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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagctatacatcatacatgtttatttccgactgataactagcgtcaatgccagGCTTTGGGATCTTGGGCAGCAACGTTGTGTTCATTCATATGCTGTGCACACTGACTCAGTGTGGACAATGGCGAGCACATCCTCTTTTAGTCACGTTTAC

Basic information

species Selaginella moellendorffii
transcript EFJ37688
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ37688 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: GRMZM2G167999_T02 (Zea mays), 3'ss of exon 8
--------------------------------------------gtagc-tatacatcata-catgttt---atttccgactgataactagcgtcaatgc-cagGCTTTGGGATCTTGGGCAGCAACGTTGTGTTCATTCATATGCTGTGCACACTGACTCAGTGTGGACAATGGCGAGCACATCCTCTTTTAGTCACGTTTAC
                                             |||| || |     |   | ||||   ||    ||   |||  |    | | |   ||| || |||||||| || ||||| |||||||||||||| ||||||||||| ||||| || || ||| || | || |||||  |  | ||| |||| || |||
gtaaacacacagctctaacatctcaaccatctccctctctcatgttagcataaatgctgtggtaagtttgacatcatagatacatatttttatttactttgcagACTATGGGATCTAGGACAGCAGCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTAC

upper sequence: EFJ37688 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: GLYMA10G30050.1 (Glycine max), 3'ss of exon 7
-------------gtagctataca-tcatacatgtttatttc-----cgactgata--actagcgtcaatgccagGCTTTGGGATCTTGGGCAGCAACGTTGTGTTCATTCATATGCTGTGCACACTGACTCAGTGTGGACAATGGCGAGCACATCCTCTTTTAGTCACGTTTAC
              | | | || | | ||   | ||| |||        ||| ||   || | | |  ||   ||||||||||||||||| |||||||| ||||| ||||| ||||| || || || || ||  | ||| |  | || ||||| ||  | |||||||| ||||| 
gtaatgcgtgtatatggttttataataatttctttttgttttatggtttactaatctcaccatctttcatcatagGCTTTGGGATCTTGGTCAGCAACGCTGTGTGCATTCTTATGCAGTTCATACAGATTCTATTTGGGCTCTTGCAAGCACTTCAACATTTAGTCATGTTTAT
















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|169114159|gb|FE516838.1|FE516838
EST:     ATTATGTTTGTCAGGGTCTTCAGATTCAATTATCAG                         GCTTTGGGATCTTGGGCAGCAACGTTGTGTTCATTCATATGCTGTGCACAC
genomic: ATTATGTTTGTCAGGGTCTTCAGATTCAATTATCAGgtagctatac ... tcaatgccagGCTTTGGGATCTTGGGCAGCAACGTTGTGTTCATTCATATGCTGTGCACAC
EST: gi|169026297|gb|FE433388.1|FE433388
EST:     ATTATGTTTGTCAGGGTCTTCAGATTCAATTATCAG                         GCTTTGGGATCTTGGGCAGCAACGTTGTGTTCATTCATATGCTGTGCACAC
genomic: ATTATGTTTGTCAGGGTCTTCAGATTCAATTATCAGgtagctatac ... tcaatgccagGCTTTGGGATCTTGGGCAGCAACGTTGTGTTCATTCATATGCTGTGCACAC
EST: gi|169087203|gb|FE493111.1|FE493111
EST:     ATTATGTTTGTCAGGGTCTTCAGATTCAATTATCAG                         GCTTTGGGATCTTGGGCAGCAACGTTGTGTTCATTCGTATGCTGTGCACAC
genomic: ATTATGTTTGTCAGGGTCTTCAGATTCAATTATCAGgtagctatac ... tcaatgccagGCTTTGGGATCTTGGGCAGCAACGTTGTGTTCATTCATATGCTGTGCACAC
EST: gi|169099050|gb|FE501771.1|FE501771
EST:     ATTATGTTTGTCAGGGTCTTCAGATTCAATTATCAG                         GCTTTGGGATCTTGGGCAGCAACGTTGTGTTCATTCGTATGCTGTGCACAC
genomic: ATTATGTTTGTCAGGGTCTTCAGATTCAATTATCAGgtagctatac ... tcaatgccagGCTTTGGGATCTTGGGCAGCAACGTTGTGTTCATTCATATGCTGTGCACAC
EST: gi|169025642|gb|FE436555.1|FE436555
EST:     ATTATGTTTGTCAGGGTCTTCAGATTCAATTATCAG                         GCTTTGGGATCTTGGGCAGCAACGTTGTGTTCATTCGTATGCTGTGCACAC
genomic: ATTATGTTTGTCAGGGTCTTCAGATTCAATTATCAGgtagctatac ... tcaatgccagGCTTTGGGATCTTGGGCAGCAACGTTGTGTTCATTCATATGCTGTGCACAC

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), 24 (downstream exon)
Score: 10

ATTATGTTTGTCAGGGTCTTCAGATTCAATTATCAGgtagctatac ... tcaatgccagGCTTTGGGATCTTGGGCAGCAACGTTGTGTTCATTCATATGCTGTGCACACTGACTCAGTGTGGACAATGGCGAGCACATCCTCTTTTAGTCACGTTTAC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtagctatacatcatacatgtttatttccgactgataactagcgtcaatgccagGCTTTGGGATCTTGGGCAGCAACGTTGTGTTCATTCATATGCTGTGCACACTGACTCAGTGTGGACAATGGCGAGCACATCCTCTTTTAGTCACGTTTAC
                                 tgataac  putative branch site (score: 10)
               atacatgtttattt  TA-rich tract