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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAACTCAACAACTTGGATGTTGTTTACACACCGTGGTATAATCTGAGGAAGACTCAAAGCATGGACGTTGGCCAAGTTGGCTTTCATAACTCCAAGCTTgtaagagtttgtagacccttgtctttgttttcaacaaagattggtgtactattgatatcttcaggttcatggacctcgaattagactaagttggtacggccttatggcag

Basic information

species Physcomitrella patens
transcript PP1S199_23V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S199_23V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os05g13440.1 (Oryza sativa), 5'ss of exon 4
TAAACTCAACAACTTGGATGTTGTTTACACACCGTGGTATAATCTGAGGAAGACTCAAAGCATGGACGTTGGCCAAGTTGGCTTTCATAACTCCAAGCTTgtaaga-gtttgtagacccttgtctttgttttcaacaaagattggtgtactattgatatcttcaggttcatggacctcgaattagactaagttggtacggccttatggcag
|||    || ||| | ||||| ||||| ||||| ||||||||||| | |||||||| |  |||||| || || |||||||| ||||| ||||| ||  | || ||| | || |   || |  |   ||| ||   ||   | |   |||  | |   || |         | || | |  ||     || ||| ||   |  |||||    
TAAGACTAATAACATTGATGTGGTTTATACACCATGGTATAATCTAAAGAAGACTCCATCCATGGATGTGGGTCAAGTTGGTTTTCACAACTCTAAATTGgtgagaagcttatttcccttacttcctgtgttaggcatgtaatttagtataacttgcatttat-------ttgaacgcttatacatttaggtttgtctagtgttatg----
















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|37852008|gb|BJ610016.1|BJ610016
EST:     AGACTCAAAGCATGGACGTTGGCCAAGTTGGCTTTCATAACTCCAAGCTT                         GTGCGTACAGTCAAGGTTGAGACACGCAAGAATGAAATTGTGAATCGGTTG
genomic: AGACTCAAAGCATGGACGTTGGCCAAGTTGGCTTTCATAACTCCAAGCTTgtaagagttt ... cttatggcagGTGCGTACAGTCAAGGTTGAGACACGCAAGAATGAAATTGTGAATCGGTTG
EST: gi|37852535|gb|BJ610543.1|BJ610543
EST:     AGACTCAAAGCATGGACGTTGGCCAAGTTGGCTTTCATAACTCCAAGCTT                         GTGCGTACAGTCAAGGTTGAGACACGCAAGAATGAAATTGTGAATCGGTTG
genomic: AGACTCAAAGCATGGACGTTGGCCAAGTTGGCTTTCATAACTCCAAGCTTgtaagagttt ... cttatggcagGTGCGTACAGTCAAGGTTGAGACACGCAAGAATGAAATTGTGAATCGGTTG
EST: gi|37837061|gb|BJ595069.1|BJ595069
EST:     AGACTCAAAGCATGGACGTTGGCCAAGTTGGCTTTCATAACTCCAAGCTT                         GTGCGTACAGTCAAGGTTGAGACACGCAAGAATGAAATTGTGAATCGGTTG
genomic: AGACTCAAAGCATGGACGTTGGCCAAGTTGGCTTTCATAACTCCAAGCTTgtaagagttt ... cttatggcagGTGCGTACAGTCAAGGTTGAGACACGCAAGAATGAAATTGTGAATCGGTTG
EST: gi|162235148|gb|FC411244.1|FC411244
EST:     AGACTCAAAGCATGGACGTTGGCCAAGTTGGCTTTCATAACTCCAAGCTT                         GTGCGTACAGTCAAGGTTGAGACACGCAAGAATGAAATTGTGAATCGGTTG
genomic: AGACTCAAAGCATGGACGTTGGCCAAGTTGGCTTTCATAACTCCAAGCTTgtaagagttt ... cttatggcagGTGCGTACAGTCAAGGTTGAGACACGCAAGAATGAAATTGTGAATCGGTTG
EST: gi|37848004|gb|BJ606012.1|BJ606012
EST:     AGACTCAAAGCATGGACGTTGGCCAAGTTGGCTTTCATAACTCCAAGCTT                         GTGCGTACAGTCAAGGTTGAGACACGCAAGAATGAAATTGTGAATCGGTTG
genomic: AGACTCAAAGCATGGACGTTGGCCAAGTTGGCTTTCATAACTCCAAGCTTgtaagagttt ... cttatggcagGTGCGTACAGTCAAGGTTGAGACACGCAAGAATGAAATTGTGAATCGGTTG
EST: gi|37830821|gb|BJ588833.1|BJ588833
EST:     AGACTCAAAGCATGGACGTTGGCCAAGTTGGCTTTCATAACTCCAAGCTT                         GTGCGTACAGTCAAGGTTGAGACACGCAAGAATGAAATTGTGAATCGGTTG
genomic: AGACTCAAAGCATGGACGTTGGCCAAGTTGGCTTTCATAACTCCAAGCTTgtaagagttt ... cttatggcagGTGCGTACAGTCAAGGTTGAGACACGCAAGAATGAAATTGTGAATCGGTTG
EST: gi|18359130|gb|BJ191190.1|BJ191190
EST:     AGACTCAAAGCATGGACGTTGGCCAAGTTGGCTTTCATAACTCCAAGCTT                         GTGCGTACAGTCAAGGTTGAGACACGCAAGAATGAAATTGTGAATCGGTTG
genomic: AGACTCAAAGCATGGACGTTGGCCAAGTTGGCTTTCATAACTCCAAGCTTgtaagagttt ... cttatggcagGTGCGTACAGTCAAGGTTGAGACACGCAAGAATGAAATTGTGAATCGGTTG
EST: gi|18351476|gb|BJ183528.1|BJ183528
EST:     AGACTCAAAGCATGGACGTTGGCCAAGTTGGCTTTCATAACTCCAAGCTT                         GTGCGTACAGTCAAGGTTGAGACACGCAAGAATGAAATTGTGAA
genomic: AGACTCAAAGCATGGACGTTGGCCAAGTTGGCTTTCATAACTCCAAGCTTgtaagagttt ... cttatggcagGTGCGTACAGTCAAGGTTGAGACACGCAAGAATGAAATTGTGAA
EST: gi|18371814|gb|BJ203416.1|BJ203416
EST:     AGACTCAAAGCATGGACGTTGGCCAAGTTGGCTTTCATAACTCCAAGCTT                         GTGCGTACAGTCAAG
genomic: AGACTCAAAGCATGGACGTTGGCCAAGTTGGCTTTCATAACTCCAAGCTTgtaagagttt ... cttatggcagGTGCGTACAGTCAAG
EST: gi|162235149|gb|FC411245.1|FC411245
EST:     AGACTCAAAGCATGGACGTTGGCCAAGTTGGCTTTCATAACTCCAAGCTT                         GTGCGTACAGTCAAGGTTGAGACACGCAAGAATGAAATTGTGAATCGGTTG
genomic: AGACTCAAAGCATGGACGTTGGCCAAGTTGGCTTTCATAACTCCAAGCTTgtaagagttt ... cttatggcagGTGCGTACAGTCAAGGTTGAGACACGCAAGAATGAAATTGTGAATCGGTTG
EST: gi|18367505|gb|BJ199588.1|BJ199588
EST:     AGACTCAAAGCATGGACGTTGGCCAAGTTGGCTTTCATAACTCCAAGCTT                         GTGCGTACAGTCAAG
genomic: AGACTCAAAGCATGGACGTTGGCCAAGTTGGCTTTCATAACTCCAAGCTTgtaagagttt ... cttatggcagGTGCGTACAGTCAAG
EST: gi|208346849|gb|DC913088.1|DC913088
EST:     AGACTCAAAGCATGGACGTTGGCCAAGTTGGCTTTCATAACTCCAAGCTT                         GTGCGTACAGTCAAGGTTGAGACACGCAAGAATGAAATTGTGAATCGGTTG
genomic: AGACTCAAAGCATGGACGTTGGCCAAGTTGGCTTTCATAACTCCAAGCTTgtaagagttt ... cttatggcagGTGCGTACAGTCAAGGTTGAGACACGCAAGAATGAAATTGTGAATCGGTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAACTCAACAACTTGGATGTTGTTTACACACCGTGGTATAATCTGAGGAAGACTCAAAGCATGGACGTTGGCCAAGTTGGCTTTCATAACTCCAAGCTTgtaagagtttgtagacccttgtctttgttttcaacaaagattggtgtactattgatatcttcaggttcatggacctcgaattagactaagttggtacggccttatggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT