GATAGTAGCTGTGAGTTTGGTTACCG
genomic: AGCCTGGAGCAGTTGTCATTGATGTTGGAACAACTCCAGTCGAGgtaaaaacga ... aatattgcagGATAGTAGCTGTGAGTTTGGTTACCG
EST: gi|86084888|gb|DR380647.1|DR380647
EST:     GGCTTAAGCCTGGAGCAGTTGTCATTGATGTTGGAACAACTCCAGTCGAG                         GATAGTAGCTGTGAGTTTGGTTACCGTCTTGTCGGGGATGTATGTTACGAG
genomic: GGCTTAAGCCTGGAGCAGTTGTCATTGATGTTGGAACAACTCCAGTCGAGgtaaaaacga ... aatattgcagGATAGTAGCTGTGAGTTTGGTTACCGTCTTGTCGGGGATGTATGTTACGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgttttcttgtttctgattagacattgaagcatgacgtgttataatattgcagGATAGTAGCTGTGAGTTTGGTTACCGTCTTGTCGGGGATGTATGTTACGAGGAAGCGTTAGGTGTTGCCTCGGCTATCACTCCCGTACCGGGAGGAGTTG
             ttctgat  putative branch site (score: 3)
                                       tgttataatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaacgaaactattttccttaactgatcaaaagtcttaatactttccaatgaaaaaagacttataccatagcttgaatccaatctgatatagaaaacgttaaactgaattagagcttgaaatgtttttccttcagattgttttcttgtttctgattagacattgaagcatgacgtgttataatattgcagGATAGTAGCTGTGAGTTTGGTTACCGTCTTGTCGGGGATGTATGTTACGAGGAAGCGTTAGGTGTTGCCTCGGCTATCACTCCCGTACCGGGAGGAGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG