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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaaatgttctcgagccctagtggtgataatggatctgtgtgatctcaccgtattcacaaattgacgagttggcctgtttttctttttcctcgtatgaagAATTCCTATACCACGAAGCAGTGATCAAGGGCTGAGAATCGATCCGTCTCGATTAAAGCTACTGGCTGTAGGCCAGTAAGCAATGGCCACTAAGTCCAGC

Basic information

species Physcomitrella patens
transcript PP1S90_134V6.1
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|18363008|gb|BJ195080.1|BJ195080
EST:     CCTCCTGAGTGTGTCGCACAGCTTCTTCTGCTTGTTCCTGCAGCTGCGAG                         AATTCCTATACCACGAAGCAGTGATCAAGGGCTGAGAATCGATCCGTCTCG
genomic: CCTCCTGAGTGTGTCGCACAGCTTCTTCTGCTTGTTCCTGCAGCTGCGAGgtgctcttac ... tcgtatgaagAATTCCTATACCACGAAGCAGTGATCAAGGGCTGAGAATCGATCCGTCTCG
EST: gi|18372531|gb|BJ204133.1|BJ204133
EST:     CCTCCTGAGTGTGTCGCACAGCTTCTTCTGCTTGTTCCTGCAGCTGCGAG                         AATTCCTATACCACGAAGCAGTGATCAAGGGCTGAGAATCGATCCGTCTCG
genomic: CCTCCTGAGTGTGTCGCACAGCTTCTTCTGCTTGTTCCTGCAGCTGCGAGgtgctcttac ... tcgtatgaagAATTCCTATACCACGAAGCAGTGATCAAGGGCTGAGAATCGATCCGTCTCG
EST: gi|18366005|gb|BJ198083.1|BJ198083
EST:     CCTCCTGAGTGTGTCGCACAGCTTCTTCTGCTTGTTCCTGCAGCTGCGAG                         AATTCCTATACCACGAAGCAGTGATCAAGGGCTGAGAATCGATCCGTCTCG
genomic: CCTCCTGAGTGTGTCGCACAGCTTCTTCTGCTTGTTCCTGCAGCTGCGAGgtgctcttac ... tcgtatgaagAATTCCTATACCACGAAGCAGTGATCAAGGGCTGAGAATCGATCCGTCTCG
EST: gi|100424327|gb|BY958429.1|BY958429
EST:     CCTCCTGAGTGTGTCGCACAGCTTCTTCTGCTTGTTCCTGCAGCTGCGAG                         AATTCCTATACCACGAAGCAGTGATCAAGGGCTGAGAATCGATCCGTCTCG
genomic: CCTCCTGAGTGTGTCGCACAGCTTCTTCTGCTTGTTCCTGCAGCTGCGAGgtgctcttac ... tcgtatgaagAATTCCTATACCACGAAGCAGTGATCAAGGGCTGAGAATCGATCCGTCTCG
EST: gi|18360741|gb|BJ192804.1|BJ192804
EST:     CCTCCTGAGTGTGTCGCACAGCTTCTTCTGCTTGTTCCTGCAGCTGCGAG                         AATTCCTATACCACGAAGCAGTGATCAAGGGCTGAGAATCGATCCGTCTCG
genomic: CCTCCTGAGTGTGTCGCACAGCTTCTTCTGCTTGTTCCTGCAGCTGCGAGgtgctcttac ... tcgtatgaagAATTCCTATACCACGAAGCAGTGATCAAGGGCTGAGAATCGATCCGTCTCG
EST: gi|18360443|gb|BJ192505.1|BJ192505
EST:     CCTCCTGAGTGTGTCGCACAGCTTCTTCTGCTTGTTCCTGCAGCTGCGAG                         AATTCCTATACCACGAAGCAGTGATCAAGGGCTGAGAATCGATCCGTCTCG
genomic: CCTCCTGAGTGTGTCGCACAGCTTCTTCTGCTTGTTCCTGCAGCTGCGAGgtgctcttac ... tcgtatgaagAATTCCTATACCACGAAGCAGTGATCAAGGGCTGAGAATCGATCCGTCTCG
EST: gi|67574551|gb|BJ947375.1|BJ947375
EST:     CCTCCTGAGTGTGTCGCACAGCTTCTTCTGCTTGTTCCTGCAGCTGCGAG                         AATTCCTATACCACGAAGCAGTGATCAAGGGCTGAGAATCGATCCGTCTCG
genomic: CCTCCTGAGTGTGTCGCACAGCTTCTTCTGCTTGTTCCTGCAGCTGCGAGgtgctcttac ... tcgtatgaagAATTCCTATACCACGAAGCAGTGATCAAGGGCTGAGAATCGATCCGTCTCG
EST: gi|18358297|gb|BJ190356.1|BJ190356
EST:     CCTCCTGAGTGTGTCGCACAGCTTCTTCTGCTTGTTCCTGCAGCTGCGAG                         AATTCCTATACCACGAAGCAGTGATCAAGGGCTGAGAATCGATCCGTCTCG
genomic: CCTCCTGAGTGTGTCGCACAGCTTCTTCTGCTTGTTCCTGCAGCTGCGAGgtgctcttac ... tcgtatgaagAATTCCTATACCACGAAGCAGTGATCAAGGGCTGAGAATCGATCCGTCTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaccgtattcacaaattgacgagttggcctgtttttctttttcctcgtatgaagAATTCCTATACCACGAAGCAGTGATCAAGGGCTGAGAATCGATCCGTCTCGATTAAAGCTACTGGCTGTAGGCCAGTAAGCAATGGCCACTAAGTCCAGC
              aattgac  putative branch site (score: 3)
                        ttggcctgtttttctt  putative PPT
                                tttttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaaatgttctcgagccctagtggtgataatggatctgtgtgatctcaccgtattcacaaattgacgagttggcctgtttttctttttcctcgtatgaagAATTCCTATACCACGAAGCAGTGATCAAGGGCTGAGAATCGATCCGTCTCGATTAAAGCTACTGGCTGTAGGCCAGTAAGCAATGGCCACTAAGTCCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA