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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaattttaaaattatgcaactgtaatgctaaatattggataaactgaaatactcacttcctcaatttctgtacagACCGAGCTGTTGATACAAGCCCAGTTAACTCGTGAATCAGGAGTCCTGTCTCCAGCCCTTCAGGGTGATTTCAGGCGTGTGCTAGAGCTTGCACCTCGCC

Basic information

species Arabidopsis thaliana
transcript AT1G79940.3
intron # 7
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|116420065|gb|EG462657.1|EG462657
EST:     TGAAGCAAGAGCAAGCTAAGTTTTGGAAACAGCATCCTGCCATAGTGAAG                         ACCGAGCTGTTGATACAAGCCCAGTTAACTCGTGAATCAGGAGTCCTGTCT
genomic: TGAAGCAAGAGCAAGCTAAGTTTTGGAAACAGCATCCTGCCATAGTGAAGgtgaatttta ... ttctgtacagACCGAGCTGTTGATACAAGCCCAGTTAACTCGTGAATCAGGAGTCCTGTCT
EST: gi|116473043|gb|EG515635.1|EG515635
EST:     TGAAGCAAGAGCAAGCTAAGTTTTGGAAACAGCATCCTGCCATAGTGAAG                         ACCGAGCTGTTGATACAAGCCCAGTTAACTCGTGAATCACGAGTCCTGTCT
genomic: TGAAGCAAGAGCAAGCTAAGTTTTGGAAACAGCATCCTGCCATAGTGAAGgtgaatttta ... ttctgtacagACCGAGCTGTTGATACAAGCCCAGTTAACTCGTGAATCAGGAGTCCTGTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaatgctaaatattggataaactgaaatactcacttcctcaatttctgtacagACCGAGCTGTTGATACAAGCCCAGTTAACTCGTGAATCAGGAGTCCTGTCTCCAGCCCTTCAGGGTGATTTCAGGCGTGTGCTAGAGCTTGCACCTCGCC
                             tactcac  putative branch site (score: 1)
                                   cttcctcaatttct  CT-rich tract
        taaatattggataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaattttaaaattatgcaactgtaatgctaaatattggataaactgaaatactcacttcctcaatttctgtacagACCGAGCTGTTGATACAAGCCCAGTTAACTCGTGAATCAGGAGTCCTGTCTCCAGCCCTTCAGGGTGATTTCAGGCGTGTGCTAGAGCTTGCACCTCGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT