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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatttacgagcgaactctattcccatgaatcagaagttgtttccattgctgttcttccaccccaaagtctcactgaagttctacattgaattttgcgtagCTCTCTTTCCTACCAATAGGGTTCCGTGTCGAAAATCCGCATCATCTTGAAGTATGGAATTGAGCGCCGTCAAGTGGCCCTGAATCACGCTTCATTTGAG

Basic information

species Physcomitrella patens
transcript PP1S239_45V6.1
intron # 9
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|67692428|gb|BJ952661.1|BJ952661
EST:     TCTCTGTGACAATGCCCCCAAAGCGTGATCGAGAAAGGATCTTCCTGCAG                         CTCTCTTTCCTACCAATAGGGTTCCGTGTCGAAAATCCGCATCATCTTGAA
genomic: TCTCTGTGACAATGCCCCCAAAGCGTGATCGAGAAAGGATCTTCCTGCAGgttgtgggtg ... ttttgcgtagCTCTCTTTCCTACCAATAGGGTTCCGTGTCGAAAATCCGCATCATCTTGAA
EST: gi|162260919|gb|FC437976.1|FC437976
EST:     TCTCTGTGACAATGCCCCCAAAGCGTGATCGAGAAAGGATCTTCCTGCAG                         CTCTCTTTCCTACCAATAGGGTTCCGTGTCGAAAATCCGCATCATCTTGAA
genomic: TCTCTGTGACAATGCCCCCAAAGCGTGATCGAGAAAGGATCTTCCTGCAGgttgtgggtg ... ttttgcgtagCTCTCTTTCCTACCAATAGGGTTCCGTGTCGAAAATCCGCATCATCTTGAA
EST: gi|162260897|gb|FC437954.1|FC437954
EST:     TCTCTGTGACAATGCCCCCAAAGCGTGATCGAGAAAGGATCTTCCTGCAG                         CTCTCTTTCCTACCAATAGGGTTCCGTGTCGAAAATCCGCATCATCTTGAA
genomic: TCTCTGTGACAATGCCCCCAAAGCGTGATCGAGAAAGGATCTTCCTGCAGgttgtgggtg ... ttttgcgtagCTCTCTTTCCTACCAATAGGGTTCCGTGTCGAAAATCCGCATCATCTTGAA
EST: gi|7583575|gb|AW699484.1|AW699484
EST:     TCTCTGTGACAATGCCCCCAAAGCGTGATCGAGAAAGGATCTTCCTGCAG                         CTCTCTTTCCTACCAATAGGGTTCCGTGTCGAAAATCCGCATCATCTTGAA
genomic: TCTCTGTGACAATGCCCCCAAAGCGTGATCGAGAAAGGATCTTCCTGCAGgttgtgggtg ... ttttgcgtagCTCTCTTTCCTACCAATAGGGTTCCGTGTCGAAAATCCGCATCATCTTGAA
EST: gi|162182562|gb|FC357537.1|FC357537
EST:     TCTCTGTGACAATGCCCCCAAAGCGTGATCGAGAAAGGATCTTCCTGCAG                         CTCTCTTTCCTACCAATAGGGTTCCGTGTCGAAAATCCGCATCATCTTGAA
genomic: TCTCTGTGACAATGCCCCCAAAGCGTGATCGAGAAAGGATCTTCCTGCAGgttgtgggtg ... ttttgcgtagCTCTCTTTCCTACCAATAGGGTTCCGTGTCGAAAATCCGCATCATCTTGAA
EST: gi|67507641|gb|BJ940521.1|BJ940521
EST:     TCTCTGTGACAATGCCCCCAAAGCGTGATCGAGAAAGGATCTTCCTGCAG                         CTCTCTTTCCTACCAATAGGGTTCCGTGTCGAAAATCCGCATCATCTTGAA
genomic: TCTCTGTGACAATGCCCCCAAAGCGTGATCGAGAAAGGATCTTCCTGCAGgttgtgggtg ... ttttgcgtagCTCTCTTTCCTACCAATAGGGTTCCGTGTCGAAAATCCGCATCATCTTGAA
EST: gi|162182563|gb|FC357538.1|FC357538
EST:     TCTCTGTGACAATGCCCCCAAAGCGTGATCGAGAAAGGATCTTCCTGCAG                         CTCTCTTTCCTACCAATAGGGTTCCGTGTCGAANATCCGCATCATCTTGAA
genomic: TCTCTGTGACAATGCCCCCAAAGCGTGATCGAGAAAGGATCTTCCTGCAGgttgtgggtg ... ttttgcgtagCTCTCTTTCCTACCAATAGGGTTCCGTGTCGAAAATCCGCATCATCTTGAA

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: 32 (upstream exon), 35 (downstream exon)
Score: 10

AAGGACGCGATCATCCCTCACGGAACAATCATCTAAGCTCTCACCGCCTTTCTCTGTGACAATGCCCCCAAAGCGTGATCGAGAAAGGATCTTCCTGCAGgttgtgggtg ... ttttgcgtagCTCTCTTTCCTACCAATAGGGTTCCGTGTCGAAAATCCGCATCATCTTGAAGTATGGAATTGAGCGCCGTCAAGTGGCCCTGAATCACGCTTCATTTGAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctgttcttccaccccaaagtctcactgaagttctacattgaattttgcgtagCTCTCTTTCCTACCAATAGGGTTCCGTGTCGAAAATCCGCATCATCTTGAAGTATGGAATTGAGCGCCGTCAAGTGGCCCTGAATCACGCTTCATTTGAG
                     gtctcac  putative branch site (score: 10)
                                       attgaatttt  TA-rich tract