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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatatcattggattctcccgtttcatttttttttattttgtaggctgacatttttgtcactgttcataagttccatcgttgtcgagatgacccttaaattgactctggctggtaacgtgtgcagAAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACTACAGGTTCAGTTCTCGTAAGATGAGAAGAGCTTTTTCAGGTTACTGGTC

Basic information

species Physcomitrella patens
transcript PP1S98_36V6.1
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|208398476|gb|DC924746.1|DC924746
EST:     GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTG                         AAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
genomic: GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTGgtaaatatca ... acgtgtgcagAAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
EST: gi|208346548|gb|DC916814.1|DC916814
EST:     GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTG                         AAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
genomic: GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTGgtaaatatca ... acgtgtgcagAAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
EST: gi|208366308|gb|DC943840.1|DC943840
EST:     GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTG                         AAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
genomic: GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTGgtaaatatca ... acgtgtgcagAAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
EST: gi|208363377|gb|DC946975.1|DC946975
EST:     GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTG                         AAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
genomic: GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTGgtaaatatca ... acgtgtgcagAAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
EST: gi|208347378|gb|DC925346.1|DC925346
EST:     GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTG                         AAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
genomic: GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTGgtaaatatca ... acgtgtgcagAAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
EST: gi|208370716|gb|DC948253.1|DC948253
EST:     GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTG                         AAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
genomic: GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTGgtaaatatca ... acgtgtgcagAAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
EST: gi|67698630|gb|BJ958863.1|BJ958863
EST:     GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTG                         AAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
genomic: GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTGgtaaatatca ... acgtgtgcagAAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
EST: gi|208365541|gb|DC954782.1|DC954782
EST:     GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTG                         AAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
genomic: GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTGgtaaatatca ... acgtgtgcagAAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
EST: gi|208368267|gb|DC951519.1|DC951519
EST:     GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTG                         AAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
genomic: GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTGgtaaatatca ... acgtgtgcagAAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
EST: gi|208392853|gb|DC928539.1|DC928539
EST:     GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTG                         AAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
genomic: GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTGgtaaatatca ... acgtgtgcagAAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
EST: gi|208345900|gb|DC921085.1|DC921085
EST:     GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTG                         AAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
genomic: GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTGgtaaatatca ... acgtgtgcagAAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
EST: gi|208373612|gb|DC952437.1|DC952437
EST:     GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTG                         AAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
genomic: GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTGgtaaatatca ... acgtgtgcagAAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
EST: gi|208393705|gb|DC946055.1|DC946055
EST:     GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTG                         AAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
genomic: GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTGgtaaatatca ... acgtgtgcagAAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
EST: gi|208367982|gb|DC951007.1|DC951007
EST:     GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTG                         AAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
genomic: GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTGgtaaatatca ... acgtgtgcagAAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
EST: gi|67579314|gb|BJ951445.1|BJ951445
EST:     CGGAAAATCACGAGTTTTTG                         AAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
genomic: CGGAAAATCACGAGTTTTTGgtaaatatca ... acgtgtgcagAAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
EST: gi|208353455|gb|DC946319.1|DC946319
EST:     GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTG                         AAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
genomic: GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTGgtaaatatca ... acgtgtgcagAAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
EST: gi|208377562|gb|DC922665.1|DC922665
EST:     GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTG                         AAATCCGTGAACTTGGGTGACCTCAAGGCATCATAAGATGAGCGCTAAACT
genomic: GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTGgtaaatatca ... acgtgtgcagAAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
EST: gi|208371846|gb|DC951838.1|DC951838
EST:     GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTG                         AAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT
genomic: GATTTGTTACTGAGTTCTCGCCAATATTGGCGGAAAATCACGAGTTTTTGgtaaatatca ... acgtgtgcagAAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttccatcgttgtcgagatgacccttaaattgactctggctggtaacgtgtgcagAAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACTACAGGTTCAGTTCTCGTAAGATGAGAAGAGCTTTTTCAGGTTACTGGTC
                                        tggtaac  putative branch site (score: 2)
                        ttaaattga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatatcattggattctcccgtttcatttttttttattttgtaggctgacatttttgtcactgttcataagttccatcgttgtcgagatgacccttaaattgactctggctggtaacgtgtgcagAAATCCGTGAACTTGGATGACCTCAAGGCATCATAAGATGAGCGCTAAACTACAGGTTCAGTTCTCGTAAGATGAGAAGAGCTTTTTCAGGTTACTGGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT