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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaaacctgtgagttctaggaatctagttttaaaagtgtcaagtatgttgcttacttattgcaagttgtgcttttgtggatccttgaccttttgcgacacATCAATCTACAGCGGAGTGTGGGCCTACCTGAGCTTCGTCGACTTCGTAGAACCTTCCTCAAATTGGCTGGGCAGTCAAGCCTGTCAGGACCTCCTCCAC

Basic information

species Physcomitrella patens
transcript PP1S95_19V6.1
intron # 8
splice site 3'
intron type U12 (go to U12 genes for details)

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|208358831|gb|DC957631.1|DC957631
EST:     GTGTTGGTGGTTTAGTGCGCAGTGTTAATCTGGGAGAAGGACTGCCTATC                         ATCAATCTACAGCGGAGTGTGGGCCTACCTGAGCTTCGTCGACTTCGTAGA
genomic: GTGTTGGTGGTTTAGTGCGCAGTGTTAATCTGGGAGAAGGACTGCCTATCatatccttta ... tttgcgacacATCAATCTACAGCGGAGTGTGGGCCTACCTGAGCTTCGTCGACTTCGTAGA
EST: gi|162227677|gb|FC402345.1|FC402345
EST:     GTGTTGGTGGTTTAGTGCGCAGTGTTAATCTGGGAGAAGGACTGCCTATC                         ATCAATCTACAGCGGAGTGTGGGCCTACCTGAGCTTCGTCGACTTCGTAGA
genomic: GTGTTGGTGGTTTAGTGCGCAGTGTTAATCTGGGAGAAGGACTGCCTATCatatccttta ... tttgcgacacATCAATCTACAGCGGAGTGTGGGCCTACCTGAGCTTCGTCGACTTCGTAGA
EST: gi|162227676|gb|FC402344.1|FC402344
EST:     GTGTTGGTGGTTTAGTGCGCAGTGTTAATCTGGGAGAAGGACTGCCTATC                         ATCAATCTACAGCGGAGTGTGGGCCTACCTGAGCTTCGTCGACTTCGTAGA
genomic: GTGTTGGTGGTTTAGTGCGCAGTGTTAATCTGGGAGAAGGACTGCCTATCatatccttta ... tttgcgacacATCAATCTACAGCGGAGTGTGGGCCTACCTGAGCTTCGTCGACTTCGTAGA
EST: gi|67699340|gb|BJ959573.1|BJ959573
EST:     GTGTTGGTGGTTTAGTGCGCAGTGTTAATCTGGGAGAAGGACTGCCTATC                         ATCAATCTACAGCGGAGTGTGGGCCTACCTGAGCTTCGTCGACTTCGTAGA
genomic: GTGTTGGTGGTTTAGTGCGCAGTGTTAATCTGGGAGAAGGACTGCCTATCatatccttta ... tttgcgacacATCAATCTACAGCGGAGTGTGGGCCTACCTGAGCTTCGTCGACTTCGTAGA
EST: gi|6166785|gb|AW145049.1|AW145049
EST:     GTTTAGTGCGCAGTGTTAATCTGGGAGAAGGACTGCCTATC                         ATCAATCTACAGCGGAGTGTGGGCCTACCTGAGCTTCGTCGACTTCGTAGA
genomic: GTTTAGTGCGCAGTGTTAATCTGGGAGAAGGACTGCCTATCatatccttta ... tttgcgacacATCAATCTACAGCGGAGTGTGGGCCTACCTGAGCTTCGTCGACTTCGTAGA
EST: gi|37830803|gb|BJ588815.1|BJ588815
EST:     GTGTTGGTGGTTTAGTGCGCAGTGTTAATCTGGGAGAAGGACTGCCTATC                         ATCAATCTACAGCGGAGTGTGGGCCTACCTGAGCTTCGTCGACTTCGTAGA
genomic: GTGTTGGTGGTTTAGTGCGCAGTGTTAATCTGGGAGAAGGACTGCCTATCatatccttta ... tttgcgacacATCAATCTACAGCGGAGTGTGGGCCTACCTGAGCTTCGTCGACTTCGTAGA
EST: gi|37853680|gb|BJ611688.1|BJ611688
EST:     GTGTTGGTGGTTTAGTGCGCAGTGTTAATCTGGGAGAAGGACTGCCTATC                         ATCAATCTACAGCGGAGTGTGGGCCTACCTGAGCTTCGTCGACTTCGTAGA
genomic: GTGTTGGTGGTTTAGTGCGCAGTGTTAATCTGGGAGAAGGACTGCCTATCatatccttta ... tttgcgacacATCAATCTACAGCGGAGTGTGGGCCTACCTGAGCTTCGTCGACTTCGTAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgcttacttattgcaagttgtgcttttgtggatccttgaccttttgcgacacATCAATCTACAGCGGAGTGTGGGCCTACCTGAGCTTCGTCGACTTCGTAGAACCTTCCTCAAATTGGCTGGGCAGTCAAGCCTGTCAGGACCTCCTCCAC
                                  atccttgac  putative branch site 
                                          ccttttgc  CT-rich tract
      ttacttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctaaacctgtgagttctaggaatctagttttaaaagtgtcaagtatgttgcttacttattgcaagttgtgcttttgtggatccttgaccttttgcgacacATCAATCTACAGCGGAGTGTGGGCCTACCTGAGCTTCGTCGACTTCGTAGAACCTTCCTCAAATTGGCTGGGCAGTCAAGCCTGTCAGGACCTCCTCCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC