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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcctgtcattgccttctaaaaaccctgaaacagaagttgaatctctagttatctttcaaaaggtacgctactgactacggaaattgatgtttgttgcagGGCAACTTTAACCTGTCTGATCATAGTCTTGCTATACATCATCATTTCGTTCTTTTGTGGTGGAATTTTTCTTCGAGGCTGCCGAGGATAAAAACGTTTA

Basic information

species Physcomitrella patens
transcript PP1S115_125V6.4
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|37832285|gb|BJ590297.1|BJ590297
EST:     CAGTCACGCCAATTGAAACAAGCCATGTGGATGAAGAATGCCAAGCTCTT                         GGCAACTTTAACCTGTCTGATCATAGTCTTGCTATACATCATCATTTCGTT
genomic: CAGTCACGCCAATTGAAACAAGCCATGTGGATGAAGAATGCCAAGCTCTTgtgagttctt ... tttgttgcagGGCAACTTTAACCTGTCTGATCATAGTCTTGCTATACATCATCATTTCGTT
EST: gi|37842940|gb|BJ600948.1|BJ600948
EST:     CAGTCACGCCAATTGAAACAAGCCATGTGGATGAAGAATGCCAAGCTCTT                         GGCAACTTTAACCTGTCTGATCATAGTCTTGCTATGCATCATCATTTCGTT
genomic: CAGTCACGCCAATTGAAACAAGCCATGTGGATGAAGAATGCCAAGCTCTTgtgagttctt ... tttgttgcagGGCAACTTTAACCTGTCTGATCATAGTCTTGCTATACATCATCATTTCGTT
EST: gi|162274387|gb|FC450414.1|FC450414
EST:     CAGTCACGCCAATTGAAACAAGCCATGTGGATGAAGAATGCCAAGCTCTT                         GGCAACTTTAACCTGTCTGATCATAGTCTTGCTATACATCATCATTTCGTT
genomic: CAGTCACGCCAATTGAAACAAGCCATGTGGATGAAGAATGCCAAGCTCTTgtgagttctt ... tttgttgcagGGCAACTTTAACCTGTCTGATCATAGTCTTGCTATACATCATCATTTCGTT
EST: gi|100393349|gb|BY989833.1|BY989833
EST:     CAGTCACGCCAATTGAAACAAGCCATGTGGATGAAGAATGCCAAGCTCTT                         GGCAACTTTAACCTGTCTGATCATAGTCTTGCTATACATCATCATTTCGTT
genomic: CAGTCACGCCAATTGAAACAAGCCATGTGGATGAAGAATGCCAAGCTCTTgtgagttctt ... tttgttgcagGGCAACTTTAACCTGTCTGATCATAGTCTTGCTATACATCATCATTTCGTT
EST: gi|162170117|gb|FC347029.1|FC347029
EST:     CAGTCACGCCAATTGAAACAAGCCATGTGGATGAAGAATGCCAAGCTCTT                         GGCAACTTTAACCTGTCTGATCATAGTCTTGGTATACATCATCATTTCGTT
genomic: CAGTCACGCCAATTGAAACAAGCCATGTGGATGAAGAATGCCAAGCTCTTgtgagttctt ... tttgttgcagGGCAACTTTAACCTGTCTGATCATAGTCTTGCTATACATCATCATTTCGTT
EST: gi|208375135|gb|DC944860.1|DC944860
EST:     CAGTCACGCCAATTGAAACAAGCCATGTGGATGAAGAATGCCAAGCTCTT                         GGCAACTTTAACCTGTCTGATCATAGTCTTGCTATACATCATCATTTCGTT
genomic: CAGTCACGCCAATTGAAACAAGCCATGTGGATGAAGAATGCCAAGCTCTTgtgagttctt ... tttgttgcagGGCAACTTTAACCTGTCTGATCATAGTCTTGCTATACATCATCATTTCGTT
EST: gi|37852861|gb|BJ610869.1|BJ610869
EST:     CAGTCACGCCAATTGAAACAAGCCATGTGGATGAAGAATGCCAAGCTCTT                         GGCAACTTTAACCTGTCTGATCATAGTCTTGCTATGCATCATCATTTCGTT
genomic: CAGTCACGCCAATTGAAACAAGCCATGTGGATGAAGAATGCCAAGCTCTTgtgagttctt ... tttgttgcagGGCAACTTTAACCTGTCTGATCATAGTCTTGCTATACATCATCATTTCGTT
EST: gi|37850241|gb|BJ608249.1|BJ608249
EST:     CAGTCACGCCAATTGAAACAAGCCATGTGGATGAAGAATGCCAAGCTCTT                         GGCAACTTTAACCTGTCTGATCATAGTCTTGCTATACATCATCATTTCGTT
genomic: CAGTCACGCCAATTGAAACAAGCCATGTGGATGAAGAATGCCAAGCTCTTgtgagttctt ... tttgttgcagGGCAACTTTAACCTGTCTGATCATAGTCTTGCTATACATCATCATTTCGTT
EST: gi|162170465|gb|FC347637.1|FC347637
EST:     CAGTCACGCCAATTGAAACAAGCCATGTGGATGAAGAATGCCAAGCTCTT                         GGCAACTTTAACCTGTCTGATCATAGTCTTGCTATACATCATCATTTCGTT
genomic: CAGTCACGCCAATTGAAACAAGCCATGTGGATGAAGAATGCCAAGCTCTTgtgagttctt ... tttgttgcagGGCAACTTTAACCTGTCTGATCATAGTCTTGCTATACATCATCATTTCGTT
EST: gi|37852406|gb|BJ610414.1|BJ610414
EST:     CAGTCACGCCAATTGAAACAAGCCATGTGGATGAAGAATGCCAAGCTCTT                         GGCAACTTTAACCTGTCTGATCATAGTCTTGCTATACATCATCATTTCGTT
genomic: CAGTCACGCCAATTGAAACAAGCCATGTGGATGAAGAATGCCAAGCTCTTgtgagttctt ... tttgttgcagGGCAACTTTAACCTGTCTGATCATAGTCTTGCTATACATCATCATTTCGTT
EST: gi|37845521|gb|BJ603529.1|BJ603529
EST:     CAGTCACGCCAATTGAAACAAGCCATGTGGATGAAGAATGCCAAGCTCTT                         GGCAACTTTAACCTGTCTGATCATAGTCTTGCTATACATCATCATTTCGTT
genomic: CAGTCACGCCAATTGAAACAAGCCATGTGGATGAAGAATGCCAAGCTCTTgtgagttctt ... tttgttgcagGGCAACTTTAACCTGTCTGATCATAGTCTTGCTATACATCATCATTTCGTT
EST: gi|37844806|gb|BJ602814.1|BJ602814
EST:     CAGTCACGCCAATTGAAACAAGCCATGTGGATGAAGAATGCCAAGCTCTT                         GGCAACTTTAACCTGTCTGATCATAGTCTTGCTATACATCATCATTTCGTT
genomic: CAGTCACGCCAATTGAAACAAGCCATGTGGATGAAGAATGCCAAGCTCTTgtgagttctt ... tttgttgcagGGCAACTTTAACCTGTCTGATCATAGTCTTGCTATACATCATCATTTCGTT
EST: gi|18335867|gb|BJ167888.1|BJ167888
EST:     CAGTCACGCCAATTGAAACAAGCCATGTGGATGAAGAATGCCAAGCTCTT                         GGCAACTTTAACCTGTCTGATCATAGTCTTGCTATACATCATCATTTCGTT
genomic: CAGTCACGCCAATTGAAACAAGCCATGTGGATGAAGAATGCCAAGCTCTTgtgagttctt ... tttgttgcagGGCAACTTTAACCTGTCTGATCATAGTCTTGCTATACATCATCATTTCGTT
EST: gi|7207413|gb|AW561415.1|AW561415
EST:     CAGTCACGCCAATTGAAACAAGCCATGTGGATGAAGAATGCCAAGCTCTT                         GGCAACTTTAACCTGTCTGATCATAGTCTTGCTATACATCATCATTTCGTT
genomic: CAGTCACGCCAATTGAAACAAGCCATGTGGATGAAGAATGCCAAGCTCTTgtgagttctt ... tttgttgcagGGCAACTTTAACCTGTCTGATCATAGTCTTGCTATACATCATCATTTCGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagttatctttcaaaaggtacgctactgactacggaaattgatgtttgttgcagGGCAACTTTAACCTGTCTGATCATAGTCTTGCTATACATCATCATTTCGTTCTTTTGTGGTGGAATTTTTCTTCGAGGCTGCCGAGGATAAAAACGTTTA
         tttcaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcctgtcattgccttctaaaaaccctgaaacagaagttgaatctctagttatctttcaaaaggtacgctactgactacggaaattgatgtttgttgcagGGCAACTTTAACCTGTCTGATCATAGTCTTGCTATACATCATCATTTCGTTCTTTTGTGGTGGAATTTTTCTTCGAGGCTGCCGAGGATAAAAACGTTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT