Skip to another splice site:
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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttctggtgttcaatcagcttggaaatgtgcttggctgtcgggtaagctcgtattccagcgagatatctgatcgatcgtttgtgaagatcccgtttgcagACATTGTTGTAGATAACTGCGCCATCTGCCGCAACCATATCATGGACCTGTGTATTGAGTGCCAAGCAAATCAAGCTAGTGCAACGAGCGAGGAGTGTAC

Basic information

species Physcomitrella patens
transcript PP1S42_194V6.1
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|22133119|gb|BQ827553.1|BQ827553
EST:     GAAGCGTTTCGAGATCAAGAAGTGGAATGCTGTGGCTCTTTGGGCATGGG                         ACATTGTTGTAGATAACTGCGCCATCTGCCGCAACCATATCATGGACCTGT
genomic: GAAGCGTTTCGAGATCAAGAAGTGGAATGCTGTGGCTCTTTGGGCATGGGgtaagcgtgc ... ccgtttgcagACATTGTTGTAGATAACTGCGCCATCTGCCGCAACCATATCATGGACCTGT
EST: gi|208373556|gb|DC941111.1|DC941111
EST:     GAAGCGTTTCGAGATCAAGAAGTGGAATGCTGTGGCTCTTTGGGCATGGG                         ACATTGTTGTAGATAACTGCGCCATCTGCCGCAACCATATCATGGACCTGT
genomic: GAAGCGTTTCGAGATCAAGAAGTGGAATGCTGTGGCTCTTTGGGCATGGGgtaagcgtgc ... ccgtttgcagACATTGTTGTAGATAACTGCGCCATCTGCCGCAACCATATCATGGACCTGT
EST: gi|18356397|gb|BJ188456.1|BJ188456
EST:     GAAGCGTTTCGAGATCAAGAAGTGGAATGCTGTGGCTCTTTGGGCAT-GG                         ACATTGCTGTAGATAACTGCGCCATCTGCCGCAACCATATCATGGACCTGT
genomic: GAAGCGTTTCGAGATCAAGAAGTGGAATGCTGTGGCTCTTTGGGCATGGGgtaagcgtgc ... ccgtttgcagACATTGTTGTAGATAACTGCGCCATCTGCCGCAACCATATCATGGACCTGT
EST: gi|37833333|gb|BJ591345.1|BJ591345
EST:     GAAGCGTTTCGAGATCAAGAAGTGGAATGCTGTGGCTCTTTGGGCAT-GG                         ACATTGCTGTAGATAACTGCGCCATCTGCCGCAACCATATCATGGACCTGT
genomic: GAAGCGTTTCGAGATCAAGAAGTGGAATGCTGTGGCTCTTTGGGCATGGGgtaagcgtgc ... ccgtttgcagACATTGTTGTAGATAACTGCGCCATCTGCCGCAACCATATCATGGACCTGT
EST: gi|37837666|gb|BJ595674.1|BJ595674
EST:     GAAGCGTTTCGAGATCAAGAAGTGGAATGCTGTGGCTCTTTGGGCATGGG                         ACATTGTTGTAGATAACTGCGCCATCTGCCGCAACCATATCATGGACCTGT
genomic: GAAGCGTTTCGAGATCAAGAAGTGGAATGCTGTGGCTCTTTGGGCATGGGgtaagcgtgc ... ccgtttgcagACATTGTTGTAGATAACTGCGCCATCTGCCGCAACCATATCATGGACCTGT
EST: gi|208360939|gb|DC954109.1|DC954109
EST:     GAAGCGTTTCGAGATCAAGAAGTGGAATGCTGTGGCTCTTTGGGCATGGG                         ACATTGTTGTAGATAACTGCGCCATCTGCCGCAACCATATCATGGACCTGT
genomic: GAAGCGTTTCGAGATCAAGAAGTGGAATGCTGTGGCTCTTTGGGCATGGGgtaagcgtgc ... ccgtttgcagACATTGTTGTAGATAACTGCGCCATCTGCCGCAACCATATCATGGACCTGT
EST: gi|37838351|gb|BJ596359.1|BJ596359
EST:     GAAGCGTTTCGAGATCAAGAAGTGGAATGCTGTGGCTCTTTGGGCATGGG                         ACATTGTTGTAGATAACTGCGCCAGCTGCCGCAACCATATCATGGACCTGT
genomic: GAAGCGTTTCGAGATCAAGAAGTGGAATGCTGTGGCTCTTTGGGCATGGGgtaagcgtgc ... ccgtttgcagACATTGTTGTAGATAACTGCGCCATCTGCCGCAACCATATCATGGACCTGT
EST: gi|18360634|gb|BJ192697.1|BJ192697
EST:     GAAGCGTTTCGAGATCAAGAAGTGGAATGCTGTGGCTCTTTGGGCATGGG                         ACATTGTTGTAGATAACTGCGCCATCTGCCGCAACCATATCATGGACCTGT
genomic: GAAGCGTTTCGAGATCAAGAAGTGGAATGCTGTGGCTCTTTGGGCATGGGgtaagcgtgc ... ccgtttgcagACATTGTTGTAGATAACTGCGCCATCTGCCGCAACCATATCATGGACCTGT
EST: gi|67717589|gb|BJ967848.1|BJ967848
EST:     GAAGCGTTTCGAGATCAAGAAGTGGAATGCTGTGGCTCTTTGGGCATGGG                         ACATTGTTGTAGATAACTGCGCCATCTGCCGCAACCATATCATGGACCTGT
genomic: GAAGCGTTTCGAGATCAAGAAGTGGAATGCTGTGGCTCTTTGGGCATGGGgtaagcgtgc ... ccgtttgcagACATTGTTGTAGATAACTGCGCCATCTGCCGCAACCATATCATGGACCTGT
EST: gi|67726104|gb|BJ976363.1|BJ976363
EST:     GAAGCGTTTCGAGATCAAGAAGTGGAATGCTGTGGCTCTTTGGGCATGGG                         ACATTGTTGTAGATAACTGCGCCATCTGCCGCAACCATATCATGGACCTGT
genomic: GAAGCGTTTCGAGATCAAGAAGTGGAATGCTGTGGCTCTTTGGGCATGGGgtaagcgtgc ... ccgtttgcagACATTGTTGTAGATAACTGCGCCATCTGCCGCAACCATATCATGGACCTGT
EST: gi|37852674|gb|BJ610682.1|BJ610682
EST:     GAAGCGTTTCGAGATCAAGAAGTGGAATGCTGTGGCTCTTTGGGCATGGG                         ACATTGTTGTAGATAACTGCGCCATCTGCCGCAACCATATCATGGACCTGT
genomic: GAAGCGTTTCGAGATCAAGAAGTGGAATGCTGTGGCTCTTTGGGCATGGGgtaagcgtgc ... ccgtttgcagACATTGTTGTAGATAACTGCGCCATCTGCCGCAACCATATCATGGACCTGT
EST: gi|162220969|gb|FC396154.1|FC396154
EST:     GAAGCGTTTCGAGATCAAGAAGTGGAATGCTGTGGCTCTTTGGGCATGGG                         ACATTGTTGTAGATAACTGCGCCATCTGCCGCAACCATATCATGGACCTGT
genomic: GAAGCGTTTCGAGATCAAGAAGTGGAATGCTGTGGCTCTTTGGGCATGGGgtaagcgtgc ... ccgtttgcagACATTGTTGTAGATAACTGCGCCATCTGCCGCAACCATATCATGGACCTGT
EST: gi|162220970|gb|FC396155.1|FC396155
EST:     GAAGCGTTTCGAGATCAAGAAGTGGAATGCTGTGGCTCTTTGGGCATGGG                         ACATTGTTGTAGATAACTGCGCCATCTGCCGCAACCATATCATGGACCTGT
genomic: GAAGCGTTTCGAGATCAAGAAGTGGAATGCTGTGGCTCTTTGGGCATGGGgtaagcgtgc ... ccgtttgcagACATTGTTGTAGATAACTGCGCCATCTGCCGCAACCATATCATGGACCTGT
EST: gi|162269226|gb|FC444756.1|FC444756
EST:     GAAGCGTTTCGAGATCAAGAAGTGGAATGCTGTGGCTCTTTGGGCATGGG                         ACATTGTTGTAGATAACTGCGCCATCTGCCGCAACCATATCATGGACCTGT
genomic: GAAGCGTTTCGAGATCAAGAAGTGGAATGCTGTGGCTCTTTGGGCATGGGgtaagcgtgc ... ccgtttgcagACATTGTTGTAGATAACTGCGCCATCTGCCGCAACCATATCATGGACCTGT
EST: gi|15729090|gb|BI741132.1|BI741132
EST:     GCTCTTTGGGCATGGG                         ACATTGTTGTAGATAATTGCGCCATTTGCCGCAACCATATCATGGACCTGT
genomic: GCTCTTTGGGCATGGGgtaagcgtgc ... ccgtttgcagACATTGTTGTAGATAACTGCGCCATCTGCCGCAACCATATCATGGACCTGT

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: 35 (upstream exon), 35 (downstream exon)
Score: 18

GGTGAGGGCTCCGGCGCCGGAGCAAGCTCCAGTGCGGTCTCGAAGCGTCCGAAGCGTTTCGAGATCAAGAAGTGGAATGCTGTGGCTCTTTGGGCATGGGgtaagcgtgc ... ccgtttgcagACATTGTTGTAGATAACTGCGCCATCTGCCGCAACCATATCATGGACCTGTGTATTGAGTGCCAAGCAAATCAAGCTAGTGCAACGAGCGAGGAGTGTAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctcgtattccagcgagatatctgatcgatcgtttgtgaagatcccgtttgcagACATTGTTGTAGATAACTGCGCCATCTGCCGCAACCATATCATGGACCTGTGTATTGAGTGCCAAGCAAATCAAGCTAGTGCAACGAGCGAGGAGTGTAC
                    atctgat  putative branch site (score: 18)
                                           tcccgttt  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttctggtgttcaatcagcttggaaatgtgcttggctgtcgggtaagctcgtattccagcgagatatctgatcgatcgtttgtgaagatcccgtttgcagACATTGTTGTAGATAACTGCGCCATCTGCCGCAACCATATCATGGACCTGTGTATTGAGTGCCAAGCAAATCAAGCTAGTGCAACGAGCGAGGAGTGTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG