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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttacatgcaaaagatgtattcaagtctttgttaaaagggctacttgatatgattgctgtacacgtatgattcactgtaaggttcggttgtgcgattacagGATGGAGATGCAATATTGAGAGAATTAACCTTCAAAAATGTAGAAGACAATGTGAAGAGGCGAGTTGCAAACAAAGCTAGAGCTTACGGTCAGGAAGTTA

Basic information

species Physcomitrella patens
transcript PP1S47_23V6.1
intron # 5
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|37827509|gb|BJ585521.1|BJ585521
EST:     CGAAGTTCATAGAGGATCCTGCGAGGTTNGAGGGCCATATCAAGGCGCAG                         GATGGAGATGCAATATTGAGAGAATTAACCTTCAAAAATGTAGAAGACAAT
genomic: CGAAGTTCATAGAGGATCCTGCGAGGTTTGAGGGCCATATCAAGGCGCAGgtacggtgcc ... gcgattacagGATGGAGATGCAATATTGAGAGAATTAACCTTCAAAAATGTAGAAGACAAT
EST: gi|208382438|gb|DC927972.1|DC927972
EST:     CGAAGTTCATAGAGGATCCTGCGAGGTTTGAGGGCCATATCAAGGCGCAG                         GATGGAGATGCAATATTGAGAGAATTAACCTTCAAAAATGTAGAAGACAAT
genomic: CGAAGTTCATAGAGGATCCTGCGAGGTTTGAGGGCCATATCAAGGCGCAGgtacggtgcc ... gcgattacagGATGGAGATGCAATATTGAGAGAATTAACCTTCAAAAATGTAGAAGACAAT
EST: gi|162223996|gb|FC400354.1|FC400354
EST:     CGAAGTTCATAGAGGATCCTGCGAGGTTTGAGGGCCATATCAAGGCGCAG                         GATGGAGATGCAATATTGAGAGAATTAACCTTCAAAAATGTAGAAGACAAT
genomic: CGAAGTTCATAGAGGATCCTGCGAGGTTTGAGGGCCATATCAAGGCGCAGgtacggtgcc ... gcgattacagGATGGAGATGCAATATTGAGAGAATTAACCTTCAAAAATGTAGAAGACAAT
EST: gi|208352569|gb|DC918278.1|DC918278
EST:     CGAAGTTCATAGAGGATCCTGCGAGGTTTGAGGGCCATATCAAGGCGCAG                         GATGGAGATGCAATATTGAGAGAATTAACCTTCAAAAATGTAGAAGACAAT
genomic: CGAAGTTCATAGAGGATCCTGCGAGGTTTGAGGGCCATATCAAGGCGCAGgtacggtgcc ... gcgattacagGATGGAGATGCAATATTGAGAGAATTAACCTTCAAAAATGTAGAAGACAAT
EST: gi|18335067|gb|BJ167085.1|BJ167085
EST:     CGAAGTTCATAGAGGATCCTGCGAGGTTTGAGGGCCATATCAAGGCGCAG                         GATGGAGATGCAATATTGAGAGAATTAACCTTCAAAAATGTAGAAGACAAT
genomic: CGAAGTTCATAGAGGATCCTGCGAGGTTTGAGGGCCATATCAAGGCGCAGgtacggtgcc ... gcgattacagGATGGAGATGCAATATTGAGAGAATTAACCTTCAAAAATGTAGAAGACAAT
EST: gi|208354231|gb|DC957437.1|DC957437
EST:     CGAAGTTCATAGAGGATCCTGCGAGGTTTGAGGGCCATATCAAGGCGCAG                         GATGGAGATGCAATATTGAGAGAATTAACCTTCAAAAATGTAGAAGACAAT
genomic: CGAAGTTCATAGAGGATCCTGCGAGGTTTGAGGGCCATATCAAGGCGCAGgtacggtgcc ... gcgattacagGATGGAGATGCAATATTGAGAGAATTAACCTTCAAAAATGTAGAAGACAAT
EST: gi|37850774|gb|BJ608782.1|BJ608782
EST:     GAAGTTCATAGAGGGATCCTGCGAGGTTTGAGGGCCATATCAAGGCGCAG                         GATGGAGATGCAATATTGAGAGAATTAACCTTCAAAAATGTAGAAGACAAT
genomic: GAAGTTCATAGA-GGATCCTGCGAGGTTTGAGGGCCATATCAAGGCGCAGgtacggtgcc ... gcgattacagGATGGAGATGCAATATTGAGAGAATTAACCTTCAAAAATGTAGAAGACAAT
EST: gi|18340006|gb|BJ172034.1|BJ172034
EST:     CGAAGTTCATAGAGGATCCTGCGAGGTTTGAGGGCCATATCAAGGCGCAG                         GATGGAGATGCAATATTGAGAGAATTAACCTTCAAAAATGTAGAAGACAAT
genomic: CGAAGTTCATAGAGGATCCTGCGAGGTTTGAGGGCCATATCAAGGCGCAGgtacggtgcc ... gcgattacagGATGGAGATGCAATATTGAGAGAATTAACCTTCAAAAATGTAGAAGACAAT
EST: gi|162223997|gb|FC400355.1|FC400355
EST:     CGAAGTTCATAGAGGATCCTGCGAGGTTTGAGGGCCATATCAAGGCGCAG                         GATGGAGATGCAATATTGAGAGAATTAACCTTCAAAAATGTAGAAGACAAT
genomic: CGAAGTTCATAGAGGATCCTGCGAGGTTTGAGGGCCATATCAAGGCGCAGgtacggtgcc ... gcgattacagGATGGAGATGCAATATTGAGAGAATTAACCTTCAAAAATGTAGAAGACAAT
EST: gi|18332684|gb|BJ164697.1|BJ164697
EST:     TGCGAGGTTTGAGGGCCATATCAAGGCGCAG                         GATGGAGATGCAATATTGAGAGAATTAACCTTCAAAAATGTAGAAGACAAT
genomic: TGCGAGGTTTGAGGGCCATATCAAGGCGCAGgtacggtgcc ... gcgattacagGATGGAGATGCAATATTGAGAGAATTAACCTTCAAAAATGTAGAAGACAAT
EST: gi|208351995|gb|DC925804.1|DC925804
EST:     CGAAGTTCATAGAGGATCCTGCGAGGTTTGAGGGCCATATCAAGGCGCAG                         GATGGAGATGCAATATTGAGAGAATTAACCTTCAAAAATGTAGAAGACAAT
genomic: CGAAGTTCATAGAGGATCCTGCGAGGTTTGAGGGCCATATCAAGGCGCAGgtacggtgcc ... gcgattacagGATGGAGATGCAATATTGAGAGAATTAACCTTCAAAAATGTAGAAGACAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatatgattgctgtacacgtatgattcactgtaaggttcggttgtgcgattacagGATGGAGATGCAATATTGAGAGAATTAACCTTCAAAAATGTAGAAGACAATGTGAAGAGGCGAGTTGCAAACAAAGCTAGAGCTTACGGTCAGGAAGTTA
 acttgat  putative branch site (score: 5)
                   tatgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttacatgcaaaagatgtattcaagtctttgttaaaagggctacttgatatgattgctgtacacgtatgattcactgtaaggttcggttgtgcgattacagGATGGAGATGCAATATTGAGAGAATTAACCTTCAAAAATGTAGAAGACAATGTGAAGAGGCGAGTTGCAAACAAAGCTAGAGCTTACGGTCAGGAAGTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT