Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tataattcttgctaaaaccttaaactatgaggaatcttgtaaatctgggcaaaatgtgttagcaacaaaaatgacttaccggctgagttgttatgaacagTTTTTGAACGACCTGATCCAAGATGAAAGCAAACCACCTCAGAAAAGTTTATTTGAGCTACGCATCAAACTGCTTGAAGAGCTTGAGTGGCCACACCTGG

Basic information

species Physcomitrella patens
transcript PP1S500_5V6.1
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|162152753|gb|FC329759.1|FC329759
EST:     TAACTGTGAAACGAGAAAAGCGCAGTGGTCGTTTCGGAAATGCTTTTAAG                         TTTTTGAACGCCCTGATCCAAGATGAAAGCAAACCCCCTCAGAAAAGTTTA
genomic: TAACTGTGAAACGAGAAAAGCGCAGTGGTCGTCTCGGAAATGCTTTTAAGgtaaagcatg ... ttatgaacagTTTTTGAACGACCTGATCCAAGATGAAAGCAAACCACCTCAGAAAAGTTTA
EST: gi|162208045|gb|FC384227.1|FC384227
EST:     TAACTGTGAAACGAGAAAAGCGCAGTGGTCGTCTCGGAAATGCTTTTAAG                         TTTTTGAACGACCTGATCCAAGATGAAAGCAAACCACCTCAGAAAAGTTTA
genomic: TAACTGTGAAACGAGAAAAGCGCAGTGGTCGTCTCGGAAATGCTTTTAAGgtaaagcatg ... ttatgaacagTTTTTGAACGACCTGATCCAAGATGAAAGCAAACCACCTCAGAAAAGTTTA
EST: gi|162237769|gb|FC413384.1|FC413384
EST:     TAACTGTGAAACGAGAAAAGCGCAGTGGTCGTCTCGGAAATGCTTTTAAG                         TTTTTGAACGACCTGATCCAAGATGAAAGCAAACCACCTCAGAAAAGTTTA
genomic: TAACTGTGAAACGAGAAAAGCGCAGTGGTCGTCTCGGAAATGCTTTTAAGgtaaagcatg ... ttatgaacagTTTTTGAACGACCTGATCCAAGATGAAAGCAAACCACCTCAGAAAAGTTTA
EST: gi|37829105|gb|BJ587117.1|BJ587117
EST:     TAACTGTGAAACGAGAAAAGCGCAGTGGTCGTCTCGGAAATGCTTTTAAG                         TTTTTGAACGACCTGATCCAAGATGAAAGCAAACCACCTCAGAAAAGTTTA
genomic: TAACTGTGAAACGAGAAAAGCGCAGTGGTCGTCTCGGAAATGCTTTTAAGgtaaagcatg ... ttatgaacagTTTTTGAACGACCTGATCCAAGATGAAAGCAAACCACCTCAGAAAAGTTTA
EST: gi|162236706|gb|FC413385.1|FC413385
EST:     TAACTGTGAAACGAGAAAAGCGCAGTGGTCGTCTCGGAAATGCTTTTAAG                         TTTTTGAACGACCTGATCCAAGATGAAAGCAAACCACCTCAGAAAAGTTTA
genomic: TAACTGTGAAACGAGAAAAGCGCAGTGGTCGTCTCGGAAATGCTTTTAAGgtaaagcatg ... ttatgaacagTTTTTGAACGACCTGATCCAAGATGAAAGCAAACCACCTCAGAAAAGTTTA
EST: gi|162158638|gb|FC335031.1|FC335031
EST:     TAACTGTGAAACGAGAAAAGCGCAGTGGTCGTCTCGGAAATGCTTTTAAG                         TTTTTGAACGACCTGATCCAAGATGAAAGCAAACCACCTCAGAAAAGTTTA
genomic: TAACTGTGAAACGAGAAAAGCGCAGTGGTCGTCTCGGAAATGCTTTTAAGgtaaagcatg ... ttatgaacagTTTTTGAACGACCTGATCCAAGATGAAAGCAAACCACCTCAGAAAAGTTTA
EST: gi|7286684|gb|AW599171.1|AW599171
EST:     GCGCAGTGGTCGTCTCGGAAATGCTTTTAAG                         TTTTTGAACGACCTGATCCAAGATGAAAGCAAACCACCTCAGAAAAGTTTA
genomic: GCGCAGTGGTCGTCTCGGAAATGCTTTTAAGgtaaagcatg ... ttatgaacagTTTTTGAACGACCTGATCCAAGATGAAAGCAAACCACCTCAGAAAAGTTTA
EST: gi|162161459|gb|FC337639.1|FC337639
EST:     TAACTGTGAAACGAGAAAAGCGCAGTGGTCGTCTCGGAAATGCTTTTAAG                         TTTTTGAACGACCTGATCCAAGATGAAAGCAAACCACCTCAGAAAAGTTTA
genomic: TAACTGTGAAACGAGAAAAGCGCAGTGGTCGTCTCGGAAATGCTTTTAAGgtaaagcatg ... ttatgaacagTTTTTGAACGACCTGATCCAAGATGAAAGCAAACCACCTCAGAAAAGTTTA
EST: gi|162208044|gb|FC384226.1|FC384226
EST:     TAACTGTGAAACGAGAAAAGCGCAGTGGTCGTCTCGGAAATGCTTTTAAG                         TTTTTGAACGACCTGATCCAAGATGAAAGCAAACCACTTCAGAAAAGTTTA
genomic: TAACTGTGAAACGAGAAAAGCGCAGTGGTCGTCTCGGAAATGCTTTTAAGgtaaagcatg ... ttatgaacagTTTTTGAACGACCTGATCCAAGATGAAAGCAAACCACCTCAGAAAAGTTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgggcaaaatgtgttagcaacaaaaatgacttaccggctgagttgttatgaacagTTTTTGAACGACCTGATCCAAGATGAAAGCAAACCACCTCAGAAAAGTTTATTTGAGCTACGCATCAAACTGCTTGAAGAGCTTGAGTGGCCACACCTGG
                           gacttac  putative branch site (score: 2)
                  aacaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tataattcttgctaaaaccttaaactatgaggaatcttgtaaatctgggcaaaatgtgttagcaacaaaaatgacttaccggctgagttgttatgaacagTTTTTGAACGACCTGATCCAAGATGAAAGCAAACCACCTCAGAAAAGTTTATTTGAGCTACGCATCAAACTGCTTGAAGAGCTTGAGTGGCCACACCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT