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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACCTAGGTTTAGATTGGAGAATGGGAGGCGAGTGGTTTGAGACGTGCCTTCTCGATTATGATCCTTGCTCAAATTATGGCAATTGGACATATGGTGCTGgtaaaaaatatacttacttccaaacttatacacttttaaatttctgttacactggtgtttcgaatactgtgaatttaggttgtctaatgtcattttgaac...

Basic information

species Physcomitrella patens
transcript PP1S488_10V6.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S488_10V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: Vv04s0008g02670.t01 (Vitis vinifera), 5'ss of exon 11
GACCTAGGTTTAGATTGGAGAATGGGAGGCGAGTGGTTTGAGACGTGCCTTCTCGATTATGATCCTTGCTCAAATTATGGCAATTGGACATATGGTGCTGgtaaaaaatatacttacttccaaacttatacacttttaaatttctgttacactggtgtttcgaatactgtgaatttaggttgtctaatgt-cattttgaac-------------------
||| | ||  | || ||| | |||||||  || ||||||||||| ||||| |||||||| || ||||| || |||||||| |||||||| ||||| || ||| |   | ||    |||     |   ||| |   |||  ||| | |   | |   | |  ||| ||     || |  |       || | |||||| |                     
GACATGGGCATTGACTGGCGTATGGGAGCTGAATGGTTTGAGACTTGCCTCCTCGATTACGACCCTTGTTCCAATTATGGAAATTGGACCTATGGAGCAGgtgattcacatcacaactaatgtagacatatatccttatgtttttatgtaaatttagatgagaacac-acatatctgtgcatctatatatgcattttaatatcctatcctgttttattag
















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|162185125|gb|FC362259.1|FC362259
EST:     TCTCGATTATGATCCTTGCTCAAATTATGGCAATTGGACATATGGTGCTG                         GCGTAGGCAATGATCCTCGAGAAGATCGCTACTTCAGCATTCCAAAGCAG
genomic: TCTCGATTATGATCCTTGCTCAAATTATGGCAATTGGACATATGGTGCTGgtaaaaaata ... ctgattgtagGCGTAGGCAATGATCCTCGAGAAGATCGCTACTTCAGCATTCCAAAGCAG
EST: gi|208349448|gb|DC921936.1|DC921936
EST:     TCTCGATTATGATCCTTGCTCAAATTATGGCAATTGGACATATGGTGCTG                         GCGTAGGCAATGATCCTCGAGAAGATCGCTACTTCAGCATTCCAAAGCAG
genomic: TCTCGATTATGATCCTTGCTCAAATTATGGCAATTGGACATATGGTGCTGgtaaaaaata ... ctgattgtagGCGTAGGCAATGATCCTCGAGAAGATCGCTACTTCAGCATTCCAAAGCAG
EST: gi|37823251|gb|BJ581317.1|BJ581317
EST:     TCTCGATTATGATCCTTGCTCAAATTATGGCAATTGGACATATGGTGCTG                         GCGTAGGCAATGATCCTCGAGAAGATCGCTACTTCAGCATTCCAAAGCAG
genomic: TCTCGATTATGATCCTTGCTCAAATTATGGCAATTGGACATATGGTGCTGgtaaaaaata ... ctgattgtagGCGTAGGCAATGATCCTCGAGAAGATCGCTACTTCAGCATTCCAAAGCAG
EST: gi|162236499|gb|FC413074.1|FC413074
EST:     TCTCGATTATGATCCTTGCTCAAATTATGGCAATTGGACATATGGTGCTG                         GCGTAGGCAATGATCCTCGAGAAGATCGCTACTTCAGCATTCCAAAGCAG
genomic: TCTCGATTATGATCCTTGCTCAAATTATGGCAATTGGACATATGGTGCTGgtaaaaaata ... ctgattgtagGCGTAGGCAATGATCCTCGAGAAGATCGCTACTTCAGCATTCCAAAGCAG

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: 34 (upstream exon), 23 (downstream exon)
Score: 3

GACCTAGGTTTAGATTGGAGAATGGGAGGCGAGTGGTTTGAGACGTGCCTTCTCGATTATGATCCTTGCTCAAATTATGGCAATTGGACATATGGTGCTGgtaaaaaata ... ctgattgtagGCGTAGGCAATGATCCTCGAGAAGATCGCTACTTCAGCATTCCAAAGCAG




<











<


<