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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCCAAGACCAGCTTCAAAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTGATGGATTAGCCAAGgtatgaatgctcgaatatcttttactctctggttgtgcctgttattttttagactaacccagggcggccatgacagtggtcgatcctgactaagcaaact...

Basic information

species Physcomitrella patens
transcript PP1S352_68V6.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S352_68V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: GLYMA15G15310.1 (Glycine max), 5'ss of exon 12
ACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCCAAGACCAGCTTCAAAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTGATGGATTAGCCAAGgtatgaatgctcgaatatct---tttactctctggttgtgcctgttattttttagactaacccagggcggccatgacagtggtcgatcctgactaagcaaact
   ||||||||||||||| ||  ||||||| |||||||| || || || ||||| || || |||||  ||||||||||||| || || ||  | |||||||| |  ||    | || | |   || |  || |  || | |      || |  ||  |      |||     | ||  ||    ||    |  | |  | |  
GAAAGCTGAAAAGGAGGGTTTTGAAGTAAGTGTTGCCAAAACAAGTTTTAAAGCTAACACAAAGGCCTTAGCTGAAAACGAAGGGGAGGGTCTTGCCAAGgt-tatatttctgtatctttcccttgatactattattctacaaaagcttataaagtgtttgtttgggttttta-gattgtaaaggaaatggttttaaaacat-

upper sequence: PP1S352_68V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: GLYMA09G04270.1 (Glycine max), 5'ss of exon 7
ACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCCAAGACCAGCTTCAAAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTGATGGATTAGCCAAGgtatgaatgctcgaatatcttttactctctggttgtgcctgttattttttagactaacccagggcggccatgacagtggtcgatcctgactaagcaaact---
   ||||||||||||||| ||  ||||||| |||||||| || || || ||||| || || |||||  ||||||||||||| || || ||  | ||||||||   | | ||  |   |    |     ||| |  ||      |  || || | | |    |   ||  | ||  || |  ||    |  | |  | | |   
GAAAGCTGAAAAGGAGGGTTTTGAAGTAAGTGTTGCCAAAACAAGTTTTAAAGCTAACACAAAGGCCTTAGCTGAAAACGAAGGGGAGGGTCTTGCCAAGgttatatttctgtatctttcccttgatactgttcttgtacaaaagcttataaagtgatt--gtttgggta-gattgtagaggaaatggttttaaaacatttgg

upper sequence: PP1S352_68V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: Vv14s0060g01330.t01 (Vitis vinifera), 5'ss of exon 12
ACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCCAAGACCAGCTTCAAAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTGATGGATTAGCCAAGgtatgaatgc--------tcgaatatcttttactctctggt-tgtgcctgtta----ttttttagactaacccagggcggccatga-cagtggtcgatcctgactaa---gcaaact------------
|  ||||||||||||||||||  ||||||| |||||||||||  | || || || || || ||||  ||||| ||||| || || || ||| | || ||||| |  || |        |      | || || ||||||||   ||   |||     |||| |    | ||       ||   | |  |||  ||   ||||   ||    |||| |            
AAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCCAAGACTGGTTTTAAGGCTAACACAAAGGTCCTAGCCGAAAATGAAGGGGAGGGACTTGCTAAGgtgtatatacaactccttttattcctgttctattctctggtacatgatagtttctacttttcttttgttactggaataggtggtaagtagttttctcacctgttaaaaacacaaagtgtttttatgcag

upper sequence: PP1S352_68V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 5'ss of exon 12
ACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCCAAGACCAGCTTCAAAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTGATGGATTAGCCAAGgtatgaatgctcgaatatcttttactctctggttgtgcctgttattttttagactaacccagggcggccatgacagtggtcgatcctgactaagcaaact-------
   ||||||||||||||||||  ||||||| ||||| ||||| ||||| || || || || ||||| ||||| ||||| || || || ||| | || ||||||  | | ||  |        | ||||          ||||  |   |  |  ||| |  |   ||  || |  |   |   |  |||  | |  | ||       
GAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCAAAGACAAGCTTTAAGGCTAACACAAAGGCCCTAGCAGAAAATGAAGGAGAGGGACTTGCTAAGgtaatatttcttaa-----cccttctcttccaacacttctgtgttgactccgcataatct-gaatggtaataattgattttctttatgag-atgttatctgaaatgt

upper sequence: PP1S352_68V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: Vv14s0060g01410.t01 (Vitis vinifera), 5'ss of exon 5
ACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCCAAGACCAGCTTCAAAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTGATGGATTAGCCAAGgtatgaatgctcgaatatcttttactctctggttgtgc-ctgttattttttagactaacccagggcggcc-atgacagtggtcgatcctgactaagcaaact-
|  ||||||||||||||||||  ||||||| ||||||||||| || || || || || || ||||| ||||| ||||| || || |  ||  | || ||||| |  ||     ||   |||||| ||      | | | ||| ||  |  | |  |   |            | || |   | | |  | | ||         
AAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCCAAGACTAGTTTTAAGGCTAACACAAAGGCCCTAGCCGAAAATGAAGGGGCGGGGCTTGCTAAGgtgtatatat---aactccttttattccagttctattctctggtacatgatggtttcttctttttttttttgttactggaataggtggtaagtagttttctcg

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|162191185|gb|FC367863.1|FC367863
EST:     AAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTGATGGATTAGCCAAG                         ATGATTTATAGACCCGACACTGGAGAGATTTTAGGGGTACATATCCTCGGT
genomic: AAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTGATGGATTAGCCAAGgtatgaatgc ... tggttggcagATGATTTATAGACCCGACACTGGAGAGATTTTAGGGGTACATATCCTCGGT
EST: gi|37832281|gb|BJ590293.1|BJ590293
EST:     AAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTGATGGATTAGCCAAG                         ATGATTTATAGACCCGACACTGGAGAGATTTTAGGGGTACATATCCTCGGT
genomic: AAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTGATGGATTAGCCAAGgtatgaatgc ... tggttggcagATGATTTATAGACCCGACACTGGAGAGATTTTAGGGGTACATATCCTCGGT
EST: gi|162246422|gb|FC421089.1|FC421089
EST:     AAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTGATGGATTAGCCAAG                         ATGATTTATAGACCCGACACTGGAGAGATTTTAGGGGTACATATCCTCGGT
genomic: AAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTGATGGATTAGCCAAGgtatgaatgc ... tggttggcagATGATTTATAGACCCGACACTGGAGAGATTTTAGGGGTACATATCCTCGGT
EST: gi|162183079|gb|FC360645.1|FC360645
EST:     AAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTGATGGATTAGCCAAG                         ATGATTTATAGACCCGACACTGGAGAGATTTTAGGGGTACATATCCTCGGT
genomic: AAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTGATGGATTAGCCAAGgtatgaatgc ... tggttggcagATGATTTATAGACCCGACACTGGAGAGATTTTAGGGGTACATATCCTCGGT
EST: gi|162186605|gb|FC363577.1|FC363577
EST:     AAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTGATGGATTAGCCAAG                         ATGATTTATAGACCCGACACTGGAGAGATTTTAGGGGTACATATCCTCGGT
genomic: AAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTGATGGATTAGCCAAGgtatgaatgc ... tggttggcagATGATTTATAGACCCGACACTGGAGAGATTTTAGGGGTACATATCCTCGGT
EST: gi|162191186|gb|FC367864.1|FC367864
EST:     AAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTGATGGATTAGCCAAG                         ATGATTTATAGACCCGACACTGGAGAGATTTTAGGGGTACATATCCTCGGT
genomic: AAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTGATGGATTAGCCAAGgtatgaatgc ... tggttggcagATGATTTATAGACCCGACACTGGAGAGATTTTAGGGGTACATATCCTCGGT
EST: gi|162166471|gb|FC343168.1|FC343168
EST:     AAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTGATGGATTAGCCAAG                         ATGATTTATAGACCCGACACTGGAGAGATTTTAGGGGTACATATCCTCGGT
genomic: AAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTGATGGATTAGCCAAGgtatgaatgc ... tggttggcagATGATTTATAGACCCGACACTGGAGAGATTTTAGGGGTACATATCCTCGGT
EST: gi|162186604|gb|FC363576.1|FC363576
EST:     AAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTGATGGATTAGCCAAG                         ATGATTTATAGACCCGACACTGGAGAGATTTTAGGGGTACATATCCTCGGT
genomic: AAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTGATGGATTAGCCAAGgtatgaatgc ... tggttggcagATGATTTATAGACCCGACACTGGAGAGATTTTAGGGGTACATATCCTCGGT
EST: gi|208368657|gb|DC947932.1|DC947932
EST:     AAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTGATGGATTAGCCAAG                         ATGATTTATAGACCCGACACTGGAGAGATTTTAGGGGTACATATCCTCGGT
genomic: AAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTGATGGATTAGCCAAGgtatgaatgc ... tggttggcagATGATTTATAGACCCGACACTGGAGAGATTTTAGGGGTACATATCCTCGGT
EST: gi|67700043|gb|BJ960276.1|BJ960276
EST:     AAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTGATGGATTAGCCAAG                         ATGATTTATAGACCCGACACTGGAGAGATTTTAGGGGTACATATCCTCGGT
genomic: AAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTGATGGATTAGCCAAGgtatgaatgc ... tggttggcagATGATTTATAGACCCGACACTGGAGAGATTTTAGGGGTACATATCCTCGGT

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: 20 (upstream exon), 35 (downstream exon)
Score: 7

ACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCCAAGACCAGCTTCAAAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTGATGGATTAGCCAAGgtatgaatgc ... tggttggcagATGATTTATAGACCCGACACTGGAGAGATTTTAGGGGTACATATCCTCGGTCTTCACGCTGCTGATCTCATTCATGAAGCTTCAAATGCTATAGCTATGG




<











<


<









Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCCAAGACCAGCTTCAAAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTGATGGATTAGCCAAGgtatgaatgctcgaatatcttttactctctggttgtgcctgttattttttagactaacccagggcggccatgacagtggtcgatcctgactaagcaaact

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA