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

...aggcgtacatgttgtatcacgtaaataacggccattttgtacatatattctgcgagacttatctttgtggcgtcgctcttgatttgcgttctggttacagTGAGGTCGATGAAATATACAAAATCTGTTCTGTGATCGGGACTCCTACTCATCAAACATGGCCTGATGGCATGAAGCTGGCAACTTCTTTGAACTTTCAG

Basic information

species Physcomitrella patens
transcript PP1S28_184V6.2
intron # 6
splice site 3'
intron type U2

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|162172239|gb|FC348804.1|FC348804
EST:     GCTATAATGGCTGAACTTTTCACTTTTCGCCCACTTTTTCCTGGAGCAAG                         TGAGGTCGATGAAATATACAAAATCTGTTCTGTGATCGGGACTCCTACTCA
genomic: GCTATAATGGCTGAACTTTTCACTTTTCGCCCACTTTTTCCTGGAGCAAGgtacagtatc ... ctggttacagTGAGGTCGATGAAATATACAAAATCTGTTCTGTGATCGGGACTCCTACTCA
EST: gi|100452665|gb|CJ975383.1|CJ975383
EST:     GCTATAATGGCTGAACTTTTCACTTTTCGCCCACTTTTTCCTGGAGCAAG                         TGAGGTCGATGAAATATACAAAATCTGTTCTGTGATCGGGACTCCTACTCA
genomic: GCTATAATGGCTGAACTTTTCACTTTTCGCCCACTTTTTCCTGGAGCAAGgtacagtatc ... ctggttacagTGAGGTCGATGAAATATACAAAATCTGTTCTGTGATCGGGACTCCTACTCA
EST: gi|162171440|gb|FC346715.1|FC346715
EST:     GCTATAATGGCTGAACTTTTCACTTTTCGCCCACTTTTTCCTGGAGCAAG                         TGAGGTCGATGAAATATACAAAATCTGTTCTGTGATCGGGACTCCTACTCA
genomic: GCTATAATGGCTGAACTTTTCACTTTTCGCCCACTTTTTCCTGGAGCAAGgtacagtatc ... ctggttacagTGAGGTCGATGAAATATACAAAATCTGTTCTGTGATCGGGACTCCTACTCA
EST: gi|100445020|gb|BY964319.1|BY964319
EST:     GCTATAATGGCTGAACTTTTCACTTTTCGCCCACTTTTTCCTGGAGCAAG                         TGAGGTCGATGAAATATACAAAATCTGTTCTGTGATCGGGACTCCTACTCA
genomic: GCTATAATGGCTGAACTTTTCACTTTTCGCCCACTTTTTCCTGGAGCAAGgtacagtatc ... ctggttacagTGAGGTCGATGAAATATACAAAATCTGTTCTGTGATCGGGACTCCTACTCA
EST: gi|162169093|gb|FC345983.1|FC345983
EST:     GCTATAATGGCTGAACTTTTCACTTTTCGCCCACTTTTTCCTGGAGCAAG                         TGAGGTCGATGAAATATACAAAATCTGTTCTGTGATCGGGACTCCTACTCA
genomic: GCTATAATGGCTGAACTTTTCACTTTTCGCCCACTTTTTCCTGGAGCAAGgtacagtatc ... ctggttacagTGAGGTCGATGAAATATACAAAATCTGTTCTGTGATCGGGACTCCTACTCA
EST: gi|100434800|gb|BY960838.1|BY960838
EST:     GCTATAATGGCTGAACTTTTCACTTTTCGCCCACTTTTTCCTGGAGCAAG                         TGAGGTCGATGAAATGTACAAAATCTGTTCTGTGATCGGGACTCCTACTCA
genomic: GCTATAATGGCTGAACTTTTCACTTTTCGCCCACTTTTTCCTGGAGCAAGgtacagtatc ... ctggttacagTGAGGTCGATGAAATATACAAAATCTGTTCTGTGATCGGGACTCCTACTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattctgcgagacttatctttgtggcgtcgctcttgatttgcgttctggttacagTGAGGTCGATGAAATATACAAAATCTGTTCTGTGATCGGGACTCCTACTCATCAAACATGGCCTGATGGCATGAAGCTGGCAACTTCTTTGAACTTTCAG
                               tcttgat  putative branch site (score: 4)
             ttatcttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggcgtacatgttgtatcacgtaaataacggccattttgtacatatattctgcgagacttatctttgtggcgtcgctcttgatttgcgttctggttacagTGAGGTCGATGAAATATACAAAATCTGTTCTGTGATCGGGACTCCTACTCATCAAACATGGCCTGATGGCATGAAGCTGGCAACTTCTTTGAACTTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG