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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttagtttctgcttgatccttgtggtgtagagtaaggaatgtcacatgcagactcgggtgtggtacgattgatgttaaaggtggtttccgtttgtgtagGACTCGTTGATGCCGTCACTTTATCTGAGTTGGAGAGTTCATTCAACGCATTTGGCATTGTGAAACATCACCTAGCCAGTGCATGGCATGATCTACAAGC

Basic information

species Physcomitrella patens
transcript PP1S54_317V6.1
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|18329064|gb|BJ161070.1|BJ161070
EST:     GTCTTGTCGCTGGGGAGCTTTGCCGATTCATCGCCGTAGTATCAACTTAG                         GACTCGTTGATGCCGTCACTTTATCTGAGTTGGAGAGTTCATTCAACGCAT
genomic: GTCTTGTCGCTGGGGAGCTTTGCCGATTCATCGCCGTAGTATCAACTTAGgtaagcgaga ... gtttgtgtagGACTCGTTGATGCCGTCACTTTATCTGAGTTGGAGAGTTCATTCAACGCAT
EST: gi|67576799|gb|BJ949623.1|BJ949623
EST:     GTCTTGTCGCTGGGGAGCTTTGCCGATTCATCGCCGTAGTATCAACTTAG                         GACTCGTTGATGCCGTCACTTTATCTGAGTTGGAGAGTTCATTCAACGCAT
genomic: GTCTTGTCGCTGGGGAGCTTTGCCGATTCATCGCCGTAGTATCAACTTAGgtaagcgaga ... gtttgtgtagGACTCGTTGATGCCGTCACTTTATCTGAGTTGGAGAGTTCATTCAACGCAT
EST: gi|67571047|gb|BJ943871.1|BJ943871
EST:     GTCTTGTCGCTGGGGAGCTTTGCCGATTCATCGCCGTAGTATCAACTTAG                         GACTCGTTGATGCCGTCACTTTATCTGAGTTGGAGAGTTCATTCAACGCAT
genomic: GTCTTGTCGCTGGGGAGCTTTGCCGATTCATCGCCGTAGTATCAACTTAGgtaagcgaga ... gtttgtgtagGACTCGTTGATGCCGTCACTTTATCTGAGTTGGAGAGTTCATTCAACGCAT
EST: gi|100427036|gb|BY958941.1|BY958941
EST:     GTCTTGTCGCTGGGGAGCTTTGCCGATTCATCGCCGTAGTATCAACTTAG                         GACTCGTTGATGCCGTCACTTTATCTGAGTTGGAGAGTTCATTCAACGCAT
genomic: GTCTTGTCGCTGGGGAGCTTTGCCGATTCATCGCCGTAGTATCAACTTAGgtaagcgaga ... gtttgtgtagGACTCGTTGATGCCGTCACTTTATCTGAGTTGGAGAGTTCATTCAACGCAT
EST: gi|100436023|gb|BY979341.1|BY979341
EST:     GTCTTGTCGCTGGGGAGCTTTGCCGATTCATCGCCGTAGTATCAACTTAG                         GACTCGTTGATGCCGTCACTTTATCTGAGTTGGAGAGTTCATTCAACGCAT
genomic: GTCTTGTCGCTGGGGAGCTTTGCCGATTCATCGCCGTAGTATCAACTTAGgtaagcgaga ... gtttgtgtagGACTCGTTGATGCCGTCACTTTATCTGAGTTGGAGAGTTCATTCAACGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgcagactcgggtgtggtacgattgatgttaaaggtggtttccgtttgtgtagGACTCGTTGATGCCGTCACTTTATCTGAGTTGGAGAGTTCATTCAACGCATTTGGCATTGTGAAACATCACCTAGCCAGTGCATGGCATGATCTACAAGC
                      gattgat  putative branch site (score: 4)
                                        tttccgttt  putative PPT
                           atgttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttagtttctgcttgatccttgtggtgtagagtaaggaatgtcacatgcagactcgggtgtggtacgattgatgttaaaggtggtttccgtttgtgtagGACTCGTTGATGCCGTCACTTTATCTGAGTTGGAGAGTTCATTCAACGCATTTGGCATTGTGAAACATCACCTAGCCAGTGCATGGCATGATCTACAAGC

- - - - - - - - - - - - - - - - - - - - - -cacatgc