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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagactttggttaaaactctgtattgatgaggttttagctctatatgtacaattcactgatcttcctttaaaatcttctcagATAAAAGAAATGAAATAGAAAATCGGGTGGACGATCAAACAGAAACTTCTTTAGCTTCTTCTGCACAAGATCAGCCTCAAGGCAATAACAATGCAGCTGA

Basic information

species Arabidopsis thaliana
transcript AT4G29000.1
intron # 6
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|116429125|gb|EG471717.1|EG471717
EST:     TTGCTCTGTTTTAGTCACTGTAGCCGGAGAAGCAGCAAAGACATCAACAG                         ATAAAAGAAATGAAATAGAAAATCGGGTGGACGATCAAACAGAAACTTCTT
genomic: TTGCTCTGTTTTAGTCACTGTAGCCGGAGAAGCAGCAAAGACATCAACAGgtgagacttt ... atcttctcagATAAAAGAAATGAAATAGAAAATCGGGTGGACGATCAAACAGAAACTTCTT
EST: gi|116399763|gb|EG442355.1|EG442355
EST:     TTGCTCTGTTTTAGTCACTGTAGCCGGAGAAGCAGCAAAGACATCAACAG                         ATAAAAGAAATGAAATAGAAAATCGGGTGGACGATCAAACAGAAACTTCTT
genomic: TTGCTCTGTTTTAGTCACTGTAGCCGGAGAAGCAGCAAAGACATCAACAGgtgagacttt ... atcttctcagATAAAAGAAATGAAATAGAAAATCGGGTGGACGATCAAACAGAAACTTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaggttttagctctatatgtacaattcactgatcttcctttaaaatcttctcagATAAAAGAAATGAAATAGAAAATCGGGTGGACGATCAAACAGAAACTTCTTTAGCTTCTTCTGCACAAGATCAGCCTCAAGGCAATAACAATGCAGCTGA
                           cactgat  putative branch site (score: 3)
                                              tcttctc  putative PPT
                                       tttaaaatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagactttggttaaaactctgtattgatgaggttttagctctatatgtacaattcactgatcttcctttaaaatcttctcagATAAAAGAAATGAAATAGAAAATCGGGTGGACGATCAAACAGAAACTTCTTTAGCTTCTTCTGCACAAGATCAGCCTCAAGGCAATAACAATGCAGCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA