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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcctttcagactgagaatatgaatggtgaatttaggatcacaatgtggctttgaaagattgatgacattgatgaattatgtattgattggtctgtgcagGCTGCATATGCCAGAGCAAAAAAAGCTGAATCAACAGCACCTCCACGTGGCTCTGCAAGACCAGGAGGTATGCCAGGATTTCCAGGCGGCATGCCTGCAG

Basic information

species Physcomitrella patens
transcript PP1S9_386V6.2
intron # 8
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|67726410|gb|BJ976669.1|BJ976669
EST:     ACGGCGTGCTGAGGCTCAG                         GCTGCATATGCCAGAGCNNNNNNNGCTGAATCAACAGCACCTCCACGTGGC
genomic: ACGGCGTGCTGAGGCTCAGgttattcagt ... gtctgtgcagGCTGCATATGCCAGAGCAAAAAAAGCTGAATCAACAGCACCTCCACGTGGC
EST: gi|208390138|gb|DC949448.1|DC949448
EST:     ATGAAAAAAGAGCGGCTCGGGAAAGGGAACAACGGCGTGCTGAGGCTCAG                         GCTGCATATGCCAGAGCNNNNNNNGCTGAATCAACAGCACCTCCACGTGGC
genomic: ATGAAAAAAGAGCGGCTCGGGAAAGGGAACAACGGCGTGCTGAGGCTCAGgttattcagt ... gtctgtgcagGCTGCATATGCCAGAGCAAAAAAAGCTGAATCAACAGCACCTCCACGTGGC
EST: gi|208348679|gb|DC926354.1|DC926354
EST:     GGAACAACGGCGTGNTGAGGCTCAG                         GCTGCATATGCCAGAGCNNNNNNNNGCTGAATCAACAGCACCTCCACGTGG
genomic: GGAACAACGGCGTGCTGAGGCTCAGgttattcagt ... gtctgtgcagGCTGCATATGCCAGAGC-AAAAAAAGCTGAATCAACAGCACCTCCACGTGG
EST: gi|37853178|gb|BJ611186.1|BJ611186
EST:     GAACAACGGCGTGCCTGAGGCTCAG                         GCTGCATATGCCAGAGCNNNNNNNNGCTGAATCAACAGCACCTCCACGTGG
genomic: GAACAACGGCGTG-CTGAGGCTCAGgttattcagt ... gtctgtgcagGCTGCATATGCCAGAGC-AAAAAAAGCTGAATCAACAGCACCTCCACGTGG
EST: gi|162275961|gb|FC452029.1|FC452029
EST:     GGGAAAGGGAACAACGGCGTGCTGAGGCTCAG                         GCTGCATATGCCAGAGCNNNNNNNNGCTGAATCAACAGCACCTCCACGTGG
genomic: GGGAAAGGGAACAACGGCGTGCTGAGGCTCAGgttattcagt ... gtctgtgcagGCTGCATATGCCAGAGC-AAAAAAAGCTGAATCAACAGCACCTCCACGTGG
EST: gi|37834841|gb|BJ592853.1|BJ592853
EST:     GAACAACGGCGTGCTGAGGCTCAG                         GCTGCATATGCCAGAGCNNNNNNNGCTGAATCAACAGCACCTCCACGTGGC
genomic: GAACAACGGCGTGCTGAGGCTCAGgttattcagt ... gtctgtgcagGCTGCATATGCCAGAGCAAAAAAAGCTGAATCAACAGCACCTCCACGTGGC
EST: gi|208364064|gb|DC950384.1|DC950384
EST:     ATGNAAAAAGAGCGGCTCGGGAAAGGGAACAACGGCGTGCTGAGGCTCAG                         GCTGCATATGCCAGAGCNNNNNNNGCTGAATCAACAGCACCTCCACGTGGC
genomic: ATGAAAAAAGAGCGGCTCGGGAAAGGGAACAACGGCGTGCTGAGGCTCAGgttattcagt ... gtctgtgcagGCTGCATATGCCAGAGCAAAAAAAGCTGAATCAACAGCACCTCCACGTGGC
EST: gi|162164760|gb|FC340482.1|FC340482
EST:     ATGAAAAAAGAGCGGCTCGGGAAAGGGAACAACGGCGTGCTGAGGCTCAG                         GCTGCATATGCCAGAGCNNNNNNNGCTGAATCAACAGCACCTCCACGTGGC
genomic: ATGAAAAAAGAGCGGCTCGGGAAAGGGAACAACGGCGTGCTGAGGCTCAGgttattcagt ... gtctgtgcagGCTGCATATGCCAGAGCAAAAAAAGCTGAATCAACAGCACCTCCACGTGGC
EST: gi|67727845|gb|BJ978104.1|BJ978104
EST:     ATGAAAAAAGAGCGGCTCGGGAAAGGGAACAACGGCGTGCTGAGGCTCAG                         GCTGCATATGCCAGAGCNNNNNNNNGCTGAATCAACAGCACCTCCACGTGG
genomic: ATGAAAAAAGAGCGGCTCGGGAAAGGGAACAACGGCGTGCTGAGGCTCAGgttattcagt ... gtctgtgcagGCTGCATATGCCAGAGC-AAAAAAAGCTGAATCAACAGCACCTCCACGTGG
EST: gi|208395724|gb|DC924218.1|DC924218
EST:     ATGAAAAAAGAGCGGCTCGGGAAAGGGAACAACGGCGTGCTGAGGCTCAG                         GCTGCGTATGCCAGAGCNNNNNNNGCTGAATCAACAGCACCTCCACGTGGC
genomic: ATGAAAAAAGAGCGGCTCGGGAAAGGGAACAACGGCGTGCTGAGGCTCAGgttattcagt ... gtctgtgcagGCTGCATATGCCAGAGCAAAAAAAGCTGAATCAACAGCACCTCCACGTGGC
EST: gi|208371038|gb|DC955914.1|DC955914
EST:     ATGAAAAAAGAGCGGCTCGGGAAAGGGAACAACGGCGTGCTGAGGCTCAG                         GCTGCATATGCCAGAGCNNNNNNNGCTGAATCAACAGCACCTCCACGTGGC
genomic: ATGAAAAAAGAGCGGCTCGGGAAAGGGAACAACGGCGTGCTGAGGCTCAGgttattcagt ... gtctgtgcagGCTGCATATGCCAGAGCAAAAAAAGCTGAATCAACAGCACCTCCACGTGGC
EST: gi|37840179|gb|BJ598187.1|BJ598187
EST:     ATGAAAAAAGAGCGGCTCGGGAAAGGGAACAACGGCGTGCTGAGGCTCAG                         GCTGCATATGCCAGAGCNNNNNNNNGCTGAATCAACAGCACCTCCACGTGG
genomic: ATGAAAAAAGAGCGGCTCGGGAAAGGGAACAACGGCGTGCTGAGGCTCAGgttattcagt ... gtctgtgcagGCTGCATATGCCAGAGC-AAAAAAAGCTGAATCAACAGCACCTCCACGTGG
EST: gi|208354412|gb|DC926603.1|DC926603
EST:     ATGAAAAAAGAGCGGCTCGGGAAAGGGAACAACGGCGTGCTGAGGCTCAG                         GCTGCATATGCCAGAGCNNNNNNNGCTGAATCAACAGCACCTCCACGTGGC
genomic: ATGAAAAAAGAGCGGCTCGGGAAAGGGAACAACGGCGTGCTGAGGCTCAGgttattcagt ... gtctgtgcagGCTGCATATGCCAGAGCAAAAAAAGCTGAATCAACAGCACCTCCACGTGGC
EST: gi|162168430|gb|FC344107.1|FC344107
EST:     ATGAAAAAAGAGCGGCTCGGGAAAGGGAACAACGGCGTGCTGAGGCTCAG                         GCTGCATATGCCAGAGCNNNNNNNGCTGAATCAACAGCACCTCCACGTGGC
genomic: ATGAAAAAAGAGCGGCTCGGGAAAGGGAACAACGGCGTGCTGAGGCTCAGgttattcagt ... gtctgtgcagGCTGCATATGCCAGAGCAAAAAAAGCTGAATCAACAGCACCTCCACGTGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggctttgaaagattgatgacattgatgaattatgtattgattggtctgtgcagGCTGCATATGCCAGAGCAAAAAAAGCTGAATCAACAGCACCTCCACGTGGCTCTGCAAGACCAGGAGGTATGCCAGGATTTCCAGGCGGCATGCCTGCAG
                                    tattgat  putative branch site (score: 3)
                             aattatgtattgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcctttcagactgagaatatgaatggtgaatttaggatcacaatgtggctttgaaagattgatgacattgatgaattatgtattgattggtctgtgcagGCTGCATATGCCAGAGCAAAAAAAGCTGAATCAACAGCACCTCCACGTGGCTCTGCAAGACCAGGAGGTATGCCAGGATTTCCAGGCGGCATGCCTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG