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

gtgcgtctcaagcttgtaccattgtgatttcactcttgagatgtgattgctagtgtcgcatttacctctctgtatttcttattttcatcatcaaatgtgattagggcttgtctcctaaccttgatggctggcgcgggtctttctgcagTACTCTTGGTGGCAGTCATGGTGTTCCTCGCGTACATTACAAAGGTCGACAAGGCGACTACTACGTCATG

Basic information

species Physcomitrella patens
transcript PP1S131_16V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 3
gtgcgtctcaagcttgtaccattgtgatttcactcttgagatgtgattgctagtgtcgcatttacctctctgtatttcttattttcatcatcaaatgt--gattagggcttgtctcctaaccttgatggctggcgcgggtctttctgcagTACTCTTGGTGGCAGTCATGGTGTTCCTCGCGTACATTACAAAGGTCGACAAGGCGACTACTACGTCATG
                                     | || |    | ||  | ||    ||| || ||||  |  | | | |||      |  | |  |||         | |  |    ||  | |||  |   | | || ||||||| | ||||||||||| |||||||| || || ||||||||||| || |||||||| |||||||| ||||||
-------------------------------------gtgaggcatcttctgatttctt-cttatctgtctgattggcatgtattccatggtagctattggatatatatacatgtgatggtattatttgctttctttgat-ttcctgcagTGCACTTGGTGGCAGCCATGGTGTGCCACGGGTACATTACAAGGGCCGACAAGGTGACTACTATGTCATG
















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|162252531|gb|FC427340.1|FC427340
EST:     CAGGTTTACAC                         TACTCTTGGTGGCAGTCATGGTGTTCCTCGCGTACATTACAAAGGTCGACA
genomic: CAGGTTTACACgtgcgtctca ... ctttctgcagTACTCTTGGTGGCAGTCATGGTGTTCCTCGCGTACATTACAAAGGTCGACA
EST: gi|162228110|gb|FC405692.1|FC405692
EST:     AGTAGTAAGGGCTGCAATTATGGTCCTCCTTATGAGTGGCAGGTTTACAC                         TACTCTTGGTGGCAGTCATGGTGTTCCTCGCGTACATTACAAAGGTCGACA
genomic: AGTAGTAAGGGCTGCAATTATGGTCCTCCTTATGAGTGGCAGGTTTACACgtgcgtctca ... ctttctgcagTACTCTTGGTGGCAGTCATGGTGTTCCTCGCGTACATTACAAAGGTCGACA
EST: gi|162257792|gb|FC433990.1|FC433990
EST:     AGTAGTAAGGGCTGCAATTATGGTCCTCCTTATGAGTGGCAGGTTTACAC                         TACTCTTGGTGGCAGTCATGGTGTTCCTCGCGTACATTACAAAGGTCGACA
genomic: AGTAGTAAGGGCTGCAATTATGGTCCTCCTTATGAGTGGCAGGTTTACACgtgcgtctca ... ctttctgcagTACTCTTGGTGGCAGTCATGGTGTTCCTCGCGTACATTACAAAGGTCGACA
EST: gi|162257871|gb|FC434069.1|FC434069
EST:     AGTAGTAAGGGCTGCAATTATGGTCCTCCTTATGAGTGGCAGGTTTACAC                         TACTCTTGGTGGCAGTCATGGTGTTCCTCGCGTACATTACAAAGGTCGACA
genomic: AGTAGTAAGGGCTGCAATTATGGTCCTCCTTATGAGTGGCAGGTTTACACgtgcgtctca ... ctttctgcagTACTCTTGGTGGCAGTCATGGTGTTCCTCGCGTACATTACAAAGGTCGACA

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: 21 (upstream exon), 32 (downstream exon)
Score: 11

GTTGCGTTGAAGTTCGAGCATCGGAGTAGTAAGGGCTGCAATTATGGTCCTCCTTATGAGTGGCAGGTTTACACgtgcgtctca ... ctttctgcagTACTCTTGGTGGCAGTCATGGTGTTCCTCGCGTACATTACAAAGGTCGACAAGGCGACTACTACGTCATG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgtgattagggcttgtctcctaaccttgatggctggcgcgggtctttctgcagTACTCTTGGTGGCAGTCATGGTGTTCCTCGCGTACATTACAAAGGTCGACAAGGCGACTACTACGTCATG
                                            tctttctgc  CT-rich tract