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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgttgattgattcagtctctttcttttatggattagaataacacctattaggttgaaagaatctcttactagttttattgactttgtttatcttcaaaaaattgaattattgtagGAGAAAAGGAGTGTGAGTTTCGAGTATGGTCGTTATGGTAACCCTACGACTGTGGTACTTGAAGATAAGATAAG

Basic information

species Arabidopsis thaliana
transcript AT3G01120.1
intron # 2
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|164010300|gb|ES047166.1|ES047166
EST:     ACACATCTGCCTACTTCTTCAAGAAAACTGCTGAGCTTATTGACTTCAAG                         GAGAAAAGGAGTG
genomic: ACACATCTGCCTACTTCTTCAAGAAAACTGCTGAGCTTATTGACTTCAAGgtccgttgat ... attattgtagGAGAAAAGGAGTG
EST: gi|124856105|gb|EH940542.1|EH940542
EST:     CTGCCTACTTCTTCAAGAAAACTGCTGAGCTTATTGACTTCAAG                         GAGAAAAGGAGTGTGAGTTTCGAGTATGGTCGTTATGGTAACCCTACGACT
genomic: CTGCCTACTTCTTCAAGAAAACTGCTGAGCTTATTGACTTCAAGgtccgttgat ... attattgtagGAGAAAAGGAGTGTGAGTTTCGAGTATGGTCGTTATGGTAACCCTACGACT
EST: gi|164155793|gb|EL984458.1|EL984458
EST:     ACACATCTGCCTACTTCTTCAAGAAAACTGCTGAGCTTATTGACTTCAAG                         GAGAAAAGGAGTGTGA
genomic: ACACATCTGCCTACTTCTTCAAGAAAACTGCTGAGCTTATTGACTTCAAGgtccgttgat ... attattgtagGAGAAAAGGAGTGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctcttactagttttattgactttgtttatcttcaaaaaattgaattattgtagGAGAAAAGGAGTGTGAGTTTCGAGTATGGTCGTTATGGTAACCCTACGACTGTGGTACTTGAAGATAAGATAAG
               tattgac  putative branch site (score: 2)
                      tttgtttatcttcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccgttgattgattcagtctctttcttttatggattagaataacacctattaggttgaaagaatctcttactagttttattgactttgtttatcttcaaaaaattgaattattgtagGAGAAAAGGAGTGTGAGTTTCGAGTATGGTCGTTATGGTAACCCTACGACTGTGGTACTTGAAGATAAGATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA