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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttctgattcaatttcgttttctttttttccgtttttgtatcttttgtcatggattttttgatttcaagaattcaccttcattgctttccacgtttcagACCCGTTATTTGCTTCAACCAGAACTTGTGTTGGAGGACGTTAGTCAAGACCATGCACGCAAGACG

Basic information

species Physcomitrella patens
transcript PP1S62_116V6.3
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S62_116V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA12G00830.5 (Glycine max), 3'ss of exon 5
----tcttctgattcaatttcgttttctttttttccgttt--ttgtatcttttgtcatggattttttgatttcaagaattcaccttcattgctttccacgtttcagACCCGTTATTTGCTTCAACCAGAACTTGTGTTGGAGGACGTTAGTCAAGACCATGCACGCAAGACG
    | |||| ||| ||     |  || |||      ||   || |||  ||||        ||  ||||||   || | ||  |||| | |||    |  |  ||    | |  ||  | ||||||||||||||  | || || ||||||||||||||||||||||| |||
attatattctcatttaaccctttcatcatttccaaatttcaattctatactttgcagacttgttactgatttagtgattccatgttcaat-cttgtggcagTCAAG----GATGCTT-TTGCAACCAGAACTTGTTCTTGAAGATGTTAGTCAAGACCATGCACGCAAAACG
















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|208393991|gb|DC928743.1|DC928743
EST:     ACGACCAGTACTATCAAACGCCTCGCGTGTGGCTAACCGGTTATGATGAG                         ACCCGTTATTTGCTTCAACCAGAACTTGTGTTGGAGGACGTTAGTCAAGAC
genomic: ACGACAAGTACTATCAAACGCCTCGCGTGTGGCTAACCGGTTATGATGAGgtacaattgg ... cacgtttcagACCCGTTATTTGCTTCAACCAGAACTTGTGTTGGAGGACGTTAGTCAAGAC
EST: gi|37825564|gb|BJ583630.1|BJ583630
EST:     ACGACAAGTACTATCAAACGCCTCGCGTGTGGCTAACCGGTTATGATGAG                         ACCCGTTATTTGCTTCAACCAGAACTTGTGTTGGAGGACGTTAGTCAAGAC
genomic: ACGACAAGTACTATCAAACGCCTCGCGTGTGGCTAACCGGTTATGATGAGgtacaattgg ... cacgtttcagACCCGTTATTTGCTTCAACCAGAACTTGTGTTGGAGGACGTTAGTCAAGAC
EST: gi|162165647|gb|FC341486.1|FC341486
EST:     AACCGGTTATGATGAG                         ACCCGTTATTTGCTTCAACCAGAACTTGTGTTGGAGGACGTTAGTCAAGAC
genomic: AACCGGTTATGATGAGgtacaattgg ... cacgtttcagACCCGTTATTTGCTTCAACCAGAACTTGTGTTGGAGGACGTTAGTCAAGAC
EST: gi|208396622|gb|DC920358.1|DC920358
EST:     GTTATGATGAG                         ACCCGTTATTTGCTTCAACCAGAACNTGTGTTGGAGGACGTTAGTCAAGAC
genomic: GTTATGATGAGgtacaattgg ... cacgtttcagACCCGTTATTTGCTTCAACCAGAACTTGTGTTGGAGGACGTTAGTCAAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtcatggattttttgatttcaagaattcaccttcattgctttccacgtttcagACCCGTTATTTGCTTCAACCAGAACTTGTGTTGGAGGACGTTAGTCAAGACCATGCACGCAAGACG
            ttttgat  putative branch site (score: 4)
                               ccttcattgctttcc  putative PPT
         attttttgatttcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttctgattcaatttcgttttctttttttccgtttttgtatcttttgtcatggattttttgatttcaagaattcaccttcattgctttccacgtttcagACCCGTTATTTGCTTCAACCAGAACTTGTGTTGGAGGACGTTAGTCAAGACCATGCACGCAAGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA