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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggctgtctaaccctctgtaggtctaacctttcatcaagtttttagttatttctctcatttaagaccatagcttcataaacttgttaattctgcatacctttttggatgcgaagaccggagcgtccataagtagaaccagctgccttgttgctatttgattgctagaatgcctcctattttttgctgtgtgcagAACGGTATGAAAGCAATGCTCCTGACCTTGCAAAAAAGGAACGTTCGGGCTTTGGCTTTCTACACTGGGAAATTAAG

Basic information

species Physcomitrella patens
transcript PP1S98_98V6.2
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|162279490|gb|FC455606.1|FC455606
EST:     AGGGGCTTGGCAAGTTTTTGATGCAGTTTCTTGAGTTGATTGCCCGCAAG                         AACGGTATGAAAGCAATGCTCCTGACCTTGCAAAAAAGGAACGTTCGGGCT
genomic: AGGGGCTTGGCAAGTTTTTGATGCAGTTTCTTGAGTTGATTGCCCGCAAGgttggctgtc ... ctgtgtgcagAACGGTATGAAAGCAATGCTCCTGACCTTGCAAAAAAGGAACGTTCGGGCT
EST: gi|37826808|gb|BJ584820.1|BJ584820
EST:     AGGGGCTTGNCAAGTTTTTGATGCAGTTTCTTGAGTTGATTGCCCGCAAG                         AACGGTATGAAAGCAATGCTCCTGACCTTGCAAAAAAGGAACGTTCGGGCT
genomic: AGGGGCTTGGCAAGTTTTTGATGCAGTTTCTTGAGTTGATTGCCCGCAAGgttggctgtc ... ctgtgtgcagAACGGTATGAAAGCAATGCTCCTGACCTTGCAAAAAAGGAACGTTCGGGCT
EST: gi|162279489|gb|FC455605.1|FC455605
EST:     AGGGGCTTGGCAAGTTTTTGATGCAGTTTCTTGAGTTGATTGCCCGCAAG                         AACGGTATGAAAGCAATGCTCCTGACCTTGCAAAAAAGGAACGTTCGGGCT
genomic: AGGGGCTTGGCAAGTTTTTGATGCAGTTTCTTGAGTTGATTGCCCGCAAGgttggctgtc ... ctgtgtgcagAACGGTATGAAAGCAATGCTCCTGACCTTGCAAAAAAGGAACGTTCGGGCT
EST: gi|162245726|gb|FC420744.1|FC420744
EST:     AGGGGCTTGGCAAGTTTTTGATGCAGTTTCTTGAGTTGATTGCCCGCAAG                         AACGGTATGAAAGCAATGCTCCTGACCTTGCAAAAAAGGAACGTTCGGGCT
genomic: AGGGGCTTGGCAAGTTTTTGATGCAGTTTCTTGAGTTGATTGCCCGCAAGgttggctgtc ... ctgtgtgcagAACGGTATGAAAGCAATGCTCCTGACCTTGCAAAAAAGGAACGTTCGGGCT
EST: gi|162245725|gb|FC420743.1|FC420743
EST:     TTGATGCAGTTTCTTGAGTTGATTGCCCGCAAG                         AACGGTATGAAAGCAATGCTCCTGACCTTGCAAAAAAGGAACGTTCGGGCT
genomic: TTGATGCAGTTTCTTGAGTTGATTGCCCGCAAGgttggctgtc ... ctgtgtgcagAACGGTATGAAAGCAATGCTCCTGACCTTGCAAAAAAGGAACGTTCGGGCT
EST: gi|162227714|gb|FC402668.1|FC402668
EST:     AGGGGCTTGGCAAGTTTTTGATGCAGTTTCTTGAGTTGATTGCCCGCAAG                         AACGGTATGAAAGCAATGCTCCTGACCTTGCAAAAAAGGAACGTTCGGGCT
genomic: AGGGGCTTGGCAAGTTTTTGATGCAGTTTCTTGAGTTGATTGCCCGCAAGgttggctgtc ... ctgtgtgcagAACGGTATGAAAGCAATGCTCCTGACCTTGCAAAAAAGGAACGTTCGGGCT
EST: gi|162227713|gb|FC402667.1|FC402667
EST:     AGGGGCTTGGCAAGTTTTTGATGCAGTTTCTTGAGTTGATTGCCCGCAAG                         AACGGTATGAAAGCAATGCTCCTGACCTTGCAAAAAAGGAACGTTCGGGCT
genomic: AGGGGCTTGGCAAGTTTTTGATGCAGTTTCTTGAGTTGATTGCCCGCAAGgttggctgtc ... ctgtgtgcagAACGGTATGAAAGCAATGCTCCTGACCTTGCAAAAAAGGAACGTTCGGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgccttgttgctatttgattgctagaatgcctcctattttttgctgtgtgcagAACGGTATGAAAGCAATGCTCCTGACCTTGCAAAAAAGGAACGTTCGGGCTTTGGCTTTCTACACTGGGAAATTAAG
              atttgat  putative branch site (score: 5)
                               cctcctattttttgct  putative PPT
                                    tatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggctgtctaaccctctgtaggtctaacctttcatcaagtttttagttatttctctcatttaagaccatagcttcataaacttgttaattctgcatacctttttggatgcgaagaccggagcgtccataagtagaaccagctgccttgttgctatttgattgctagaatgcctcctattttttgctgtgtgcagAACGGTATGAAAGCAATGCTCCTGACCTTGCAAAAAAGGAACGTTCGGGCTTTGGCTTTCTACACTGGGAAATTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA