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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctacattttcaaaatggtttgagcgttggtgaaggattctgtgtttttttggtaacattggtgggtattggaacatctgttttttttgttgtgtgcagGGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGAATCAACAGAAGTTATTCTGAATGCGGCCATCAAATACGCACTGAGGCGG

Basic information

species Physcomitrella patens
transcript PP1S90_133V6.1
intron # 5
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|67693566|gb|BJ953799.1|BJ953799
EST:     ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAG                         GGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
genomic: ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAGgtaatgttcc ... ttgtgtgcagGGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
EST: gi|67696530|gb|BJ956763.1|BJ956763
EST:     ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAG                         GGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
genomic: ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAGgtaatgttcc ... ttgtgtgcagGGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
EST: gi|162180804|gb|FC358305.1|FC358305
EST:     ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAG                         GGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
genomic: ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAGgtaatgttcc ... ttgtgtgcagGGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
EST: gi|162231958|gb|FC409032.1|FC409032
EST:     ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAG                         GGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
genomic: ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAGgtaatgttcc ... ttgtgtgcagGGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
EST: gi|162168678|gb|FC343940.1|FC343940
EST:     ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAG                         GGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
genomic: ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAGgtaatgttcc ... ttgtgtgcagGGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
EST: gi|162276390|gb|FC452445.1|FC452445
EST:     ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAG                         GGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
genomic: ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAGgtaatgttcc ... ttgtgtgcagGGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
EST: gi|208373198|gb|DC945152.1|DC945152
EST:     ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAG                         GGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
genomic: ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAGgtaatgttcc ... ttgtgtgcagGGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
EST: gi|162276389|gb|FC452444.1|FC452444
EST:     ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAG                         GGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
genomic: ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAGgtaatgttcc ... ttgtgtgcagGGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
EST: gi|162256711|gb|FC433229.1|FC433229
EST:     ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAG                         GGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
genomic: ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAGgtaatgttcc ... ttgtgtgcagGGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
EST: gi|162201557|gb|FC377439.1|FC377439
EST:     ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAG                         GGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
genomic: ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAGgtaatgttcc ... ttgtgtgcagGGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
EST: gi|67700956|gb|BJ961189.1|BJ961189
EST:     ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAG                         GGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
genomic: ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAGgtaatgttcc ... ttgtgtgcagGGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
EST: gi|162184089|gb|FC358835.1|FC358835
EST:     ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAG                         GGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
genomic: ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAGgtaatgttcc ... ttgtgtgcagGGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
EST: gi|162256710|gb|FC433228.1|FC433228
EST:     ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAG                         GGGTTTAATTCCTTTCTTGGCGGAAGGTTCAGCAAGATTTACTGATTTGGA
genomic: ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAGgtaatgttcc ... ttgtgtgcagGGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
EST: gi|162168677|gb|FC343939.1|FC343939
EST:     ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAG                         GGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
genomic: ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAGgtaatgttcc ... ttgtgtgcagGGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
EST: gi|162238393|gb|FC417352.1|FC417352
EST:     ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAG                         GGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
genomic: ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAGgtaatgttcc ... ttgtgtgcagGGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
EST: gi|19778710|gb|BQ039344.1|BQ039344
EST:     ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAG                         GGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
genomic: ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAGgtaatgttcc ... ttgtgtgcagGGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
EST: gi|162238394|gb|FC417353.1|FC417353
EST:     ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAG                         GGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
genomic: ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAGgtaatgttcc ... ttgtgtgcagGGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
EST: gi|162188470|gb|FC365068.1|FC365068
EST:     ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAG                         GGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
genomic: ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAGgtaatgttcc ... ttgtgtgcagGGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
EST: gi|67570295|gb|BJ943119.1|BJ943119
EST:     ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAG                         GGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA
genomic: ACCTGGACTTGCAGCGAGGAGTCCCCAGCTCATCACAGCTTAGTGGTCAGgtaatgttcc ... ttgtgtgcagGGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttttggtaacattggtgggtattggaacatctgttttttttgttgtgtgcagGGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGAATCAACAGAAGTTATTCTGAATGCGGCCATCAAATACGCACTGAGGCGG
      tggtaac  putative branch site (score: 2)
                                tctgttttttttgtt  putative PPT
                                    ttttttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctacattttcaaaatggtttgagcgttggtgaaggattctgtgtttttttggtaacattggtgggtattggaacatctgttttttttgttgtgtgcagGGGTTTAATTCCTCTCTTGGCGGAAGGTTCAGCAAGATCTACTGATTCGGAATCAACAGAAGTTATTCTGAATGCGGCCATCAAATACGCACTGAGGCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT