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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtagatacactaatcgtgaaacagaagagagctccccacgaattcagagacacgaatgtctctcactctcgatttgatattctcttgtaatgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAGCGCTTGCTTATGGTACAATCGCAGCAACGATGCTGGTTGGACTCGCCAA

Basic information

species Physcomitrella patens
transcript PP1S485_2V6.1
intron # 1
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|18354959|gb|BJ187018.1|BJ187018
EST:     GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAGgtgaaccttg ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|100400045|gb|BY990751.1|BY990751
EST:     GCCACGAGAGCCAAAGCTCGCACGTCCTTATCA---T----TT--TA-AG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAGgtgaaccttg ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|208350029|gb|DC910264.1|DC910264
EST:     GCCACGAGAGCCAAAGCTCGCACGTCCTTATCA---T----TT--TA-AG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAGgtgaaccttg ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|208383770|gb|DC911480.1|DC911480
EST:     GCCACGAGAGCCAAAGCTCGCACGTCCTTATCA---T----TT--TA-AG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAGgtgaaccttg ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|162270839|gb|FC446868.1|FC446868
EST:     GCCACGAGAGCCAAAGCTCGCACGTCCTTATCA---T----TT--TA-AG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAGgtgaaccttg ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|18365780|gb|BJ197858.1|BJ197858
EST:     GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAGgtgaaccttg ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|100421006|gb|BY993569.1|BY993569
EST:     GCCACGAGAGCCAAAGCTCGCACGTCCTTATCA---T----TT--TA-AG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAGgtgaaccttg ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|18356091|gb|BJ188150.1|BJ188150
EST:     GCCACGAGAGCCAAAGCTCGCACGTCCTTATCA---T----TT--TA-AG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAGgtgaaccttg ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|162208832|gb|FC384968.1|FC384968
EST:     GCCACGAGAGCCAAAGCTCGCACGTCCTTAACATTTTAAGGTTAATAAAG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTGGTGTAAACGTCAATTTAG
genomic: GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAGgtgaaccttg ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|208388919|gb|DC932947.1|DC932947
EST:     GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAGgtgaaccttg ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|100401340|gb|BY990953.1|BY990953
EST:     GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAGgtgaaccttg ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|18368542|gb|BJ200627.1|BJ200627
EST:     GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAGgtgaaccttg ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|18343504|gb|BJ175542.1|BJ175542
EST:     GCCACGAGAGCCAAAGCTCGCACGTCCTTATCA---T----TT--TA-AG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAGgtgaaccttg ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|100410297|gb|BY992036.1|BY992036
EST:     GCCACGAGAGCCAAAGCTCGCACGTCCTTATCA---T----TT--TA-AG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAGgtgaaccttg ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|18368327|gb|BJ200412.1|BJ200412
EST:     GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAGgtgaaccttg ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|208377449|gb|DC906676.1|DC906676
EST:     AAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: AAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAGgtgaaccttg ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|100419722|gb|BY957690.1|BY957690
EST:     GCCACGAGAGCCAAAGCTCGCACGTCCTTATCA---T----TT--TA-AG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAGgtgaaccttg ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|18361207|gb|BJ193272.1|BJ193272
EST:     GCCACGAGAGCCAAAGCTCGCACGTCCTTATCA---T----TT--TA-AG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAGgtgaaccttg ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|100431820|gb|BY978522.1|BY978522
EST:     GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAGgtgaaccttg ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|100415879|gb|BY956969.1|BY956969
EST:     GCCACGAGAGCCAAAGCTCGCACGTCCTTATCA---T----TT--TA-AG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAGgtgaaccttg ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|208383925|gb|DC907316.1|DC907316
EST:     GCCACGAGAGCCAAAGCTCGCACGTCCTTATCA---T----TT--TA-AG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAGgtgaaccttg ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|100361681|gb|BY947769.1|BY947769
EST:     GCCACGAGAGCCAAAGCTCGCACGTCCTTATCA---T----TT--TA-AG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAGgtgaaccttg ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|100357038|gb|BY983663.1|BY983663
EST:     GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAGgtgaaccttg ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|18351413|gb|BJ183465.1|BJ183465
EST:     GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAGgtgaaccttg ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|100379676|gb|BY949888.1|BY949888
EST:     GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAGgtgaaccttg ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|208348000|gb|DC905323.1|DC905323
EST:     GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: GCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAGgtgaaccttg ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagagacacgaatgtctctcactctcgatttgatattctcttgtaatgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAGCGCTTGCTTATGGTACAATCGCAGCAACGATGCTGGTTGGACTCGCCAA
                           atttgatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtagatacactaatcgtgaaacagaagagagctccccacgaattcagagacacgaatgtctctcactctcgatttgatattctcttgtaatgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAGCGCTTGCTTATGGTACAATCGCAGCAACGATGCTGGTTGGACTCGCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG