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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attcaatattcagtccaagtgatagttcccagttacatgtatcaatatcatattttgtgatacgttattgacacagaaatcgggcctcgtgtggctgcagGGCAAGGGACTTCAACGTGCAATCACTTCTGAACCACATGTTGAGCGCTGAAATGGAGAAGAACAAGTCTTGAGTATTGTGAGAACAACATCTAACGCTC

Basic information

species Physcomitrella patens
transcript PP1S45_277V6.2
intron # 22
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|162185545|gb|FC361477.1|FC361477
EST:     GCCGACAGGTTCAACCCGCGGCGCAGAGCAAAGAG                         GGCAAGGGACTTCAACGTGCAATCACTTCTGAACCACATGTTGAGCGCTGA
genomic: GCCGACAGGTTCAACCCGCGGCGCAGAGCAAAGAGgtatcattct ... gtggctgcagGGCAAGGGACTTCAACGTGCAATCACTTCTGAACCACATGTTGAGCGCTGA
EST: gi|162163012|gb|FC338402.1|FC338402
EST:     GCCGACAGGTTCAACCCGCGGCGCAGAGCAAAGAG                         GGCAAGGGACTTCAACGTGCAATCACTTCTGAACCACATGTTGAGCGCTGA
genomic: GCCGACAGGTTCAACCCGCGGCGCAGAGCAAAGAGgtatcattct ... gtggctgcagGGCAAGGGACTTCAACGTGCAATCACTTCTGAACCACATGTTGAGCGCTGA
EST: gi|37846978|gb|BJ604986.1|BJ604986
EST:     GCCGACAGGTTCAACCCGCGGCGCAGAGCAAAGAG                         GGCAAGGGACTTCAACGTGCAATCACTTCTGAACCACATGTTGAGCGCTGA
genomic: GCCGACAGGTTCAACCCGCGGCGCAGAGCAAAGAGgtatcattct ... gtggctgcagGGCAAGGGACTTCAACGTGCAATCACTTCTGAACCACATGTTGAGCGCTGA
EST: gi|37843463|gb|BJ601471.1|BJ601471
EST:     GCCGACAGGTTCAACCCGCGGCGCAGAGCAAAGAG                         GGCAAGGGACTTCAACGTGCAATCACTTCTGAACCACATGTTGAGCGCTGA
genomic: GCCGACAGGTTCAACCCGCGGCGCAGAGCAAAGAGgtatcattct ... gtggctgcagGGCAAGGGACTTCAACGTGCAATCACTTCTGAACCACATGTTGAGCGCTGA
EST: gi|18335079|gb|BJ167097.1|BJ167097
EST:     GCCGACAGGTTCAACCCGCGGCGCAGAGCAAAGAG                         GGCAAGGGACTTCAACGTGCAATCACTTCTGAACCACATGTTGAGCGCTGA
genomic: GCCGACAGGTTCAACCCGCGGCGCAGAGCAAAGAGgtatcattct ... gtggctgcagGGCAAGGGACTTCAACGTGCAATCACTTCTGAACCACATGTTGAGCGCTGA
EST: gi|37851600|gb|BJ609608.1|BJ609608
EST:     GCCGACAGGTTCAACCCGCGGCGCAGAGCAAAGAG                         GGCAAGGGACTTCAACGTGCAATCACTTCTGAACCACATGTTGAGCGCTGA
genomic: GCCGACAGGTTCAACCCGCGGCGCAGAGCAAAGAGgtatcattct ... gtggctgcagGGCAAGGGACTTCAACGTGCAATCACTTCTGAACCACATGTTGAGCGCTGA
EST: gi|37847156|gb|BJ605164.1|BJ605164
EST:     GCCGACAGGTTCAACCCGCGGCGCAGAGCAAAGAG                         GGCAAGGGACTTCAACGTGGCAATCACTTCTGAACCACATGTTGAGCGCTG
genomic: GCCGACAGGTTCAACCCGCGGCGCAGAGCAAAGAGgtatcattct ... gtggctgcagGGCAAGGGACTTCAACGT-GCAATCACTTCTGAACCACATGTTGAGCGCTG
EST: gi|37850950|gb|BJ608958.1|BJ608958
EST:     GCCGACAGGTTCAACCCGCGGCGCAGAGCAAAGAG                         GGCAAGGGACTTCAACGTGCAATCACTTCTGAACCACATGTTGAGCGCTGA
genomic: GCCGACAGGTTCAACCCGCGGCGCAGAGCAAAGAGgtatcattct ... gtggctgcagGGCAAGGGACTTCAACGTGCAATCACTTCTGAACCACATGTTGAGCGCTGA
EST: gi|37848518|gb|BJ606526.1|BJ606526
EST:     GCCGACAGGTTCAACCCGCGGCGCAGAGCAAAGAG                         GGCAAGGGACTTCAACGTGCAATCACTTCTGAACCACATGTTGAGCGCTGA
genomic: GCCGACAGGTTCAACCCGCGGCGCAGAGCAAAGAGgtatcattct ... gtggctgcagGGCAAGGGACTTCAACGTGCAATCACTTCTGAACCACATGTTGAGCGCTGA
EST: gi|37853036|gb|BJ611044.1|BJ611044
EST:     GCCGACAGGTTCAACCCGCGGCGCAGAGCAAAGAG                         GGCAAGGGACTTCAACGTGCAATCACTTCTGAACCACATGTTGAGCGCTGA
genomic: GCCGACAGGTTCAACCCGCGGCGCAGAGCAAAGAGgtatcattct ... gtggctgcagGGCAAGGGACTTCAACGTGCAATCACTTCTGAACCACATGTTGAGCGCTGA
EST: gi|37850034|gb|BJ608042.1|BJ608042
EST:     GCCGACAGGTTCAACCCGCGGCGCAGAGCAAAGAG                         GGCAAGGGACTTCAACGTGCAATCACTTCTGAACCACATGTTGAGCGCTGA
genomic: GCCGACAGGTTCAACCCGCGGCGCAGAGCAAAGAGgtatcattct ... gtggctgcagGGCAAGGGACTTCAACGTGCAATCACTTCTGAACCACATGTTGAGCGCTGA
EST: gi|162241089|gb|FC414133.1|FC414133
EST:     GCCGACAGGTTCAACCCGCGGCGCAGAGCAAAGAG                         GGCAAGGGACTTCAACGTGCAATCACTTCTGAACCACATGTTGAGCGCTGA
genomic: GCCGACAGGTTCAACCCGCGGCGCAGAGCAAAGAGgtatcattct ... gtggctgcagGGCAAGGGACTTCAACGTGCAATCACTTCTGAACCACATGTTGAGCGCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcatattttgtgatacgttattgacacagaaatcgggcctcgtgtggctgcagGGCAAGGGACTTCAACGTGCAATCACTTCTGAACCACATGTTGAGCGCTGAAATGGAGAAGAACAAGTCTTGAGTATTGTGAGAACAACATCTAACGCTC
                    tattgac  putative branch site (score: 2)
     tattttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attcaatattcagtccaagtgatagttcccagttacatgtatcaatatcatattttgtgatacgttattgacacagaaatcgggcctcgtgtggctgcagGGCAAGGGACTTCAACGTGCAATCACTTCTGAACCACATGTTGAGCGCTGAAATGGAGAAGAACAAGTCTTGAGTATTGTGAGAACAACATCTAACGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC