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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attctgaactcaacctaaatggatgtcctctacttgtctcttctgctcacacgatggcctttaacttgttcctgacgtggtttatgtgtgaatattgcagGGGTCCATGAGACTAGGTTGATGCTGGTCACACCTTAAGTAGATGCATCAAATGGCATTGATTTGCCGTAGGTCTTAGAGAGGGTTACTGTAACATTATA

Basic information

species Physcomitrella patens
transcript PP1S42_153V6.1
intron # 4
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|37835806|gb|BJ593818.1|BJ593818
EST:     NNNCCGATAAAAATCGCCTTGAACAAGACAAGCCGGATTCACTTTAAATG                         GGGTCCATGAGACTAGGTTGATGCTGGTCACACCTTAAGTAGATGCATCAA
genomic: TTTCCGATAAAAATCGCCTTGAACAAGACAAGCCGGATTCACTTTAAATGgtaatcctct ... aatattgcagGGGTCCATGAGACTAGGTTGATGCTGGTCACACCTTAAGTAGATGCATCAA
EST: gi|37841823|gb|BJ599831.1|BJ599831
EST:     NNNCCGATAAAAATCGCCTTGAACAAGACAAGCCGGATTCACTTTAAATG                         GGGTCCATGAGACTAGGTTGATGCTGGTCACACCTTAAGTAGATGCATCAA
genomic: TTTCCGATAAAAATCGCCTTGAACAAGACAAGCCGGATTCACTTTAAATGgtaatcctct ... aatattgcagGGGTCCATGAGACTAGGTTGATGCTGGTCACACCTTAAGTAGATGCATCAA
EST: gi|37851864|gb|BJ609872.1|BJ609872
EST:     NNNCCGATAAAAATCGCCTTGAACAAGACAAGCCGGATTCACTTTAAATG                         GGGTCCATGAGACTAGGTTGATGCTGGTCACACCTTAAGTAGATGCATCAA
genomic: TTTCCGATAAAAATCGCCTTGAACAAGACAAGCCGGATTCACTTTAAATGgtaatcctct ... aatattgcagGGGTCCATGAGACTAGGTTGATGCTGGTCACACCTTAAGTAGATGCATCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcacacgatggcctttaacttgttcctgacgtggtttatgtgtgaatattgcagGGGTCCATGAGACTAGGTTGATGCTGGTCACACCTTAAGTAGATGCATCAAATGGCATTGATTTGCCGTAGGTCTTAGAGAGGGTTACTGTAACATTATA
                        tcctgac  putative branch site (score: 2)
              tttaactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attctgaactcaacctaaatggatgtcctctacttgtctcttctgctcacacgatggcctttaacttgttcctgacgtggtttatgtgtgaatattgcagGGGTCCATGAGACTAGGTTGATGCTGGTCACACCTTAAGTAGATGCATCAAATGGCATTGATTTGCCGTAGGTCTTAGAGAGGGTTACTGTAACATTATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - ctgctca