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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taggtgtgacttttgtactgccgctctggtcttgctgcaatacaagtgtttttgtaaatacacttgcgtcaactctaatgagcccaatttcgcactgcagGTGCTGAGGCAACTTGACGCAGATGCTCAAGCGCTTGAACGGGAACTCAGGGTGGCCAGGGCTGAGCTTGAG

Basic information

species Physcomitrella patens
transcript PP1S9_480V6.2
intron # 3
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|162176764|gb|FC353311.1|FC353311
EST:     ATCGCATCGCTTATAGAACCATGAAAGGGTTAGATGATTCCGGAAGCAGA                         GTGCTGAGGCAACTTGACGCAGATGCTCAAGCGCTTGAACGGGAACTCAGG
genomic: ATCGCATCGCTTATAGAACCATGAAAGGGTTAGATGATTCCGGAAGCAGAgtgagtaaca ... cgcactgcagGTGCTGAGGCAACTTGACGCAGATGCTCAAGCGCTTGAACGGGAACTCAGG
EST: gi|162175773|gb|FC352075.1|FC352075
EST:     ATCGCATCGCTTATAGAACCATGAAAGGGTTAGATGATTCCGGAAGCAGA                         GTGCTGAGGCAACTTGACGCAGATGCTCAAGCGCTTGAACGGGAACTCAGG
genomic: ATCGCATCGCTTATAGAACCATGAAAGGGTTAGATGATTCCGGAAGCAGAgtgagtaaca ... cgcactgcagGTGCTGAGGCAACTTGACGCAGATGCTCAAGCGCTTGAACGGGAACTCAGG
EST: gi|100385240|gb|BY950832.1|BY950832
EST:     ATCGCATCGCTTATAGAACCATGAAAGGGT-AGATGATTCCGGAAGCAGA                         GTGCTGAGGCNACTTGACGCAGATGCTCAAGCGCTTGAACGGG
genomic: ATCGCATCGCTTATAGAACCATGAAAGGGTTAGATGATTCCGGAAGCAGAgtgagtaaca ... cgcactgcagGTGCTGAGGCAACTTGACGCAGATGCTCAAGCGCTTGAACGGG
EST: gi|162184006|gb|FC359376.1|FC359376
EST:     ATCGCATCGCTTATAGAACCATGAAAGGGTTAGATGATTCCGGAAGCAGA                         GTGCTGAGGCAACTTGACGCAGATGCTCAAGCGCTTGAACGGGAACTCAGG
genomic: ATCGCATCGCTTATAGAACCATGAAAGGGTTAGATGATTCCGGAAGCAGAgtgagtaaca ... cgcactgcagGTGCTGAGGCAACTTGACGCAGATGCTCAAGCGCTTGAACGGGAACTCAGG
EST: gi|162175772|gb|FC352074.1|FC352074
EST:     ATCGCATCGCTTATAGAACCATGAAAGGGTTAGATGATTCCGGAAGCAGA                         GTGCTGAGGCAACTTGACGCAGATGCTCAAGCGCTTGAACGGGAACTCAGG
genomic: ATCGCATCGCTTATAGAACCATGAAAGGGTTAGATGATTCCGGAAGCAGAgtgagtaaca ... cgcactgcagGTGCTGAGGCAACTTGACGCAGATGCTCAAGCGCTTGAACGGGAACTCAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtttttgtaaatacacttgcgtcaactctaatgagcccaatttcgcactgcagGTGCTGAGGCAACTTGACGCAGATGCTCAAGCGCTTGAACGGGAACTCAGGGTGGCCAGGGCTGAGCTTGAG
                           ctctaat  putative branch site (score: 3)
     tttgtaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taggtgtgacttttgtactgccgctctggtcttgctgcaatacaagtgtttttgtaaatacacttgcgtcaactctaatgagcccaatttcgcactgcagGTGCTGAGGCAACTTGACGCAGATGCTCAAGCGCTTGAACGGGAACTCAGGGTGGCCAGGGCTGAGCTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT