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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaaaaaggcaactgttctcatgcttaaagtttttgtaatttcttatttagttaccaacagtcacaatagtttcttttaaacagGAGAAGTCCATTGATTCGACAAAGCAAGTAAAGCTTGGATTTCTTACCGGATTAGTGCCTCGTGAAAAGTCTATGGTCTTTGAGAGGATTCTGTTCCGTG

Basic information

species Arabidopsis thaliana
transcript AT4G39080.1
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|125308928|gb|EL323013.1|EL323013
EST:     AATCACAACAAGCGGATGAAGATCTGCTGGAGTCTCCTTTGTTACAGGAA                         GAGAAGTCCATTGATTCGACAAAGCA
genomic: AATCACAACAAGCGGGTGAAGATCTGCTGGAGTCTCCTTTGTTACAGGAAgtatgaaaaa ... ttttaaacagGAGAAGTCCATTGATTCGACAAAGCA
EST: gi|116448634|gb|EG491226.1|EG491226
EST:     AATCACAACAAGCGGGTGAAGATCTGCTGGAGTCTCCTTTGTTACAGGAA                         GAGAAGTCCATTGATTCGACAAAGCAAGTAAAGCTTGGATTTCTTACCGGA
genomic: AATCACAACAAGCGGGTGAAGATCTGCTGGAGTCTCCTTTGTTACAGGAAgtatgaaaaa ... ttttaaacagGAGAAGTCCATTGATTCGACAAAGCAAGTAAAGCTTGGATTTCTTACCGGA
EST: gi|86064751|gb|DR360508.1|DR360508
EST:     AATCACAACAAGCGGGTGAAGATCTGCTGGAGTCTCCTTTGTTACAGGAA                         GAGAAGTCCATTGATTCGACAAAGCAAGTAAAGCTTGNATTTCTTACCGGA
genomic: AATCACAACAAGCGGGTGAAGATCTGCTGGAGTCTCCTTTGTTACAGGAAgtatgaaaaa ... ttttaaacagGAGAAGTCCATTGATTCGACAAAGCAAGTAAAGCTTGGATTTCTTACCGGA
EST: gi|116444120|gb|EG486712.1|EG486712
EST:     AATCACAACAAGCGGGTGAAGATCTGCTGGAGTCTCCTTTGTTACAGGAA                         GAGAAGTCCATTGATTCGACAAAGCAAGTAAAGCTTGGATTTCTTACCGGA
genomic: AATCACAACAAGCGGGTGAAGATCTGCTGGAGTCTCCTTTGTTACAGGAAgtatgaaaaa ... ttttaaacagGAGAAGTCCATTGATTCGACAAAGCAAGTAAAGCTTGGATTTCTTACCGGA
EST: gi|116415767|gb|EG458359.1|EG458359
EST:     AATCACAACAAGCGGGTGAAGATCTGCTGGAGTCTCCTTTGTTACAGGAA                         GAGAAGTCCATTGATTCGACAAAGCAAGTAAAGCTTGGATTTCTTACCGGA
genomic: AATCACAACAAGCGGGTGAAGATCTGCTGGAGTCTCCTTTGTTACAGGAAgtatgaaaaa ... ttttaaacagGAGAAGTCCATTGATTCGACAAAGCAAGTAAAGCTTGGATTTCTTACCGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttttgtaatttcttatttagttaccaacagtcacaatagtttcttttaaacagGAGAAGTCCATTGATTCGACAAAGCAAGTAAAGCTTGGATTTCTTACCGGATTAGTGCCTCGTGAAAAGTCTATGGTCTTTGAGAGGATTCTGTTCCGTG
                                         tttctttt  CT-rich tract
       taatttcttatttagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaaaaaggcaactgttctcatgcttaaagtttttgtaatttcttatttagttaccaacagtcacaatagtttcttttaaacagGAGAAGTCCATTGATTCGACAAAGCAAGTAAAGCTTGGATTTCTTACCGGATTAGTGCCTCGTGAAAAGTCTATGGTCTTTGAGAGGATTCTGTTCCGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT