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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtatctgataataggtgaagttaggtgcaaatttcttcatctgtatcacggtacatgaacttttatggatttattttgacgttgaggataacaattccagGTTGTAGATCACTACGACAATCCTCGGAATGTTGGGTCATTCGACAAGAACGACCCTAATGTTGGAACTGGCTTGGTAGGTGCTCCTGCTTGTGGAGATG

Basic information

species Physcomitrella patens
transcript PP1S76_212V6.1
intron # 2
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|18325020|gb|BJ157016.1|BJ157016
EST:     AAGCTGGCCGGGTATCTCTTGTATCTGGACAGAGGTTCTACCACGAGAAG                         GTTGTAGATCACTACGACAATCCTCGGAATGTTGGGTCATTCGACAAGAAC
genomic: AAGCTGGCCGGGTATCTCTTGTATCTGGACAGAGGTTCTACCACGAGAAGgtatgtattg ... acaattccagGTTGTAGATCACTACGACAATCCTCGGAATGTTGGGTCATTCGACAAGAAC
EST: gi|18348082|gb|BJ180129.1|BJ180129
EST:     AAGCTGGCCGGGTATCTCTTGTATCTGGACAGAGGTTCTACCACGAGAAG                         GTTGTAGATCACTACGACAATCCTCGGAATGTTGGGTCATTCGACAAGAAC
genomic: AAGCTGGCCGGGTATCTCTTGTATCTGGACAGAGGTTCTACCACGAGAAGgtatgtattg ... acaattccagGTTGTAGATCACTACGACAATCCTCGGAATGTTGGGTCATTCGACAAGAAC
EST: gi|67508569|gb|BJ941432.1|BJ941432
EST:     AAGCTGGCCGGGTATCTCTTGTATCTGGACAGAGGTTCTACCACGAGAAG                         GTTGTAGATCACTACGACAATCCTCGGAATGTTGGGTCATTCGACAAGAAC
genomic: AAGCTGGCCGGGTATCTCTTGTATCTGGACAGAGGTTCTACCACGAGAAGgtatgtattg ... acaattccagGTTGTAGATCACTACGACAATCCTCGGAATGTTGGGTCATTCGACAAGAAC
EST: gi|18345107|gb|BJ177148.1|BJ177148
EST:     AAGCTGGCCGGGTATCTCTTGTATCTGGACAGAGGTTCTACCACGAGAAG                         GTTGTAGATCACTACGACAATCCTCGGAATGTTGGGTCATTCGACAAGAAC
genomic: AAGCTGGCCGGGTATCTCTTGTATCTGGACAGAGGTTCTACCACGAGAAGgtatgtattg ... acaattccagGTTGTAGATCACTACGACAATCCTCGGAATGTTGGGTCATTCGACAAGAAC
EST: gi|37827453|gb|BJ585465.1|BJ585465
EST:     AAGCTGGCCGGGTATCTCTTGTATCTGGACAGAGGTTCTACCACGAGAAG                         GTTGTAGATCACTACGACAATCCTCGGAATGTTGGGTCATTCGACAAGAAC
genomic: AAGCTGGCCGGGTATCTCTTGTATCTGGACAGAGGTTCTACCACGAGAAGgtatgtattg ... acaattccagGTTGTAGATCACTACGACAATCCTCGGAATGTTGGGTCATTCGACAAGAAC
EST: gi|37824297|gb|BJ582363.1|BJ582363
EST:     TATCTGGACAGAGGTTNTACCACGAGAAG                         GTTGTAGATCACTACGACAATCCTCGGAATGTTGGGTCATTCGACAAGAAC
genomic: TATCTGGACAGAGGTTCTACCACGAGAAGgtatgtattg ... acaattccagGTTGTAGATCACTACGACAATCCTCGGAATGTTGGGTCATTCGACAAGAAC
EST: gi|162177238|gb|FC353395.1|FC353395
EST:     AAGCTGGCCGGGTATCTCTTGTATCTGGACAGAGGTTCTACCACGAGAAG                         GTTGTAGATCACTACGACAATCCTCGGAATGTTGGGTCATTCGACAAGAAC
genomic: AAGCTGGCCGGGTATCTCTTGTATCTGGACAGAGGTTCTACCACGAGAAGgtatgtattg ... acaattccagGTTGTAGATCACTACGACAATCCTCGGAATGTTGGGTCATTCGACAAGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacggtacatgaacttttatggatttattttgacgttgaggataacaattccagGTTGTAGATCACTACGACAATCCTCGGAATGTTGGGTCATTCGACAAGAACGACCCTAATGTTGGAACTGGCTTGGTAGGTGCTCCTGCTTGTGGAGATG
                                        ggataac  putative branch site (score: 3)
               ttttatggatttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatctgataataggtgaagttaggtgcaaatttcttcatctgtatcacggtacatgaacttttatggatttattttgacgttgaggataacaattccagGTTGTAGATCACTACGACAATCCTCGGAATGTTGGGTCATTCGACAAGAACGACCCTAATGTTGGAACTGGCTTGGTAGGTGCTCCTGCTTGTGGAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG