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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttgtgatttttgtgcaagtcgtgggctacactgtcctttaaggatgcgacagagttgttgctctctagctgatttgttttgctgcggggtatttgcagAATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGAATCTCCGGGACCGTGTCACTGGAATCCGGTTTCAGAGCAATA

Basic information

species Physcomitrella patens
transcript PP1S62_157V6.4
intron # 1
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|100451228|gb|CJ974660.1|CJ974660
EST:     TGTGCACTTCTTTGTTTCGTTAAAAGTTGTGTGTGCAAGTTGGGTTTGTG                         AATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
genomic: TGTGCACTTCTTTGTTTCGTTAAAAGTTGTGTGTGCAAGTTGGGTTTGTGgtgggttctc ... gtatttgcagAATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
EST: gi|18329484|gb|BJ161490.1|BJ161490
EST:     TGTGCACTTCTTTGTTTCGTTAAAAGTTGTGTGTGCAAGTTGGGTTTGTG                         AATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
genomic: TGTGCACTTCTTTGTTTCGTTAAAAGTTGTGTGTGCAAGTTGGGTTTGTGgtgggttctc ... gtatttgcagAATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
EST: gi|18354978|gb|BJ187037.1|BJ187037
EST:     TGTGCACTTCTTTGTTTCGTTAAAAGTTGTGTGTGCAAGTTGGGTTTGTG                         AATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
genomic: TGTGCACTTCTTTGTTTCGTTAAAAGTTGTGTGTGCAAGTTGGGTTTGTGgtgggttctc ... gtatttgcagAATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
EST: gi|100409386|gb|BY991986.1|BY991986
EST:     TGTGCACTTCTTTGTTTCGTTAAAAGTTGTGTGTGCAAGTTGGGTTTGTG                         AATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
genomic: TGTGCACTTCTTTGTTTCGTTAAAAGTTGTGTGTGCAAGTTGGGTTTGTGgtgggttctc ... gtatttgcagAATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
EST: gi|18328096|gb|BJ160100.1|BJ160100
EST:     TGTGCACTTCTTTGTTTCGTTAAAAGTTGTGTGTGCAAGTTGGGTTTGTG                         AATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
genomic: TGTGCACTTCTTTGTTTCGTTAAAAGTTGTGTGTGCAAGTTGGGTTTGTGgtgggttctc ... gtatttgcagAATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
EST: gi|18363878|gb|BJ195950.1|BJ195950
EST:     GTGCAAGTTGGGTTTGTG                         AATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
genomic: GTGCAAGTTGGGTTTGTGgtgggttctc ... gtatttgcagAATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
EST: gi|162179792|gb|FC356383.1|FC356383
EST:     TGTGCACTTCTTTGTTTCGTTAAAAGTTGTGTGTGCAAGTTGGGTTTGTG                         AATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
genomic: TGTGCACTTCTTTGTTTCGTTAAAAGTTGTGTGTGCAAGTTGGGTTTGTGgtgggttctc ... gtatttgcagAATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcgacagagttgttgctctctagctgatttgttttgctgcggggtatttgcagAATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGAATCTCCGGGACCGTGTCACTGGAATCCGGTTTCAGAGCAATA
                       agctgat  putative branch site (score: 4)
                            atttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttgtgatttttgtgcaagtcgtgggctacactgtcctttaaggatgcgacagagttgttgctctctagctgatttgttttgctgcggggtatttgcagAATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGAATCTCCGGGACCGTGTCACTGGAATCCGGTTTCAGAGCAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA