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

CCAAATTCGCAACCTTATCGAAATTGCTGAGCAAGAGTACGAGAAGGAGAAGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAGgtatatgtcttcatttgtttcaatcataataagaatctgttagctccctgtcgtgacagcgtccactatatattctcaaattgttccgtgttgtggtttgcacaatgaaggcctctcttgacgtgggacttcctgcgcag

Basic information

species Physcomitrella patens
transcript PP1S276_75V6.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S276_75V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 8
CCAAATTCGCAACCTTATCGAAATTGCTGAGCAAGAGTACGAGAAGGAGAAGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAGgtatatgtcttcatttgtttcaatcataataagaatctgttagctccctgtcgtgacagcgtccactatatattctcaaattgttccgtgttgtggtttgcacaatgaaggcctctcttgacgtgggacttcctgcgcag
                        ||||||||||||||| ||||| || |||||||||||||||||||| || ||||| || ||||| ||  | || ||||||   | ||            |    |||   ||| |||||| |   |      ||  |||    |||||     ||| |||  |  | ||      ||   |                                    
----------------------GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAGgtaacagactc-----------actgaaatggtaatatgttagtttggt------acgccgttgggtatat-----caacttgggcaatttttgtacatgtgtag-----------------------------------

upper sequence: PP1S276_75V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA08G18760.1 (Glycine max), 5'ss of exon 8
CCAAATTCGCAACCTTATCGAAATTGCTGAGCAAGAGTACGAGAAGGAGAAGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAGgtatatgtcttcatttgtttcaatcataataagaatctgttagctccctgtcgtgacagcgtccactatatattctcaaattgttccgtgt-tgtggtttgcacaatgaaggcctctcttgacgtgggacttcctgcgcag
                        ||||||||||||||| ||||| || |||||||||||||||||||| || || || || ||||| ||  | || ||||||   |     | |   |  |||     |   ||| | |||| |   |    || ||  ||  |  | |  |     |||| ||     | | | |                                            
----------------------GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAATTGTCTGGTGGTGTGGCTGTGATACAGgtaacag-----actcactgaaat----gtggtaatatattagtttggtactctg-caaggtatatca-acttggggcaatttttgtacatatatag--------------------------------------------

upper sequence: PP1S276_75V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: AT1G55490.2 (Arabidopsis thaliana), 5'ss of exon 9
CCAAATTCGCAACCTTATCGAAATTGCTGAGCAAGAGTACGAGAAGGAGAAGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAGgtatat----gtcttcatttgtttcaatcat--aataagaatctgttagctccctgtcgtgacagcgtccactatatattc-tcaaattgttccgtgttgtggtttgcacaatgaaggcctctcttgacgtgggacttcctgcgcag
                         || |||||||| |||||||||||||| || |||||||||||||| ||| | || || || || ||  | ||||||||| |       ||   |  |||||  |  |   || |  || ||||       | |   |  |  |  |  ||| ||||  | |||                                                            
----------------------CAAGCGGAGCAAGATTACGAGAAGGAGAAACTCAATGAGAGAATTGCAAAGCTCTCTGGTGGAGTTGCTGTGATTCAGgtaaactaaaaactatttaagtttcctttgtctgattaagatgtgtttcagagatattaagttaa-gctcgttatgtattggttaaag-----------------------------------------------------------

upper sequence: PP1S276_75V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 9
CCAAATTCGCAACCTTATCGAAATTGCTGAGCAAGAGTACGAGAAGGAGAAGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAGgtatatgtcttcatttgtttcaatcataataagaatctgttagctccctgtcgtgacagcgtccactatatattctca--aattgttccgtgttgtggtttgcacaatgaaggcctctcttgacgtgggacttcctgcgcag
                         || |||||||| ||||||||||| ||  | |||||||||||||||||| | || || || || ||  | ||||||||| |            |   ||||| |    || | | || | |   | |  |   ||  |    ||  |  ||| |  ||   ||     |  |||||                                          
----------------------CAAGCGGAGCAAGACTACGAGAAGGAAAAATTAAATGAGAGAATTGCGAAGCTCTCTGGTGGAGTTGCTGTAATTCAGgtaaa-----------atagtaatcacat--ggactttcttggatttgtatgatagaagaataagttaagtgatctaattaaagtttttacatcttggttaaag--------------------------------------

upper sequence: PP1S276_75V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: EDP03982 (Chlamydomonas reinhardtii), 5'ss of exon 12
CCAAATTCGCAACCTTATCGAAATTGCTGAGCAAGAGTACGAGAAGGAGAAGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAGgtatatgtcttcatttgtttcaatcataataagaatctgttagctccctgtcgtgacagcgtccactatatattctcaaattgttccgtgt-tgtggtttgcacaatgaaggcctctcttgacgtgggacttcctgcgcag
 || || ||||||||    |      | ||||| |||||||||||||||||||| |||||| | ||||||    | ||||| || || ||||| || |||||                  |    |     ||   | |  |||  | | |  || | |  | |  |        |  ||| | |  |||  || ||| ||| |   |   ||||  ||||                    
GCAGATCCGCAACCTGGCGGCGGAGACGGAGCAGGAGTACGAGAAGGAGAAGCTCAATGAGCGCATTGCGCGCCTGTCGGGCGGCGTGGCCATCATCCAGgtgggg--------------cggcgagggagaggggcgg--agcggcgtttt-tggctgtattcggtg---gccttggaatcgctgtgtgcatgaggtatgcgcgtcg---gccttgcttgca------------------

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|162178480|gb|FC354204.1|FC354204
EST:     AGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAG                         GTCGGAGCTCAAACCGAGACAGAGTTGAAGGAGAAGAAGCTCCGTGTTGAG
genomic: AGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAGgtatatgtct ... tcctgcgcagGTCGGAGCTCAAACCGAGACAGAGTTGAAGGAGAAGAAGCTCCGTGTTGAG
EST: gi|162176319|gb|FC353504.1|FC353504
EST:     AGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAG                         GTCGGAGCTCAAACCGAGACAGAGTTGAAGGAGAAGAAGCTCCGTGTTGAG
genomic: AGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAGgtatatgtct ... tcctgcgcagGTCGGAGCTCAAACCGAGACAGAGTTGAAGGAGAAGAAGCTCCGTGTTGAG
EST: gi|162170396|gb|FC346788.1|FC346788
EST:     AGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAG                         GTCGGAGCTCAAACCGAGACAGAGTTGAAGGAGAAGAAGCTCCGTGTTGAG
genomic: AGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAGgtatatgtct ... tcctgcgcagGTCGGAGCTCAAACCGAGACAGAGTTGAAGGAGAAGAAGCTCCGTGTTGAG
EST: gi|19790367|gb|BQ041835.1|BQ041835
EST:     AGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAG                         GTCGGAGCTCAAACCGAGACAGAGTTGAAGGAGAAGAAGCTCCGTGTTGAG
genomic: AGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAGgtatatgtct ... tcctgcgcagGTCGGAGCTCAAACCGAGACAGAGTTGAAGGAGAAGAAGCTCCGTGTTGAG
EST: gi|67571361|gb|BJ944185.1|BJ944185
EST:     AGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAG                         GTCGGAGCTCAAACCGAGACAGAGTTGAAGGAGAAGAAGCTCCGTGTTGAG
genomic: AGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAGgtatatgtct ... tcctgcgcagGTCGGAGCTCAAACCGAGACAGAGTTGAAGGAGAAGAAGCTCCGTGTTGAG
EST: gi|162169794|gb|FC346150.1|FC346150
EST:     AGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAG                         GTCGGAGCTCAAACCGAGACAGAGTTGAAGGAGAAGAAGCTCCGTGTTGAG
genomic: AGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAGgtatatgtct ... tcctgcgcagGTCGGAGCTCAAACCGAGACAGAGTTGAAGGAGAAGAAGCTCCGTGTTGAG
EST: gi|162270366|gb|FC447066.1|FC447066
EST:     AGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAG                         GTCGGAGCTCAAACCGAGACAGAGTTGAAGGAGAAGAAGCTCCGTGTTGAG
genomic: AGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAGgtatatgtct ... tcctgcgcagGTCGGAGCTCAAACCGAGACAGAGTTGAAGGAGAAGAAGCTCCGTGTTGAG
EST: gi|162179963|gb|FC356034.1|FC356034
EST:     AGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAG                         GTCGGAGCTCAAACCGAGACAGAGTTGAAGGAGAAGAAGCTCCGTGTTGAG
genomic: AGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAGgtatatgtct ... tcctgcgcagGTCGGAGCTCAAACCGAGACAGAGTTGAAGGAGAAGAAGCTCCGTGTTGAG
EST: gi|162191911|gb|FC366916.1|FC366916
EST:     AGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAN                         GTCGGAGCTCANACCGAGACAGAGTTGAAGG
genomic: AGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAGgtatatgtct ... tcctgcgcagGTCGGAGCTCAAACCGAGACAGAGTTGAAGG
EST: gi|162191910|gb|FC366915.1|FC366915
EST:     AGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAG                         GTCGGAGCTCAAACCGAGACAGAGTTGAAGGAGAAGAAGCTCCGTGTTGAG
genomic: AGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAGgtatatgtct ... tcctgcgcagGTCGGAGCTCAAACCGAGACAGAGTTGAAGGAGAAGAAGCTCCGTGTTGAG
EST: gi|162192275|gb|FC367800.1|FC367800
EST:     GAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAG                         GTCGGAGCTCAAACCGAGACAGAGTTGAAGGAGAAGAAGCTCCGTGTTGAG
genomic: GAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAGgtatatgtct ... tcctgcgcagGTCGGAGCTCAAACCGAGACAGAGTTGAAGGAGAAGAAGCTCCGTGTTGAG
EST: gi|162160105|gb|FC335975.1|FC335975
EST:     AGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAG                         GTCGGAGCTCAAACCGAGACAGAGTTGAAGGAGAAGAAGCTCCGTGTTGAG
genomic: AGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAGgtatatgtct ... tcctgcgcagGTCGGAGCTCAAACCGAGACAGAGTTGAAGGAGAAGAAGCTCCGTGTTGAG
EST: gi|162190350|gb|FC365364.1|FC365364
EST:     GAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAG                         GTCGGAGCTCAAACCGAGACAGAGTTGAAGGAGAAGAAGCTCCGTGTTGAG
genomic: GAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAGgtatatgtct ... tcctgcgcagGTCGGAGCTCAAACCGAGACAGAGTTGAAGGAGAAGAAGCTCCGTGTTGAG
EST: gi|162150108|gb|FC326821.1|FC326821
EST:     AGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAG                         GTCGGAGCTCAAACCGAGACAGAGTTGAAGGAGAAGAAGCTCCGTGTTGAG
genomic: AGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAGgtatatgtct ... tcctgcgcagGTCGGAGCTCAAACCGAGACAGAGTTGAAGGAGAAGAAGCTCCGTGTTGAG
EST: gi|162157274|gb|FC332908.1|FC332908
EST:     AGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAG                         GTCGGAGCTCAAACCGAGACAGAGTTGAAGGAGAAGAAGCTCCGTGTTGAG
genomic: AGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAGgtatatgtct ... tcctgcgcagGTCGGAGCTCAAACCGAGACAGAGTTGAAGGAGAAGAAGCTCCGTGTTGAG

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), 23 (downstream exon)
Score: 10

CCAAATTCGCAACCTTATCGAAATTGCTGAGCAAGAGTACGAGAAGGAGAAGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAGgtatatgtct ... tcctgcgcagGTCGGAGCTCAAACCGAGACAGAGTTGAAGGAGAAGAAGCTCCGTGTTGAGGATGCGCTAAATGCCACCAAGGCTGCTGTGGAGGAAGGCATCGTCGTGG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAAATTCGCAACCTTATCGAAATTGCTGAGCAAGAGTACGAGAAGGAGAAGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAGgtatatgtcttcatttgtttcaatcataataagaatctgttagctccctgtcgtgacagcgtccactatatattctcaaattgttccgtgttgtggtttgcacaatgaaggcctctcttgacgtgggacttcctgcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA