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

...gcatgagatttgcgttcactttccagcttgatagagctgtctctgactcgtcgggctatatttttaatactggtgtgtatcatgtctttgtatctggcagCGTGATCTTGTAACAGTTAAAGTTAACAAGTTAACATCGACCAAGACGCAGTTGCCGTACAACTATTATTCATTGGATTACTGTAGGCCTCCAAAGATTC

Basic information

species Physcomitrella patens
transcript PP1S73_94V6.1
intron # 2
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|18352162|gb|BJ184216.1|BJ184216
EST:     CCGCTGCAGCTTTCTACCTACCAGGCGTTGCCCCCCAGGATTTCGAAGAG                         CGTGATCTTGTAACAGTTAAAGTTAACAAGTTAACATCGACCAAGACGCAG
genomic: CCGCTGCAGCTTTCTACCTACCAGGCGTTGCCCCCCAGGATTTCGAAGAGgttctctctt ... tatctggcagCGTGATCTTGTAACAGTTAAAGTTAACAAGTTAACATCGACCAAGACGCAG
EST: gi|18359587|gb|BJ191648.1|BJ191648
EST:     CCGCTGCAGCTTTCTACCTACCAGGCGTTGCCCCCCAGGATTTCGAAGAG                         CGTGATCTTGTAACAGTTAAAGTTAACAAGTTAACATCGACCAAGACGCAG
genomic: CCGCTGCAGCTTTCTACCTACCAGGCGTTGCCCCCCAGGATTTCGAAGAGgttctctctt ... tatctggcagCGTGATCTTGTAACAGTTAAAGTTAACAAGTTAACATCGACCAAGACGCAG
EST: gi|18342920|gb|BJ174956.1|BJ174956
EST:     CCGCTGCAGCTTTCTACCTACCAGGCGTTGCCCCCCAGGATTTCGAAGAG                         CGTGATCTTGTAACAGTTAAAGTTAACAAGTTAACATCGACCAAGACGCAG
genomic: CCGCTGCAGCTTTCTACCTACCAGGCGTTGCCCCCCAGGATTTCGAAGAGgttctctctt ... tatctggcagCGTGATCTTGTAACAGTTAAAGTTAACAAGTTAACATCGACCAAGACGCAG
EST: gi|18348107|gb|BJ180154.1|BJ180154
EST:     CCGCTGCAGCTTTCTACCTACCAGGCGTTGCCCCCCAGGATTTCGAAGAG                         CGTGATCTTGTAACAGTTAAAGTTAACAAGTTAACATCGACCAAGACGCAG
genomic: CCGCTGCAGCTTTCTACCTACCAGGCGTTGCCCCCCAGGATTTCGAAGAGgttctctctt ... tatctggcagCGTGATCTTGTAACAGTTAAAGTTAACAAGTTAACATCGACCAAGACGCAG

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: 30 (upstream exon), 14 (downstream exon)
Score: 9

CATGGCTCGCCTGCCCATCTACGGCCTGTTGCTGGTGTTTCTCTTTCACTCCGCTGCAGCTTTCTACCTACCAGGCGTTGCCCCCCAGGATTTCGAAGAGgttctctctt ... tatctggcagCGTGATCTTGTAACAGTTAAAGTTAACAAGTTAACATCGACCAAGACGCAGTTGCCGTACAACTATTATTCATTGGATTACTGTAGGCCTCCAAAGATTC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actcgtcgggctatatttttaatactggtgtgtatcatgtctttgtatctggcagCGTGATCTTGTAACAGTTAAAGTTAACAAGTTAACATCGACCAAGACGCAGTTGCCGTACAACTATTATTCATTGGATTACTGTAGGCCTCCAAAGATTC
                ttttaat  putative branch site (score: 9)
                                       tctttgt  putative PPT
           tatatttttaatact  TA-rich tract