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'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgttcatttaatcgacggtcgcatctttttaatgattgcacgttactttttcgtgtgacggaaacgtgtagcaactggtgttacgtatactggaaaaactaccaactcattgaaatccaatcattcttaccaatcgtataattggttggtggtgaattgcacagGCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACACTCTACCTGCCTGGGCTAAATCAAGGGGTATTAAG

Basic information

species Physcomitrella patens
transcript PP1S12_178V6.2
intron # 21
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|162234487|gb|FC409518.1|FC409518
EST:     TGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATG                         GCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACA
genomic: TGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATGgtgcgttcat ... aattgcacagGCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACA
EST: gi|37847723|gb|BJ605731.1|BJ605731
EST:     TGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCATTGTTTCGTATATG                         GCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACA
genomic: TGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATGgtgcgttcat ... aattgcacagGCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACA
EST: gi|162231381|gb|FC406804.1|FC406804
EST:     TGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATG                         GCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACA
genomic: TGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATGgtgcgttcat ... aattgcacagGCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACA
EST: gi|162272001|gb|FC448419.1|FC448419
EST:     TGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATG                         GCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACA
genomic: TGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATGgtgcgttcat ... aattgcacagGCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACA
EST: gi|162272000|gb|FC448418.1|FC448418
EST:     TGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATG                         GCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACA
genomic: TGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATGgtgcgttcat ... aattgcacagGCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACA
EST: gi|162159914|gb|FC336167.1|FC336167
EST:     TGAGAACATTTTTCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATG                         GCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACA
genomic: TGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATGgtgcgttcat ... aattgcacagGCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACA
EST: gi|37846424|gb|BJ604432.1|BJ604432
EST:     TGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATG                         GCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACA
genomic: TGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATGgtgcgttcat ... aattgcacagGCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACA
EST: gi|162192790|gb|FC369628.1|FC369628
EST:     TGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATG                         GCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACA
genomic: TGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATGgtgcgttcat ... aattgcacagGCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACA

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: 18 (upstream exon), 19 (downstream exon)
Score: 2

AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATTGCACCGGAAAAGATTGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATGgtgcgttcat ... aattgcacagGCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACACTCTACCTGCCTGGGCTAAATCAAGGGGTATTAAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaaatccaatcattcttaccaatcgtataattggttggtggtgaattgcacagGCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACACTCTACCTGCCTGGGCTAAATCAAGGGGTATTAAG
              ttcttac  putative branch site (score: 2)
                           tataatt  TA-rich tract