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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGTAGATTTCTTGGACAAGCTTCTGCGGTATGACCATCAAGAAAGGCTTACTGCCAGGGAAGCTATGgtatgtttctattcccttatgttgcaagctggttacaaagcagttctttcacgatgtacggattttctcaaattgatccaaattcgttgagtcatacatgtcgagcttagttgtgtgatttctgatttatgtcgtatttcag

Basic information

species Physcomitrella patens
transcript PP1S165_107V6.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S165_107V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GRMZM5G845755_T01 (Zea mays), 5'ss of exon 8
GCAGTAGATTTCTTGGACAAGCTTCTGCGGTATGACCATCAAGAAAGGCTTACTGCCAGGGAAGCTATGgtatgtttctat-tcccttatgttgcaagctggttacaaagcagttctttcacgatgtacggattttctcaaattgatccaaattcgttgagtcatacatgtcgagcttagttgtgtgatttctgatttatgtcgtatttcag
||  |||||||| | ||||||||| |||| ||||| ||||| || |||||||||||  | |||||||||||| |||||  | | | | || |||   ||  || |    ||||  |    |   |  || |  |||    | |    | ||||   | | || |   ||                                           
GCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATGgtaagtttccctgtgcttaattttggtggcatgtaatttggcagcgc----aaagtacactggcttttctcactattgctaaatatttggcgtaaagtatactc---------------------------------------

upper sequence: PP1S165_107V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GRMZM2G141903_T01 (Zea mays), 5'ss of exon 9
GCAGTAGATTTCTTGGACAAGCTTCTGCGGTATGACCATCAAGAAAGGCTTACTGCCAGGGAAGCTATGgtatgtttctattcccttatgttgcaagctggttacaaagcagttctttcacgatgtacggattttctcaaattgatccaaattcgttgagtcatacatgtcgagcttagttgtgtgatt-tctgatttatgtcgtatttcag
||  |||||||  | || ||||| ||||| ||||| || ||||| |||||||||||  |||||||||||||| |   | |  |   || | | |   ||     |  || | || |||  | ||| ||     ||   |  ||||    |||  | |   | ||| |||     ||| | | | | ||   | ||   |||    |||  ||
GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGACAGGCTTACTGCACGGGAAGCTATGgtaag---ccagacagataagctac---cttagctcctagtacttgtttt-caatgaacaa---tttcaagtttgaaaagaataaggtttcttataaatgatt--cttggatttttaatggcccgacacatgaataattgtag
















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|37847463|gb|BJ605471.1|BJ605471
EST:     AGCTTNTGCGGTATGACCATCAAGAAAGGCTTACTGCCAGGGAAGCTANG                         GCTCATCCNTACTTCTATCCTGTTCGTTCCATGGAAGCAAGTAACCGTCGC
genomic: AGCTTCTGCGGTATGACCATCAAGAAAGGCTTACTGCCAGGGAAGCTATGgtatgtttct ... cgtatttcagGCTCATCCCTACTTCTATCCTGTTCGTTCCATGGAAGCAAGTAACCGTCGC
EST: gi|162271756|gb|FC448889.1|FC448889
EST:     AGCTTCTGCGGTATGACCATCAAGAAAGGCTTACTGCCAGGGAAGCTATG                         GCTCATCCCTACTTCTATCCTGTTCGTTCCATGGAAGCAAGTAACCGTCGC
genomic: AGCTTCTGCGGTATGACCATCAAGAAAGGCTTACTGCCAGGGAAGCTATGgtatgtttct ... cgtatttcagGCTCATCCCTACTTCTATCCTGTTCGTTCCATGGAAGCAAGTAACCGTCGC
EST: gi|162240845|gb|FC417516.1|FC417516
EST:     AGCTTCTGCGGTATGACCATCAAGAAAGGCTTACTGCCAGGGAAGCTATG                         GCTCATCCCTACTTCTATCCTGTTCGTTCCATGGAAGCAAGTAACCGTCGC
genomic: AGCTTCTGCGGTATGACCATCAAGAAAGGCTTACTGCCAGGGAAGCTATGgtatgtttct ... cgtatttcagGCTCATCCCTACTTCTATCCTGTTCGTTCCATGGAAGCAAGTAACCGTCGC
EST: gi|162255256|gb|FC431566.1|FC431566
EST:     AGCTTCTGCGGTATGACCATCAAGAAAGGCTTACTGCCAGGGAAGCTATG                         GCTCATCCCTACTTCTATCCTGTTCGTTCCATGGAAGCAAGTAACCGTCGC
genomic: AGCTTCTGCGGTATGACCATCAAGAAAGGCTTACTGCCAGGGAAGCTATGgtatgtttct ... cgtatttcagGCTCATCCCTACTTCTATCCTGTTCGTTCCATGGAAGCAAGTAACCGTCGC
EST: gi|37834022|gb|BJ592034.1|BJ592034
EST:     AGCTTCTGCGGTATGACCATCAAGAAAGGCTTACTGCCAGGGAAGCTATG                         GCTCATCCCTACTTCTATCCTGTTCGTTCCATGGAAGCAAGTAACCGTCGC
genomic: AGCTTCTGCGGTATGACCATCAAGAAAGGCTTACTGCCAGGGAAGCTATGgtatgtttct ... cgtatttcagGCTCATCCCTACTTCTATCCTGTTCGTTCCATGGAAGCAAGTAACCGTCGC
EST: gi|37829629|gb|BJ587641.1|BJ587641
EST:     AGCTTCTGCGGTATGACCATCAAGAAAGGCTTACTGCCAGGGAAGCTATG                         GCTCATCCCTACTTCTATCCTGTTCGTTCCATGGAAGCAAGTAACCGTCGC
genomic: AGCTTCTGCGGTATGACCATCAAGAAAGGCTTACTGCCAGGGAAGCTATGgtatgtttct ... cgtatttcagGCTCATCCCTACTTCTATCCTGTTCGTTCCATGGAAGCAAGTAACCGTCGC
EST: gi|162240846|gb|FC417517.1|FC417517
EST:     AGCTTCTGCGGTATGACCATCAAGAAAGGCTTACTGCCAGGGAAGCTATG                         GCTCATCCCTACTTCTATCCTGTTCGTTCCATGGAAGCAAGTAACCGTCGC
genomic: AGCTTCTGCGGTATGACCATCAAGAAAGGCTTACTGCCAGGGAAGCTATGgtatgtttct ... cgtatttcagGCTCATCCCTACTTCTATCCTGTTCGTTCCATGGAAGCAAGTAACCGTCGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGTAGATTTCTTGGACAAGCTTCTGCGGTATGACCATCAAGAAAGGCTTACTGCCAGGGAAGCTATGgtatgtttctattcccttatgttgcaagctggttacaaagcagttctttcacgatgtacggattttctcaaattgatccaaattcgttgagtcatacatgtcgagcttagttgtgtgatttctgatttatgtcgtatttcag

- - - - - - - - - - - - - - - - - - - - AAGAAA