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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaaagtctttacgttttctacaattggccaagtgctattgcacctcgttgtgtggaagagcttgtgtgattcttgctaactgtcgttctcgattgttagATGGTGCAGCAAGGAGGCTATAACCCTTACATGCAAGCGCAG

Basic information

species Physcomitrella patens
transcript PP1S25_89V6.2
intron # 5
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|67697971|gb|BJ958204.1|BJ958204
EST:     CATCTTCTGGCAAGAAGGAGGGAAGTGGCATGGTATCTCCTGGCGTTCAG                         ATGGTGCAGCAAGGAGGCTATAACCCTTACATGCAAGCGCAG
genomic: CATCTTCTGGCAAGAAGGAGGGAAGTGGCATGGTATCTCCTGGCGTTCAGgtgggcttgt ... cgattgttagATGGTGCAGCAAGGAGGCTATAACCCTTACATGCAAGCGCAG
EST: gi|162273472|gb|FC449617.1|FC449617
EST:     CATCTTCTGGCAAGAAGGAGGGAAGTGGCATGGTATCTCCTGGCGTTCAG                         ATGGTGCAGCAAGGAGGCTATAACCCTTACATGCAAGCGCAG
genomic: CATCTTCTGGCAAGAAGGAGGGAAGTGGCATGGTATCTCCTGGCGTTCAGgtgggcttgt ... cgattgttagATGGTGCAGCAAGGAGGCTATAACCCTTACATGCAAGCGCAG
EST: gi|208354191|gb|DC957411.1|DC957411
EST:     CATCTTCTGGCAAGAAGGAGGGAAGTGGCATGGTATCTCCTGGCGTTCAG                         ATGGTGCAGCAAGGAGGCTATAACCCTTACATGCAAGCGCAG
genomic: CATCTTCTGGCAAGAAGGAGGGAAGTGGCATGGTATCTCCTGGCGTTCAGgtgggcttgt ... cgattgttagATGGTGCAGCAAGGAGGCTATAACCCTTACATGCAAGCGCAG
EST: gi|208361426|gb|DC935113.1|DC935113
EST:     CATCTTCTGGCAAGAAGGAGGGAAGTGGCATGGTATCTCCTGGCGTTCAG                         ATGGTGCAGCAAGGAGGCTATAACCCTTACATGCANGCGCAG
genomic: CATCTTCTGGCAAGAAGGAGGGAAGTGGCATGGTATCTCCTGGCGTTCAGgtgggcttgt ... cgattgttagATGGTGCAGCAAGGAGGCTATAACCCTTACATGCAAGCGCAG
EST: gi|162273471|gb|FC449616.1|FC449616
EST:     CATCTTCTGGCAAGAAGGAGGGAAGTGGCATGGTATCTCCTGGCGTTCAG                         ATGGTGCAGCAAGGAGGCTATAACCCTTACATGCAAGCGCAG
genomic: CATCTTCTGGCAAGAAGGAGGGAAGTGGCATGGTATCTCCTGGCGTTCAGgtgggcttgt ... cgattgttagATGGTGCAGCAAGGAGGCTATAACCCTTACATGCAAGCGCAG
EST: gi|37828975|gb|BJ586987.1|BJ586987
EST:     CATCTTCTGGCAAGAAGGAGGGAAGTGGCATGGTATCTCCTGGCGTTCAG                         ATGGTGCAGCAAGGAGGCTATAACCCTTACATGCAAGCGCAG
genomic: CATCTTCTGGCAAGAAGGAGGGAAGTGGCATGGTATCTCCTGGCGTTCAGgtgggcttgt ... cgattgttagATGGTGCAGCAAGGAGGCTATAACCCTTACATGCAAGCGCAG
EST: gi|208387454|gb|DC949239.1|DC949239
EST:     CATCTTCTGGCAAGAAGGAGGGAAGTGGCATGGTATCTCCTGGCGTTCAG                         ATGGTGCAGCAAGGAGGCTATAACCCTTACATGCAAGCGCAG
genomic: CATCTTCTGGCAAGAAGGAGGGAAGTGGCATGGTATCTCCTGGCGTTCAGgtgggcttgt ... cgattgttagATGGTGCAGCAAGGAGGCTATAACCCTTACATGCAAGCGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgttgtgtggaagagcttgtgtgattcttgctaactgtcgttctcgattgttagATGGTGCAGCAAGGAGGCTATAACCCTTACATGCAAGCGCAG
                             tgctaac  putative branch site (score: 1)
                                      tcgttctc  putative PPT
                                               attgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaaagtctttacgttttctacaattggccaagtgctattgcacctcgttgtgtggaagagcttgtgtgattcttgctaactgtcgttctcgattgttagATGGTGCAGCAAGGAGGCTATAACCCTTACATGCAAGCGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG