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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttgtatagcctcttctcctatggaagcatcgattcctcttgtttgattgatttccagCAAGTCGAGCTACCATTCTCGGTGTTTGAGACCCCGCGCGTGGATCCCAAGTCGGTCGTCTCCATCATCCTGGGAGGCGGCGTTGGAACGCGATTGTTTC

Basic information

species Selaginella moellendorffii
transcript EFJ23417
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|169065580|gb|FE474833.1|FE474833
EST:     CCGCTCTGTCGTCCGCTGTTCTAGTGGATTATCCCCCGCGCGAAGCAAAG                         CAAGTCGAGCTACCATTCTCGGTGTTTGAGACCCCGCGCGTGGATCCCAAG
genomic: CCGCTCTGTCGTCCGCTGTTCTAGTGGATTATCCCCCGCGCGAAGCAAAGgtgagtttgt ... tgatttccagCAAGTCGAGCTACCATTCTCGGTGTTTGAGACCCCGCGCGTGGATCCCAAG
EST: gi|169040801|gb|FE447852.1|FE447852
EST:     CCGCTCTGTCGTCCGCTGTTCTAGTGGATTATCCCCCGCGCGAAGCAAAG                         CAAGTCGAGCTACCATTCTCGGTGTTTGAGACCCCGCGCGTGGATCCCAAG
genomic: CCGCTCTGTCGTCCGCTGTTCTAGTGGATTATCCCCCGCGCGAAGCAAAGgtgagtttgt ... tgatttccagCAAGTCGAGCTACCATTCTCGGTGTTTGAGACCCCGCGCGTGGATCCCAAG

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: 31

ATCCAAGCCGAGGATCGCCAAATGCCAGGCGGCCCAGAAAGGAGGGAATGCCGCTCTGTCGTCCGCTGTTCTAGTGGATTATCCCCCGCGCGAAGCAAAGgtgagtttgt ... tgatttccagCAAGTCGAGCTACCATTCTCGGTGTTTGAGACCCCGCGCGTGGATCCCAAGTCGGTCGTCTCCATCATCCTGGGAGGCGGCGTTGGAACGCGATTGTTTC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatagcctcttctcctatggaagcatcgattcctcttgtttgattgatttccagCAAGTCGAGCTACCATTCTCGGTGTTTGAGACCCCGCGCGTGGATCCCAAGTCGGTCGTCTCCATCATCCTGGGAGGCGGCGTTGGAACGCGATTGTTTC
                                          gattgat  putative branch site (score: 31)
                                                tttcc  CT-rich tract
                                           attgattt  TA-rich tract