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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccaatccctcgattctgcagctactttttcatgtgttttgttcaattagattcagcaggtcgtgtgatattaaccgattgaagccctgatatctggatggttcctggctttgtaaatctacagGGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG

Basic information

species Physcomitrella patens
transcript PP1S41_70V6.1
intron # 5
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|18334808|gb|BJ166825.1|BJ166825
EST:     CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAG                         GGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG
genomic: CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAGgtatccaatc ... aaatctacagGGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG
EST: gi|18326829|gb|BJ158829.1|BJ158829
EST:     CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAG                         GGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG
genomic: CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAGgtatccaatc ... aaatctacagGGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG
EST: gi|208372651|gb|DC944630.1|DC944630
EST:     CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAG                         GGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG
genomic: CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAGgtatccaatc ... aaatctacagGGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG
EST: gi|208353940|gb|DC930094.1|DC930094
EST:     CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAG                         GGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG
genomic: CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAGgtatccaatc ... aaatctacagGGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG
EST: gi|162241394|gb|FC418559.1|FC418559
EST:     CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAG                         GGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG
genomic: CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAGgtatccaatc ... aaatctacagGGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG
EST: gi|162244584|gb|FC423446.1|FC423446
EST:     CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAG                         GGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG
genomic: CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAGgtatccaatc ... aaatctacagGGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG
EST: gi|67721131|gb|BJ971390.1|BJ971390
EST:     CGGA-TTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAG                         GGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG
genomic: CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAGgtatccaatc ... aaatctacagGGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG
EST: gi|162184696|gb|FC361934.1|FC361934
EST:     CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAG                         GGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG
genomic: CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAGgtatccaatc ... aaatctacagGGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG
EST: gi|7148048|gb|AW509970.1|AW509970
EST:     CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAG                         GGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG
genomic: CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAGgtatccaatc ... aaatctacagGGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG
EST: gi|18351691|gb|BJ183743.1|BJ183743
EST:     CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAG                         GGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG
genomic: CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAGgtatccaatc ... aaatctacagGGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG
EST: gi|19780510|gb|BQ039570.1|BQ039570
EST:     CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAG                         GGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG
genomic: CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAGgtatccaatc ... aaatctacagGGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG
EST: gi|18327559|gb|BJ159562.1|BJ159562
EST:     CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAG                         GGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAGTTTG
genomic: CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAGgtatccaatc ... aaatctacagGGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAGTTTG
EST: gi|37831031|gb|BJ589043.1|BJ589043
EST:     CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAG                         GGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG
genomic: CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAGgtatccaatc ... aaatctacagGGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG
EST: gi|67720438|gb|BJ970697.1|BJ970697
EST:     CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAG                         GGAAAGCCCATACCGCTCAAATACGTCAAGTNTCAGAGTGTGNGAAG
genomic: CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAGgtatccaatc ... aaatctacagGGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG
EST: gi|67709266|gb|BJ965082.1|BJ965082
EST:     CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAG                         GGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG
genomic: CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAGgtatccaatc ... aaatctacagGGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG
EST: gi|162244583|gb|FC423445.1|FC423445
EST:     CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAG                         GGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG
genomic: CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAGgtatccaatc ... aaatctacagGGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG
EST: gi|162241395|gb|FC418560.1|FC418560
EST:     CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAG                         GGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG
genomic: CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAGgtatccaatc ... aaatctacagGGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG
EST: gi|18354254|gb|BJ186310.1|BJ186310
EST:     CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAG                         GGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG
genomic: CGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAGgtatccaatc ... aaatctacagGGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG

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: 34 (upstream exon), 34 (downstream exon)
Score: 2

CAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAGgtatccaatc ... aaatctacagGGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaaccgattgaagccctgatatctggatggttcctggctttgtaaatctacagGGAAAGCCCATACCGCTCAAATACGTCAAGTTTCAGAGTGTGCGAAG
                                        tttgtaaat  TA-rich tract