Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agactagtcaactttgatactttgatttctatcgaatactcttcgtttttgtagactatgtggggctgattctagcatgctggttgaaattgatcctcagGCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGACGCAATTCATGCAGCTGTGGTTGGAGCTCAGCGCAAGAGTTAGGTGTTG

Basic information

species Physcomitrella patens
transcript PP1S132_95V6.1
intron # 12
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|208385027|gb|DC919707.1|DC919707
EST:     CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGG                         GCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
genomic: CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGGgtacataaaa ... tgatcctcagGCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
EST: gi|162173605|gb|FC349573.1|FC349573
EST:     CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGG                         GCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
genomic: CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGGgtacataaaa ... tgatcctcagGCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
EST: gi|162182166|gb|FC358181.1|FC358181
EST:     CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGG                         GCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
genomic: CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGGgtacataaaa ... tgatcctcagGCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
EST: gi|67726923|gb|BJ977182.1|BJ977182
EST:     CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGG                         GCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
genomic: CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGGgtacataaaa ... tgatcctcagGCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
EST: gi|37831224|gb|BJ589236.1|BJ589236
EST:     CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGG                         GCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
genomic: CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGGgtacataaaa ... tgatcctcagGCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
EST: gi|37851862|gb|BJ609870.1|BJ609870
EST:     CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGG                         GCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
genomic: CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGGgtacataaaa ... tgatcctcagGCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
EST: gi|162196336|gb|FC375406.1|FC375406
EST:     CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAAATGG                         GCGTATAAGTATGGCTGGATTAAG
genomic: CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGGgtacataaaa ... tgatcctcagGCGTATAAGTATGGCTGGATTAAG
EST: gi|37839276|gb|BJ597284.1|BJ597284
EST:     CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGG                         GCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
genomic: CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGGgtacataaaa ... tgatcctcagGCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
EST: gi|208400819|gb|DC925099.1|DC925099
EST:     CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGG                         GNGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
genomic: CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGGgtacataaaa ... tgatcctcagGCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
EST: gi|162267155|gb|FC443386.1|FC443386
EST:     CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGG                         GCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
genomic: CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGGgtacataaaa ... tgatcctcagGCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
EST: gi|208350485|gb|DC926452.1|DC926452
EST:     CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGG                         GCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
genomic: CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGGgtacataaaa ... tgatcctcagGCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
EST: gi|67699338|gb|BJ959571.1|BJ959571
EST:     CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGG                         GCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
genomic: CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGGgtacataaaa ... tgatcctcagGCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
EST: gi|162205457|gb|FC381555.1|FC381555
EST:     CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGG                         GCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
genomic: CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGGgtacataaaa ... tgatcctcagGCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
EST: gi|162196335|gb|FC375405.1|FC375405
EST:     CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGG                         GCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
genomic: CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGGgtacataaaa ... tgatcctcagGCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
EST: gi|162173604|gb|FC349572.1|FC349572
EST:     CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGG                         GCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
genomic: CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGGgtacataaaa ... tgatcctcagGCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
EST: gi|208366377|gb|DC947573.1|DC947573
EST:     CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGG                         GCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
genomic: CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGGgtacataaaa ... tgatcctcagGCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
EST: gi|162175651|gb|FC351238.1|FC351238
EST:     CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGG                         GCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
genomic: CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGGgtacataaaa ... tgatcctcagGCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
EST: gi|162263808|gb|FC438427.1|FC438427
EST:     CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGG                         GCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
genomic: CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGGgtacataaaa ... tgatcctcagGCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
EST: gi|37842485|gb|BJ600493.1|BJ600493
EST:     CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGG                         GCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
genomic: CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGGgtacataaaa ... tgatcctcagGCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
EST: gi|162176138|gb|FC351087.1|FC351087
EST:     CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGG                         GCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA
genomic: CAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGGgtacataaaa ... tgatcctcagGCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGA

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), 30 (downstream exon)
Score: 11

ACGTTCTGAAGCAGATTGGAATGTTCACTTTCACGGGATTGAACAAGTCTCAAGTCGAGTTCATGACCCGTCAATATCACATCTACATGACCTCAGATGGgtacataaaa ... tgatcctcagGCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGACGCAATTCATGCAGCTGTGGTTGGAGCTCAGCGCAAGAGTTAGGTGTTG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgtagactatgtggggctgattctagcatgctggttgaaattgatcctcagGCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGACGCAATTCATGCAGCTGTGGTTGGAGCTCAGCGCAAGAGTTAGGTGTTG
                                          aattgat  putative branch site (score: 11)
                                                tcctc  CT-rich tract
                                      ttgaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agactagtcaactttgatactttgatttctatcgaatactcttcgtttttgtagactatgtggggctgattctagcatgctggttgaaattgatcctcagGCGTATAAGTATGGCTGGATTAAGCAGCAAAACTGTTCCACATTTGGCGGACGCAATTCATGCAGCTGTGGTTGGAGCTCAGCGCAAGAGTTAGGTGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA