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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtggtaaaaggatatttgattgcttgaaatcataccagattgaacaatgttttgatgttctgtgcggttatctcaaggttacggtggcttttgtgtcagGCTTTGTACAACAAGGATGACTTCTTCGATTCTCTATCCTGTGATGCAACTCACGGAGGACGTGGTGAACGCCCTAAATTCTCTGAGCAACGCAGGATTG

Basic information

species Physcomitrella patens
transcript PP1S35_182V6.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S35_182V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: EFJ22693 (Selaginella moellendorffii), 3'ss of exon 6
tgtggtaaaaggatatttgattgcttgaaatcataccagattgaacaatgttttgatgttctgtgcggttatctcaaggttacggtggcttttgtgtcagGCTTTGTACAACAAGGATGACTTCTTCGATTCTCTATCCTGTGATGC---AACTCACGGAGGACGTGGTGAACGCCCTAAATTCTCTGAGCAACGCAGGATTG
                                      |   |||  | | ||| |  || ||       ||| ||    |      |||||    |||| |  | ||   |||||||||||| ||||||||||| ||||||||  |      ||  |  ||  ||   || ||||| |  || || |||||||| | ||   
--------------------------------------gtacgaatgacgctttcacattatgg------atcacatttctgataaagctttgcattcagCCGGTATATGTCAAGGATGACTTTTTCGATTCTCTCTCCTGTGACACTCTGGATCGTGAGGGTGGTACCGAGCGCCCCAGGTTTTCAGAGCAACGTAAGA---

upper sequence: PP1S35_182V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: EFJ13073 (Selaginella moellendorffii), 3'ss of exon 6
tgtggtaaaaggatatttgattgcttgaaatcataccagattgaacaatgttttgatgttctgtgcggttatctcaaggttacggtggcttttgtgtcagGCTTTGTACAACAAGGATGACTTCTTCGATTCTCTATCCTGTGATGC---AACTCACGGAGGACGTGGTGAACGCCCTAAATTCTCTGAGCAACGCAGGATTG
                                      |   |||  | | |||||  || ||       ||| ||    |      |||||    |||| |  | |||  |||||||||||| ||||||||||| ||||||||  |      ||  |  ||  ||   || ||||| | ||| || |||||||| | ||   
--------------------------------------gtacgaatgacgctttgacattatgg------atcacatttctgataaagctttgcattcagCCGGTATACGTCAAGGATGACTTTTTCGATTCTCTCTCCTGTGACACTCTGGATCGTGAGGGTGGTACCGAGCGCCCCAGATTTTCAGAGCAACGTAAGA---
















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|162161376|gb|FC337595.1|FC337595
EST:     ACGTCGAAGCTGACGCAGCTGATTCTGCACAATCAGATGCATCAAAGAAG                         GCTTTGTACAACAAGGATGACTTCTTCGATTCTCTATCCTGTGATGCAACT
genomic: ACGTCGAAGCTGACGCAGCTGATTCTGCACAATCAGATGCATCAAAGAAGgtagttcata ... tttgtgtcagGCTTTGTACAACAAGGATGACTTCTTCGATTCTCTATCCTGTGATGCAACT
EST: gi|162154240|gb|FC330371.1|FC330371
EST:     ACGTCGAAGCTGACGCAGCTGATTCTGCACAATCAGATGCATCANAGAAG                         GCTTTGTACAACAAGGATGACTTCTTCGATTCTCTATCCTGTGATGCAACT
genomic: ACGTCGAAGCTGACGCAGCTGATTCTGCACAATCAGATGCATCAAAGAAGgtagttcata ... tttgtgtcagGCTTTGTACAACAAGGATGACTTCTTCGATTCTCTATCCTGTGATGCAACT
EST: gi|162251586|gb|FC425602.1|FC425602
EST:     ACGTCGAAGCTGACGCAGCTGATTCTGCACAATCAGATGCATCAAAGAAG                         GCTTTGTACAACAAGGATGACTTCTTCGATTCTCTATCCTGTGATGCAACT
genomic: ACGTCGAAGCTGACGCAGCTGATTCTGCACAATCAGATGCATCAAAGAAGgtagttcata ... tttgtgtcagGCTTTGTACAACAAGGATGACTTCTTCGATTCTCTATCCTGTGATGCAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatgttttgatgttctgtgcggttatctcaaggttacggtggcttttgtgtcagGCTTTGTACAACAAGGATGACTTCTTCGATTCTCTATCCTGTGATGCAACTCACGGAGGACGTGGTGAACGCCCTAAATTCTCTGAGCAACGCAGGATTG
     ttttgat  putative branch site (score: 4)
                                           cttttgt  putative PPT
     ttttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtggtaaaaggatatttgattgcttgaaatcataccagattgaacaatgttttgatgttctgtgcggttatctcaaggttacggtggcttttgtgtcagGCTTTGTACAACAAGGATGACTTCTTCGATTCTCTATCCTGTGATGCAACTCACGGAGGACGTGGTGAACGCCCTAAATTCTCTGAGCAACGCAGGATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA