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'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAACCAATAGATCCAGAGGAGGATTTGAGACTCATGGCTCAAGAAGTTCGAGATTATGTGGAGGCTGTGCTTAACAGTTTGTCTGCAAATGTTCCGAAGgtaaaatctttgcctcacgttctagagctttttgcttacccttgcatgcatggtgaagattatcatgtctaacttgaacttatatggtgtaagcatgaaa...

Basic information

species Physcomitrella patens
transcript PP1S33_163V6.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S33_163V6.1 (Physcomitrella patens), 5'ss of exon 18
lower sequence: LOC_Os02g50550.1 (Oryza sativa), 5'ss of exon 19
GAAACCAATAGATCCAGAGGAGGATTTGAGACTCATGGCTCAAGAAGTTCGAGATTATGTGGAGGCTGTGCTTAACAGTTTGTCTGCAAATGTTCCGAAGgtaaa-atctttgcctcacgttc---tagagctttttgcttacccttgcatgcatggtgaagattatcat-gtctaacttgaacttatatggtgtaagcatgaaa--
||| ||    ||||| || || ||  |  |    ||| ||||||||||||| | |||||| ||||||||  | ||||||||| | ||||||||||| |||||  | || |   ||||||  |    |  |   |  | ||     ||  |  ||   | || ||  |||| ||   | |||   |||| ||   |   |||||    
GAAGCCTGCTGATCCTGAAGAAGAACTTCGGTGGATGTCTCAAGAAGTTCGTGGTTATGTAGAGGCTGTTTTGAACAGTTTGGCAGCAAATGTTCCAAAGgtttacatttgaacctcacaattgtttcaacagtcatactattttttaaactca-atttaacatggtcatagttgcaattgttattat-tgtctttttcatgatcag

upper sequence: PP1S33_163V6.1 (Physcomitrella patens), 5'ss of exon 18
lower sequence: EFJ05623 (Selaginella moellendorffii), 5'ss of exon 19
GAAACCAATAGATCCAGAGGAGGATTTGAGACTCATGGCTCAAGAAGTTCGAGATTATGTGGAGGCTGTGCTTAACAGTTTGTCTGCAAATGTTCCGAAGgtaaaatctttgcctcacgttctagagctttttgcttacccttgcatgcatggtgaagattatcatgtctaacttgaacttatatggtgtaagcatgaaa
|| |  |  ||||||||| || ||  |  |  ||||||||||||||||||| ||||| |||||||| ||  | |||||| | || |||||  | || ||||||      | ||     |||   ||    |   || |   | || ||||                                                  
GAGAAGAGCAGATCCAGAAGAAGAGCTTCGGATCATGGCTCAAGAAGTTCGTGATTACGTGGAGGCAGTAATGAACAGTCTTTCAGCAAACATCCCCAAGgta---cgctagcaatttgtttgtgaatgctggactaaaaatcgc-tgcag-------------------------------------------------

upper sequence: PP1S33_163V6.1 (Physcomitrella patens), 5'ss of exon 18
lower sequence: EFJ28901 (Selaginella moellendorffii), 5'ss of exon 18
GAAACCAATAGATCCAGAGGAGGATTTGAGACTCATGGCTCAAGAAGTTCGAGATTATGTGGAGGCTGTGCTTAACAGTTTGTCTGCAAATGTTCCGAAGgtaaaatctttgcctcacgttctagagctttttgcttacccttgcatgcatggtgaagattatcatgtctaacttgaacttatatggtgtaagcatgaaa
|| |  |  ||||||||| || ||  |  |  ||||||||||||||||||| ||||| |||||||| ||  | |||||| | || |||||  | || ||||||      | ||     |||   ||    |   || |   | || ||||                                                  
GAGAAGAGCAGATCCAGAAGAAGAGCTTCGGATCATGGCTCAAGAAGTTCGTGATTACGTGGAGGCAGTAATGAACAGTCTTTCAGCAAACATCCCCAAGgta---cgctggcaatttgtttgtgaatgctggactaaaaatcgc-tgcag-------------------------------------------------

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|162209952|gb|FC385782.1|FC385782
EST:     GGGATTATGTGGAGGCTGTGCTTAACAGTTTGTCTGCAAATGTTCCGAAG                         GCAGTGGTCCTTTGTCAAGTGGAGAGGGCCAAGGATGCTATGCTAAATCAC
genomic: GAGATTATGTGGAGGCTGTGCTTAACAGTTTGTCTGCAAATGTTCCGAAGgtaaaatctt ... cacatttcagGCAGTGGTCCTTTGTCAAGTGGAGAGGGCCAAGGATGCTATGCTAAATCAC
EST: gi|162268866|gb|FC445701.1|FC445701
EST:     GAGATTATGTGGAGGCTGTGCTTAACAGTTTGTCTGCAAATGTTCCGAAG                         GCAGTGGTCCTTTGTCAAGTGGAGAGGGCCAAGGATGCTATGCTAAATCAC
genomic: GAGATTATGTGGAGGCTGTGCTTAACAGTTTGTCTGCAAATGTTCCGAAGgtaaaatctt ... cacatttcagGCAGTGGTCCTTTGTCAAGTGGAGAGGGCCAAGGATGCTATGCTAAATCAC
EST: gi|162268865|gb|FC445700.1|FC445700
EST:     GAGATTATGTGGAGGCTGTGCTTAACAGTTTGTCTGCAAATGTTCCGAAG                         GCAGTGGTCCTTTGTCAAGTGGAGAGGGCCAAGGATGCTATGCTAAATCAC
genomic: GAGATTATGTGGAGGCTGTGCTTAACAGTTTGTCTGCAAATGTTCCGAAGgtaaaatctt ... cacatttcagGCAGTGGTCCTTTGTCAAGTGGAGAGGGCCAAGGATGCTATGCTAAATCAC

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: 25 (upstream exon), 35 (downstream exon)
Score: 5

GAAACCAATAGATCCAGAGGAGGATTTGAGACTCATGGCTCAAGAAGTTCGAGATTATGTGGAGGCTGTGCTTAACAGTTTGTCTGCAAATGTTCCGAAGgtaaaatctt ... cacatttcagGCAGTGGTCCTTTGTCAAGTGGAGAGGGCCAAGGATGCTATGCTAAATCACCTTTATAGCTCCATCAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAACCAATAGATCCAGAGGAGGATTTGAGACTCATGGCTCAAGAAGTTCGAGATTATGTGGAGGCTGTGCTTAACAGTTTGTCTGCAAATGTTCCGAAGgtaaaatctttgcctcacgttctagagctttttgcttacccttgcatgcatggtgaagattatcatgtctaacttgaacttatatggtgtaagcatgaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG