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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactagttgccacctttctactttctacaatcctcaatcattactttagtcagcagcaacaaaccctaatcaaaacaaacacttctgcttcattttgcagCTAAATCCGAAGAAAACTTCAGGGACAAGAAACCCATCAAAGGAAGACCGAAACAGAACAGCAAAGATGCACAACAAAGACTGTGTCCTCATGGGTCTCA

Basic information

species Arabidopsis thaliana
transcript AT3G18050.1
intron # 1
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|47830825|gb|CK120509.1|CK120509
EST:     GATTCTCACCTCTTCTTGGTTGCAACAAGTGCTTGAACAGTCTCTATAAG                         CTAAATCCGAAGAAAACTTCAGGGACAAGAAACCCATCAAAGGAAGACCGA
genomic: GATTCTCACCTCTTCTTGGTTGCAACAAGTGCTTGAACAGTCTCTATAAGgtaaagtcac ... cattttgcagCTAAATCCGAAGAAAACTTCAGGGACAAGAAACCCATCAAAGGAAGACCGA
EST: gi|124881988|gb|EH960890.1|EH960890
EST:     GAACAGTCTCTATAAG                         CTAAATCCGAAGAAAACTTTCAGGGACAAGAAACCCATCAAAGGAAGACCG
genomic: GAACAGTCTCTATAAGgtaaagtcac ... cattttgcagCTAAATCCGAAGAAAAC-TTCAGGGACAAGAAACCCATCAAAGGAAGACCG
EST: gi|116483001|gb|EG525593.1|EG525593
EST:     GATTCTCACCTCTTTTTGGTTGCAACAAGTGCTTGAACAGTCTCTATAAG                         CTAAATCCGAAGAAAACTTCAGGGACAAGAAACCCATCAAAGGAA
genomic: GATTCTCACCTCTTCTTGGTTGCAACAAGTGCTTGAACAGTCTCTATAAGgtaaagtcac ... cattttgcagCTAAATCCGAAGAAAACTTCAGGGACAAGAAACCCATCAAAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagtcagcagcaacaaaccctaatcaaaacaaacacttctgcttcattttgcagCTAAATCCGAAGAAAACTTCAGGGACAAGAAACCCATCAAAGGAAGACCGAAACAGAACAGCAAAGATGCACAACAAAGACTGTGTCCTCATGGGTCTCA
                  ccctaat  putative branch site (score: 3)
                                    cttctgcttcatttt  putative PPT
                     taatcaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactagttgccacctttctactttctacaatcctcaatcattactttagtcagcagcaacaaaccctaatcaaaacaaacacttctgcttcattttgcagCTAAATCCGAAGAAAACTTCAGGGACAAGAAACCCATCAAAGGAAGACCGAAACAGAACAGCAAAGATGCACAACAAAGACTGTGTCCTCATGGGTCTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - cctttct
- - - - - - - - - - - - - - - tcctcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaaccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacaaa