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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGAGGACTCAGTGATCAAATCCGAGAGCTCCGTGAGTCAATTGAGTTGCCGCTTATGAATCCCGAGCTCTTCCTGCGAGTTGGCATTAAGCCTCCAAAGgtgtgttttaccatctgtcactaatttagactcagtttacgtagtcatctactcctattgacatgcattcctggcgactggtacctccacgatattacat...

Basic information

species Physcomitrella patens
transcript PP1S91_182V6.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S91_182V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G165817_T01 (Zea mays), 5'ss of exon 4
TGGAGGACTCAGTGATCAAATCCGAGAGCTCCGTGAGTCAATTGAGTTGCCGCTTATGAATCCCGAGCTCTTCCTGCGAGTTGGCATTAAGCCTCCAAAGgtgtgttttaccatctgtcactaatttagactcagtttacgtagtcatctactcctattgacatgcattcc---tggcgactggtac-ctccacgatattacat------
 || || ||   |||||| ||  |||||||| | ||||| |||||||| || ||||||||||| || ||||| || || || || ||||||||||| |||||       |  || |||     ||    | |  |  || |  ||||   |     || | |     ||||   |||  |    ||  ||      | ||||        
AGGTGGTCTGTCTGATCAGATTAGAGAGCTCAGGGAGTCCATTGAGTTACCACTTATGAATCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaaatatatgtt-tagatcccaattatgcatatgaggtcaaagagataaat-gtctaatgttccgactggatatcaatatgcttgtttgttttactcatccag

upper sequence: PP1S91_182V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA04G03180.1 (Glycine max), 5'ss of exon 4
TGGAGGACTCAGTGATCAAATCCGAGAGCTCCGTGAGTCAATTGAGTTGCCGCTTATGAATCCCGAGCTCTTCCTGCGAGTTGGCATTAAGCCTCCAAAGgtgtgttttaccatctgtcactaatt-tagactcagtttacgtagtcatctactcctattgacatgcattcctggcgac--tggtacctccacgatattacat-----------------------------------------------------------------------------------
||| ||  |   |||||| ||| | ||  |  | |||||||||||  |||| || |||||||| ||||||||||| |||||||| ||||| ||||||||||||  |||  |  | |    ||  || ||| ||| | || | || |  | |    |||| |   |  |||  | |   |  || ||  ||     |  |||||                                                                                   
TGGTGGCTTATCTGATCAGATCAGGGAATTGAGGGAGTCAATTGAACTGCCTCTAATGAATCCTGAGCTCTTCCTTCGAGTTGGAATTAAACCTCCAAAGgtg-atttacctttttactgctctttctagtctctgatttc-tattagtgttaatctat-gttttagatttttagtagctttgttatgtcattttttctacatatttttttagtggaagcttatttgtaatggccgtacttttgaattttacatttaatcaaaatcttttcaattctaattttcag

upper sequence: PP1S91_182V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA06G03230.1 (Glycine max), 5'ss of exon 4
TGGAGGACTCAGTGATCAAATCCGAGAGCTCCGTGAGTCAATTGAGTTGCCGCTTATGAATCCCGAGCTCTTCCTGCGAGTTGGCATTAAGCCTCCAAAGgtgtgttttaccatctgtcactaatttagactcagtttacgtagtcatctactcctattgacatgcattcctggcgactggtacctccacgatattacat--------------------------------------------------------------------------------------------
||| ||  |   |||||| ||| | ||  |  | |||||||||||  | || || |||||||| |||||||| || |||||||| ||||| ||||||||||||   ||||||  || |||||  | |      ||| |  |    | |||| |  | || |  |   ||   |     | ||| ||     ||   |  |                                                                                            
TGGTGGCTTATCTGATCAGATCAGGGAATTGAGGGAGTCAATTGAACTACCTCTGATGAATCCTGAGCTCTTTCTTCGAGTTGGAATTAAACCTCCAAAGgtga--tttacc--ctttcactgctctt--tctagtctctga---cttctattagtgttaatctatgttttagatttttagtagctttgttatgacatttttcctacatatttttttagtggaagcttacttgtaatggctgtacttttgaattttacacttgatcaaaatcttttcaattctaattttcag

upper sequence: PP1S91_182V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: Vv18s0001g13090.t01 (Vitis vinifera), 5'ss of exon 4
TGGAGGACTCAGTGATCAAATCCGAGAGCTCCGTGAGTCAATTGAGTTGCCGCTTATGAATCCCGAGCTCTTCCTGCGAGTTGGCATTAAGCCTCCAAAGgtgtgttttaccatctgtcactaatttagactcagtttacgtagtcatctact-cctattgacat-gcattcctggcgactggtacctccacg-atattacat-------------------------------------------
 || ||  |    |||||||||||||| ||| | || ||||||||| | || || |||||||| || ||||| ||  ||||||| ||||| ||||| ||||||  |  |||  |   |   || ||   | || || |     ||  |  | |  | |||||  | ||  |||| | |   |  || |  | | || |||  |                                           
GGGTGGGTTATCAGATCAAATCCGAGAACTCAGGGAATCAATTGAGCTACCTCTAATGAATCCTGAACTCTTTCTTAGAGTTGGAATTAAACCTCCCAAGgtgattcatactttaatttgttagtt---attctgtatggtctgttctgcattgtcaattgagttagccatcctagtggtggtaacatgaatggattttatttttttccttaattaaaaagtctcttaaattttatttttttgcag

upper sequence: PP1S91_182V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: EDP04786 (Chlamydomonas reinhardtii), 5'ss of exon 4
TGGAGGACTCAGTGATCAAATCCGAGAGCTCCGTGAGTCAATTGAGTTGCCGCTTATGAATCCCGAGCTCTTCCTGCGAGTTGGCATTAAGCCTCCAAAGgtg----tgttttaccatctgtcac-taatttagactcag---tttacgtagtcatctactcc--tattgacatgcattcctggcgactggtacctccacgatattacat----------------
                         ||||| || ||||| || ||| ||||||| ||||| ||||||||||||||||| || ||||| ||||| || ||||      || | |||   | | ||  |      | | | |   ||   |  | |    |||      | ||   |   |  ||| | | ||   |   | || || |                   
-------------------------GAGCTGCGCGAGTCCATCGAGCTGCCGCTCATGAACCCCGAGCTCTTCCTGCGCGTGGGCATCAAGCCGCCCAAGGGAGTGCTGCTGTACGGCCCGCCAGgtggggagggcgccgggcttggggcgggcgggcactggggcgtcgaggcgtggtgttgggggcagggggcaggagga-atgatgggaatggatggatcagc

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|67572554|gb|BJ945378.1|BJ945378
EST:     CGCTTATGAATCCCGAGCTCTTCCTGCGAGTTGGCATTAAGCCTCCAAAG                         GGTGTATTGTTGTATGGCCCCCCAGGAACCGGCAAAACCCTTCTGGCACGA
genomic: CGCTTATGAATCCCGAGCTCTTCCTGCGAGTTGGCATTAAGCCTCCAAAGgtgtgtttta ... tcttttacagGGTGTATTGTTGTATGGCCCCCCAGGAACCGGCAAAACCCTTCTGGCACGA
EST: gi|100386933|gb|BY988202.1|BY988202
EST:     CGCTTATGAATCCCGAGCTCTTCCTGCGAGTTGGCATTAAGCCTCCAAAG                         GGTGTATTGTTGTATG
genomic: CGCTTATGAATCCCGAGCTCTTCCTGCGAGTTGGCATTAAGCCTCCAAAGgtgtgtttta ... tcttttacagGGTGTATTGTTGTATG
EST: gi|100448214|gb|CJ972513.1|CJ972513
EST:     CGCTTATGAATCCCGAGCTCTTCCTGCGAGTTGGCATTAAGCCTCCAANG                         G-TGTATTGTTGTATGGCCCCCCAGGAACCGGCAAAANCCTTCTGGCACGA
genomic: CGCTTATGAATCCCGAGCTCTTCCTGCGAGTTGGCATTAAGCCTCCAAAGgtgtgtttta ... tcttttacagGGTGTATTGTTGTATGGCCCCCCAGGAACCGGCAAAACCCTTCTGGCACGA
EST: gi|67508474|gb|BJ941340.1|BJ941340
EST:     CGCTTATGAATCCCGAGCTCTTCCTGCGAGTTGGCATTAAGCCTCCAAAG                         GGTGTATTGTTGTATGGCCCCCCAGGAACCGGCAAAACCCTTCTGGCACGA
genomic: CGCTTATGAATCCCGAGCTCTTCCTGCGAGTTGGCATTAAGCCTCCAAAGgtgtgtttta ... tcttttacagGGTGTATTGTTGTATGGCCCCCCAGGAACCGGCAAAACCCTTCTGGCACGA
EST: gi|100426731|gb|BY977333.1|BY977333
EST:     CGCTTATGAATCCCGAGCTCTTCCTGCGAGTTGGCATTAAGCCTCCAAAG                         GGTGTATTGTTGTATGG
genomic: CGCTTATGAATCCCGAGCTCTTCCTGCGAGTTGGCATTAAGCCTCCAAAGgtgtgtttta ... tcttttacagGGTGTATTGTTGTATGG
EST: gi|100403562|gb|BY954988.1|BY954988
EST:     CGCTTATGAATCCCGAGCTCTTCCTGCGAGTTGGCATTAAGCCTCCAAAG                         GGTGTATTGTTGTATGGNNNNNNNAG-AACCGGCAAAACCCTTCTGGCACG
genomic: CGCTTATGAATCCCGAGCTCTTCCTGCGAGTTGGCATTAAGCCTCCAAAGgtgtgtttta ... tcttttacagGGTGTATTGTTGTATGGCCCCCC-AGGAACCGGCAAAACCCTTCTGGCACG

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: 32 (upstream exon), 34 (downstream exon)
Score: 11

TGGAGGACTCAGTGATCAAATCCGAGAGCTCCGTGAGTCAATTGAGTTGCCGCTTATGAATCCCGAGCTCTTCCTGCGAGTTGGCATTAAGCCTCCAAAGgtgtgtttta ... tcttttacagGGTGTATTGTTGTATGGCCCCCCAGGAACCGGCAAAACCCTTCTGGCACGAGCAATTGCCAGCAACATTGATGCTAATTTCTTAAAG




<











<


<