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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtaaagtaagtgtaattggccctcagtttgtttcgaatttcatcttatggtttactgtgtgactaagattttcgttatttccttttttaccgaatccagTTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAAGCGTCCAAGTTTCAAGCATTCTCTGGCAGAAAGTATTCCTTGAGGGATT

Basic information

species Physcomitrella patens
transcript PP1S245_32V6.2
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|208380268|gb|DC919104.1|DC919104
EST:     GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAG                         TTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA
genomic: GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAGgtatgatgga ... ccgaatccagTTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA
EST: gi|208373274|gb|DC948562.1|DC948562
EST:     GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAG                         TTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA
genomic: GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAGgtatgatgga ... ccgaatccagTTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA
EST: gi|208393488|gb|DC949650.1|DC949650
EST:     GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAG                         TTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA
genomic: GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAGgtatgatgga ... ccgaatccagTTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA
EST: gi|162206110|gb|FC383103.1|FC383103
EST:     GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAG                         TTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA
genomic: GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAGgtatgatgga ... ccgaatccagTTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA
EST: gi|208395706|gb|DC920268.1|DC920268
EST:     GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAG                         TTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA
genomic: GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAGgtatgatgga ... ccgaatccagTTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA
EST: gi|162206109|gb|FC383102.1|FC383102
EST:     GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAG                         TTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA
genomic: GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAGgtatgatgga ... ccgaatccagTTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA
EST: gi|67691900|gb|BJ952133.1|BJ952133
EST:     GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAG                         TTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA
genomic: GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAGgtatgatgga ... ccgaatccagTTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA
EST: gi|208365926|gb|DC951155.1|DC951155
EST:     GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAG                         TTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA
genomic: GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAGgtatgatgga ... ccgaatccagTTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA
EST: gi|162243302|gb|FC417003.1|FC417003
EST:     GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAG                         TTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA
genomic: GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAGgtatgatgga ... ccgaatccagTTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA
EST: gi|208394989|gb|DC920220.1|DC920220
EST:     GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAG                         TTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA
genomic: GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAGgtatgatgga ... ccgaatccagTTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA
EST: gi|208370760|gb|DC948269.1|DC948269
EST:     GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAG                         TTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA
genomic: GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAGgtatgatgga ... ccgaatccagTTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA
EST: gi|208374165|gb|DC945211.1|DC945211
EST:     GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAG                         TTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA
genomic: GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAGgtatgatgga ... ccgaatccagTTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA
EST: gi|208374981|gb|DC956391.1|DC956391
EST:     GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAG                         TTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA
genomic: GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAGgtatgatgga ... ccgaatccagTTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA
EST: gi|208363142|gb|DC954342.1|DC954342
EST:     GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAG                         TTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA
genomic: GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAGgtatgatgga ... ccgaatccagTTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA
EST: gi|18338628|gb|BJ170652.1|BJ170652
EST:     GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAG                         TTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA
genomic: GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAGgtatgatgga ... ccgaatccagTTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA
EST: gi|208393483|gb|DC949645.1|DC949645
EST:     GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAG                         TTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA
genomic: GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAGgtatgatgga ... ccgaatccagTTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA
EST: gi|208387581|gb|DC953323.1|DC953323
EST:     GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAG                         TTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA
genomic: GAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAGgtatgatgga ... ccgaatccagTTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAA

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: 24

TAGTGTACAGAAGCCCACTGGAACTCCACCTGCAGGAGCACAAAGACCTGGAAAGCTTGTGTTTGGTGGCGGCAGCAGTAATGCACCAGCAGCTGCAAAGgtatgatgga ... ccgaatccagTTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAAGCGTCCAAGTTTCAAGCATTCTCTGGCAGAAAGTATTCCTTGAGGGATT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatggtttactgtgtgactaagattttcgttatttccttttttaccgaatccagTTACCCAGTACAAAGAAAGAGGAGGTCAAGGAAGAAAAGAAAGAGCCTGAAGCGTCCAAGTTTCAAGCATTCTCTGGCAGAAAGTATTCCTTGAGGGATT
                        ttttcgttatttcctt  CT-rich tract
                              ttatttcctttttta  TA-rich tract