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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatacggcatcacaaaagttgaggttcatctctttaacatactgctgttttttcttttctctttcgcaagggatttaacgatctctttgtatagctcttgtcgttacagttcactgcaagggattccctttatattaagagttttaattcctctgcagATGATGAAACATCAGGCAAAGGAAAAGAGAGACCTTGCCCAAGAGAAGGACTTAGCTCAGGGTAAGAAGGACCAAGCCAACGAAACGAAAAAGAACAAGG

Basic information

species Physcomitrella patens
transcript PP1S61_4V6.1
intron # 10
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|37825026|gb|BJ583092.1|BJ583092
EST:     AAGCTCTGAAGCTTTACAAGGAGAAAGAAAAGTTGGATCAAGCTAAAAAG                         ATGATGAAACATCAGGCAAAGGAAAAGAGAGACCTTGCCCAAGAGAAGGAC
genomic: AAGCTCTGAAGCTTTACAAGGAGAAAGAAAAGTTGGATCAAGCTAAAAAGgtaatacggc ... tcctctgcagATGATGAAACATCAGGCAAAGGAAAAGAGAGACCTTGCCCAAGAGAAGGAC
EST: gi|15327478|gb|BI488232.1|BI488232
EST:     AAGCTCTGAAGCTTTACAAGGAGAAAGAAAAGTTGGATCAAGCTAAAAAG                         ATGATGAAACATCAGGCAAAGGAAAAGAGAGACCTTGCCCAAGAGAAGGAC
genomic: AAGCTCTGAAGCTTTACAAGGAGAAAGAAAAGTTGGATCAAGCTAAAAAGgtaatacggc ... tcctctgcagATGATGAAACATCAGGCAAAGGAAAAGAGAGACCTTGCCCAAGAGAAGGAC
EST: gi|208367881|gb|DC955344.1|DC955344
EST:     AAGCTCTGAAGCTTTACAAGGAGAAAGAAAAGTTGGATCAAGCTAAAAAG                         ATGATGAAACATCAGGCAAAGGAAAAGAGAGACCTTGCCCAAGAGAAGGAC
genomic: AAGCTCTGAAGCTTTACAAGGAGAAAGAAAAGTTGGATCAAGCTAAAAAGgtaatacggc ... tcctctgcagATGATGAAACATCAGGCAAAGGAAAAGAGAGACCTTGCCCAAGAGAAGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacagttcactgcaagggattccctttatattaagagttttaattcctctgcagATGATGAAACATCAGGCAAAGGAAAAGAGAGACCTTGCCCAAGAGAAGGACTTAGCTCAGGGTAAGAAGGACCAAGCCAACGAAACGAAAAAGAACAAGG
                                      ttttaat  putative branch site (score: 3)
                                            ttcctctgc  CT-rich tract
                         tttatattaagagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatacggcatcacaaaagttgaggttcatctctttaacatactgctgttttttcttttctctttcgcaagggatttaacgatctctttgtatagctcttgtcgttacagttcactgcaagggattccctttatattaagagttttaattcctctgcagATGATGAAACATCAGGCAAAGGAAAAGAGAGACCTTGCCCAAGAGAAGGACTTAGCTCAGGGTAAGAAGGACCAAGCCAACGAAACGAAAAAGAACAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC