Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATGACGAATTCTCCAGAGTTCTGCACCAGCAGATGGAATACTTCTCTAGCAATCCAAATGCAGATACGATAAACAGAGTGAAAGGGGAAATAGCAGAGgtatattatgttgcaagcgactcatgggctaggaataccttgctctttctacgcgtacttagctgaatcaccatcttttaaatctagtgatctatcgcatctgctcaaggcttgtgcgtagcttagagctgttgtttaactaagtccctctgcatcag

Basic information

species Physcomitrella patens
transcript PP1S115_125V6.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S115_125V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: AT5G22360.1 (Arabidopsis thaliana), 5'ss of exon 2
GAATGACGAATTCTCCAGAGTTCTGCACCAGCAGATGGAATACTTCTCTAGCAATCCAAATGCAGATACGATAAACAGAGTGAAAGGGGAAATAGCAGAGgtatattatgttgcaagcgactcatgggctaggaataccttgctctttctacgcgtacttagctgaatcaccat---cttttaaatctagtgatctatcgcat-ctgctcaaggcttgtgcgtagcttagagctgttgtttaactaagtccct-ctgcatcag-----------
|||||| |||||||| || ||| |||| ||||||||||| | ||||||||| ||||| | ||  |||||  | ||  | || | ||| ||| |    |||||||| | |||| |   ||  | ||        | |||   ||| | || |     |    | |||||    ||    | |||   ||  |   ||  | ||  || ||  |    ||| | | | | | || ||  ||||   ||  ||  |  ||  | |            
GAATGATGAATTCTCAAGGGTTTTGCATCAGCAGATGGAGTTCTTCTCTAGTAATCCTAGTGTTGATACTCTCAATCGTGTTAGAGGAGAAGTCAGTGAGgtataat-tgtttctt-cgtatgatctctagatattactcagctatatccattgaaaa--ggttgaatttttatgagttattacgccttcttggctcacacaggcttctttaaatctgt-cttgggtgaaagatgaagtttg-ttatctcattgttgtgttatcgtgtttacag

upper sequence: PP1S115_125V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: EFJ30194 (Selaginella moellendorffii), 5'ss of exon 2
GAATGACGAATTCTCCAGAGTTCTGCACCAGCAGATGGAATACTTCTCTAGCAATCCAAATGCAGATACGATAAACAGAGTGAAAGGGGAAATAGCAGAGgtatattatgttgcaagcgactcatgggctaggaataccttgctctttctacgcgtacttagctgaatcaccatcttttaaatctagtgatctatcgcatctgctcaaggcttgtgcgtagcttagagctgttgtttaactaagtccctctgcatcag
||| ||||| || || |||||| |||||||||||||||||||||| || |  || ||  | || || ||||| ||  | || ||||| ||  ||   ||||||       |  | | | | || |          |   | | ||||   || |   ||    |   || |  | ||  |                                                                              
GAACGACGAGTTTTCTAGAGTTTTGCACCAGCAGATGGAATACTTTTCCAATAACCCCGAGGCGGACACGATCAATCGGGTCAAAGGCGATCTAAACGAGgtagg---catgactatccattctt----------tgtttggttcttctcacactggct---gtcgctcgcggtgttccag-----------------------------------------------------------------------------

upper sequence: PP1S115_125V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: EFJ06041 (Selaginella moellendorffii), 5'ss of exon 2
GAATGACGAATTCTCCAGAGTTCTGCACCAGCAGATGGAATACTTCTCTAGCAATCCAAATGCAGATACGATAAACAGAGTGAAAGGGGAAATAGCAGAGgtatattatgttgcaagcgactcatgggctaggaataccttgctctttctacgcgtacttagctgaatcaccatcttttaaatctagtgatctatcgcatctgctcaaggcttgtgcgtagcttagagctgttgtttaactaagtccctctgcatcag
||| ||||| || || |||||| |||||||||||||||||||||| || |  || ||  | || || ||||| |   | || ||||| ||  ||   ||||||       |   | | ||   |      || ||        ||||| |  | || |||  |  | |  |  ||  |        ||| || |                                                                
GAACGACGAGTTTTCTAGAGTTTTGCACCAGCAGATGGAATACTTTTCCAATAACCCCGAGGCGGACACGATCAGTCGGGTCAAAGGCGATCTAAACGAGgtagg---catgagaggagaaaaaaaaagaagaaactatccattctttgtttg-gttcttctcacactggctgtcgctcg----cggtgttccag---------------------------------------------------------------

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|37832285|gb|BJ590297.1|BJ590297
EST:     AATCCAAATGCAGATACGATAANCAGAGTGAAAGGGGAAATAGCAGAG                         GTTCGGGCTGTCATGGTGGAGAATATCGATAAAGTGCTGGAGAGAGGTGAT
genomic: AATCCAAATGCAGATACGATAAACAGAGTGAAAGGGGAAATAGCAGAGgtatattatg ... tctgcatcagGTTCGGGCTGTCATGGTGGAGAATATCGATAAAGTGCTGGAGAGAGGTGAT
EST: gi|37842940|gb|BJ600948.1|BJ600948
EST:     GCAATCCAAATGCAGATACGATAAACAGAGTGAAAGGGGAAATAGCAGAG                         GTTCGGGCTGTCATGGTGGAGAATATCGATAAAGTGCTGGAGAGAGGTGAT
genomic: GCAATCCAAATGCAGATACGATAAACAGAGTGAAAGGGGAAATAGCAGAGgtatattatg ... tctgcatcagGTTCGGGCTGTCATGGTGGAGAATATCGATAAAGTGCTGGAGAGAGGTGAT
EST: gi|100393349|gb|BY989833.1|BY989833
EST:     GCAATCCAAATGCAGATACGATAAACAGATTGAAAGGGGAAATAGCAGAG                         GTTCGGGCTGTCATGGTGGAGAATATCGATAAAGTGCTGGAGAGAGGTGAT
genomic: GCAATCCAAATGCAGATACGATAAACAGAGTGAAAGGGGAAATAGCAGAGgtatattatg ... tctgcatcagGTTCGGGCTGTCATGGTGGAGAATATCGATAAAGTGCTGGAGAGAGGTGAT
EST: gi|162274387|gb|FC450414.1|FC450414
EST:     GCAATCCAAATGCAGATTCGATAAACAGAGTGAAAGGGGAAATAGCAGAG                         GTTCGGGCTGTCATGGTGGAGAATATCGATAAAGTGCTGGAGAGAGGTGAT
genomic: GCAATCCAAATGCAGATACGATAAACAGAGTGAAAGGGGAAATAGCAGAGgtatattatg ... tctgcatcagGTTCGGGCTGTCATGGTGGAGAATATCGATAAAGTGCTGGAGAGAGGTGAT
EST: gi|37850241|gb|BJ608249.1|BJ608249
EST:     AATCCAAATGCAGATACGATAAACAGAGTGAAAGGGGAAATAGCAGAG                         GTTCGGGCTGTCATGGTGGAGAATATCGATAAAGTGCTGGAGAGAGGTGAT
genomic: AATCCAAATGCAGATACGATAAACAGAGTGAAAGGGGAAATAGCAGAGgtatattatg ... tctgcatcagGTTCGGGCTGTCATGGTGGAGAATATCGATAAAGTGCTGGAGAGAGGTGAT
EST: gi|162170465|gb|FC347637.1|FC347637
EST:     ACGATAAACAGAGTGAAAGGGGAAATAGCAGAG                         GTTCGGGCTGTCATGGTGGAGAATATCGATAAAGTGCTGGAGAGAGGTGAT
genomic: ACGATAAACAGAGTGAAAGGGGAAATAGCAGAGgtatattatg ... tctgcatcagGTTCGGGCTGTCATGGTGGAGAATATCGATAAAGTGCTGGAGAGAGGTGAT
EST: gi|37852406|gb|BJ610414.1|BJ610414
EST:     AATGCAGATACGATAAACAGAGTGAAAGGGGAAATAGCAGAG                         GTTCGGGCTGTCATGGTGGAGAATATCGATAAAGTGCTGGAGAGAGGTGAT
genomic: AATGCAGATACGATAAACAGAGTGAAAGGGGAAATAGCAGAGgtatattatg ... tctgcatcagGTTCGGGCTGTCATGGTGGAGAATATCGATAAAGTGCTGGAGAGAGGTGAT
EST: gi|208361290|gb|DC930329.1|DC930329
EST:     GCAATCCAAATGCAGATACGATAAACAGAGTGAAAGGGGAAATAGCAGAG                         GTTCGGGCTGTCATGGTGGAGAATATCGATAAAGTGCTGGAGAGAGGTGAT
genomic: GCAATCCAAATGCAGATACGATAAACAGAGTGAAAGGGGAAATAGCAGAGgtatattatg ... tctgcatcagGTTCGGGCTGTCATGGTGGAGAATATCGATAAAGTGCTGGAGAGAGGTGAT
EST: gi|37845521|gb|BJ603529.1|BJ603529
EST:     GCAATCCAAATGCAGATACGATAAACAGAGTGAAAGGGGAAATAGCAGAG                         GTTCGGGCTGTCATGGTGGAGAATATCGATAAAGTGCTGGAGAGAGGTGAT
genomic: GCAATCCAAATGCAGATACGATAAACAGAGTGAAAGGGGAAATAGCAGAGgtatattatg ... tctgcatcagGTTCGGGCTGTCATGGTGGAGAATATCGATAAAGTGCTGGAGAGAGGTGAT
EST: gi|18335867|gb|BJ167888.1|BJ167888
EST:     ATCCAAATGCAGATACGATAAACAGAGTGAAAGGGGAAATAGCAGAG                         GTTCGGGCTGTCATGGTGGAGAATATCGATAAAGTGCTGGAGAGAGGTGAT
genomic: ATCCAAATGCAGATACGATAAACAGAGTGAAAGGGGAAATAGCAGAGgtatattatg ... tctgcatcagGTTCGGGCTGTCATGGTGGAGAATATCGATAAAGTGCTGGAGAGAGGTGAT
EST: gi|7207413|gb|AW561415.1|AW561415
EST:     AAACAGAGTGAAAGGGGAAATAGCAGAG                         GTTCGGGCTGTCATGGTGGAGAATATCGATAAAGTGCTGGAGAGAGGTGAT
genomic: AAACAGAGTGAAAGGGGAAATAGCAGAGgtatattatg ... tctgcatcagGTTCGGGCTGTCATGGTGGAGAATATCGATAAAGTGCTGGAGAGAGGTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAATGACGAATTCTCCAGAGTTCTGCACCAGCAGATGGAATACTTCTCTAGCAATCCAAATGCAGATACGATAAACAGAGTGAAAGGGGAAATAGCAGAGgtatattatgttgcaagcgactcatgggctaggaataccttgctctttctacgcgtacttagctgaatcaccatcttttaaatctagtgatctatcgcatctgctcaaggcttgtgcgtagcttagagctgttgtttaactaagtccctctgcatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT