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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatggcgcgctacgatcagagttcttggagttgatcagctcattgattttgtggttgatggtgtaatgttgatcgaggttttgtaattgtgttggtcagATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGGTGAATCCGAACGGATGCCGAAACAGCTTGTTGAAGCTCTTGGCATCCTT

Basic information

species Physcomitrella patens
transcript PP1S49_154V6.1
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|208363600|gb|DC939777.1|DC939777
EST:     TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCG                         ATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
genomic: TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCGgtgcgtgtgg ... tgttggtcagATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
EST: gi|100377587|gb|BY986312.1|BY986312
EST:     TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCG                         ATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
genomic: TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCGgtgcgtgtgg ... tgttggtcagATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
EST: gi|18351239|gb|BJ183291.1|BJ183291
EST:     TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCG                         ATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
genomic: TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCGgtgcgtgtgg ... tgttggtcagATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
EST: gi|18365619|gb|BJ197696.1|BJ197696
EST:     TTCAGGGAGGAGCGGGACACCTTTGGCCTCATTCAAGTCCCCAATGACCG                         ATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
genomic: TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCGgtgcgtgtgg ... tgttggtcagATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
EST: gi|18372221|gb|BJ203823.1|BJ203823
EST:     TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCG                         ATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
genomic: TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCGgtgcgtgtgg ... tgttggtcagATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
EST: gi|18374173|gb|BJ205751.1|BJ205751
EST:     TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCG                         ATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
genomic: TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCGgtgcgtgtgg ... tgttggtcagATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
EST: gi|18367708|gb|BJ199791.1|BJ199791
EST:     TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCG                         ATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
genomic: TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCGgtgcgtgtgg ... tgttggtcagATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
EST: gi|18362649|gb|BJ194720.1|BJ194720
EST:     TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCG                         ATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
genomic: TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCGgtgcgtgtgg ... tgttggtcagATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
EST: gi|208358694|gb|DC942916.1|DC942916
EST:     TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCG                         ATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
genomic: TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCGgtgcgtgtgg ... tgttggtcagATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
EST: gi|18372136|gb|BJ203738.1|BJ203738
EST:     TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCG                         ATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
genomic: TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCGgtgcgtgtgg ... tgttggtcagATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
EST: gi|18326303|gb|BJ158302.1|BJ158302
EST:     TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCG                         ATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
genomic: TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCGgtgcgtgtgg ... tgttggtcagATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
EST: gi|18327256|gb|BJ159258.1|BJ159258
EST:     TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCG                         ATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
genomic: TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCGgtgcgtgtgg ... tgttggtcagATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
EST: gi|18343443|gb|BJ175481.1|BJ175481
EST:     TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCG                         ATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
genomic: TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCGgtgcgtgtgg ... tgttggtcagATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
EST: gi|18370151|gb|BJ201753.1|BJ201753
EST:     TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCG                         ATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
genomic: TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCGgtgcgtgtgg ... tgttggtcagATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
EST: gi|18364496|gb|BJ196569.1|BJ196569
EST:     TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCG                         ATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
genomic: TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCGgtgcgtgtgg ... tgttggtcagATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
EST: gi|18373951|gb|BJ205529.1|BJ205529
EST:     TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCG                         ATACTGGGGTGCTCANACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
genomic: TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCGgtgcgtgtgg ... tgttggtcagATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
EST: gi|18366250|gb|BJ198328.1|BJ198328
EST:     TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCG                         ATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
genomic: TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCGgtgcgtgtgg ... tgttggtcagATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
EST: gi|18373779|gb|BJ205357.1|BJ205357
EST:     TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCG                         ATACTGGGGTGCTCANACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG
genomic: TTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCGgtgcgtgtgg ... tgttggtcagATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 27 (upstream exon), 29 (downstream exon)
Score: 6

CGCGCAATTTCACCTTCCAATTCGTCCGCTCTCTCACAGGCGGAGGTGGATTCAGGGAGGAGCGTGACACCTTTGGCCTCATTCAAGTCCCCAATGACCGgtgcgtgtgg ... tgttggtcagATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGGTGAATCCGAACGGATGCCGAAACAGCTTGTTGAAGCTCTTGGCATCCTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattttgtggttgatggtgtaatgttgatcgaggttttgtaattgtgttggtcagATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGGTGAATCCGAACGGATGCCGAAACAGCTTGTTGAAGCTCTTGGCATCCTT
                      tgttgat  putative branch site (score: 6)
                                  ttttgtaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatggcgcgctacgatcagagttcttggagttgatcagctcattgattttgtggttgatggtgtaatgttgatcgaggttttgtaattgtgttggtcagATACTGGGGTGCTCAGACTCAAAGATCTGTACAGAATTTTGAGATTGGGGGTGAATCCGAACGGATGCCGAAACAGCTTGTTGAAGCTCTTGGCATCCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC