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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAAGCAGGGAAAGCCCCCGATGTTTTCTACTGCCTGAGGCTTCTTGAGGCTACCGGAATCTCCACCGTTCCAGGTTCAGGGTTCGGCCAGAAAGAGGGgtacgttttcttgaagtcgaccttatactgcatcatgtattggcgcatatttctgaaagtctatttagctatacattactttgtgttgtttttttgaaac...

Basic information

species Physcomitrella patens
transcript PP1S341_73V6.2
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S341_73V6.2 (Physcomitrella patens), 5'ss of exon 12
lower sequence: LOC_Os07g01760.1 (Oryza sativa), 5'ss of exon 11
AGAAAGCAGGGAAAGCCCCCGATGTTTTCTACTGCCTGAGGCTTCTTGAGGCTACCGGAATCTCCACCGTTCCAGGTTCAGGGTTCGGCCAGAAAGAGGGgta--cgttttcttgaagtcgaccttatactgcatcatgtattggcgcatatttctgaaagtctatttagctatacattactttgtgttgtttttttgaaac---
| |  || || |||||  ||||||||||||||||||| | ||||||||| || || ||||| ||||| |||||||| ||||| ||||| || ||||| |||||   |||| | | |  |  ||   ||| || ||| |  |  |   ||||    | | ||     | | ||| |||| |||  |   |   |   |  | |   
AAAGGGCTGGCAAAGCGGCCGATGTTTTCTACTGCCTCAAGCTTCTTGAAGCAACTGGAATATCCACTGTTCCAGGGTCAGGTTTCGGACAAAAAGAAGGgtaggtgtttcccttacatatac---ata-tgtatctt-caaagtttcataaacatcagagatctctcaactagacatgactcaggagtacctgaatttatcctt
















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|162245385|gb|FC421287.1|FC421287
EST:     GCTACCGGAATCTCCACCGTTCCAGGTTCAGGGTTCGGCCAGAAAGAGGG                         GACCTTTCACGTGCGGACTACAATTCTGCCATCTGAGAAAGACATGCCTGG
genomic: GCTACCGGAATCTCCACCGTTCCAGGTTCAGGGTTCGGCCAGAAAGAGGGgtacgttttc ... tgttgctcagGACCTTTCACGTGCGGACTACAATTCTGCCATCTGAGAAAGACATGCCTGG
EST: gi|162165682|gb|FC342249.1|FC342249
EST:     GCTACCGGAATCTCCACCGTTCCAGGTTCAGGGTTCGGCCAGAAAGAGGG                         GACCTTTCACGTGCGGACTACAATTCTGCCATCTGAGAAAGACATGCCTGG
genomic: GCTACCGGAATCTCCACCGTTCCAGGTTCAGGGTTCGGCCAGAAAGAGGGgtacgttttc ... tgttgctcagGACCTTTCACGTGCGGACTACAATTCTGCCATCTGAGAAAGACATGCCTGG
EST: gi|18334610|gb|BJ166627.1|BJ166627
EST:     GCTACCGGAATCTCCACCGTTCCAGGTTCAGGGTTCGGCCAGAAAGAGGG                         GACCTTTCACGTGCGGACTACAATTCTGCCATCTGAGAAAGACATGCCTGG
genomic: GCTACCGGAATCTCCACCGTTCCAGGTTCAGGGTTCGGCCAGAAAGAGGGgtacgttttc ... tgttgctcagGACCTTTCACGTGCGGACTACAATTCTGCCATCTGAGAAAGACATGCCTGG
EST: gi|162245386|gb|FC421288.1|FC421288
EST:     GCTACCGGAATCTCCACCGTTCCAGGTTCAGGGTTCGGCCAGAAAGAGGG                         GACCTTTCACGTGCGGACTACAATTCTGCCATCTGAGAAAGACATGCCTGG
genomic: GCTACCGGAATCTCCACCGTTCCAGGTTCAGGGTTCGGCCAGAAAGAGGGgtacgttttc ... tgttgctcagGACCTTTCACGTGCGGACTACAATTCTGCCATCTGAGAAAGACATGCCTGG
EST: gi|162187115|gb|FC362897.1|FC362897
EST:     GCTACCGGAATCTCCACCGTTCCAGGTTCAGGGTTCGGCCAGAAAGAGGG                         GACCTTTCACGTGCGGACTACAATTCTGCCATCTGAGAAAGACATGCCTGG
genomic: GCTACCGGAATCTCCACCGTTCCAGGTTCAGGGTTCGGCCAGAAAGAGGGgtacgttttc ... tgttgctcagGACCTTTCACGTGCGGACTACAATTCTGCCATCTGAGAAAGACATGCCTGG
EST: gi|162151891|gb|FC328137.1|FC328137
EST:     GCTACCGGAATCTCCACCGTTCCAGGTTCAGGGTTCGGCCAGAAAGAGGG                         GACCTTTCACGTGCGGACTACAATTCTGCCATCTGAGAAAGACATGCCTGG
genomic: GCTACCGGAATCTCCACCGTTCCAGGTTCAGGGTTCGGCCAGAAAGAGGGgtacgttttc ... tgttgctcagGACCTTTCACGTGCGGACTACAATTCTGCCATCTGAGAAAGACATGCCTGG
EST: gi|162173952|gb|FC349752.1|FC349752
EST:     GCTACCGGAATCTCCACCGTTCCAGGTTCAGGGTTCGGCCAGAAAGAGGG                         GACCTTTCACGTGCGGACTACAATTCTGCCATCTGAGAAAGACATGCCTGG
genomic: GCTACCGGAATCTCCACCGTTCCAGGTTCAGGGTTCGGCCAGAAAGAGGGgtacgttttc ... tgttgctcagGACCTTTCACGTGCGGACTACAATTCTGCCATCTGAGAAAGACATGCCTGG
EST: gi|162158809|gb|FC335332.1|FC335332
EST:     GCTACCGGAATCTCCACCGTTCCAGGTTCAGGGTTCGGCCAGAAAGAGGG                         GACCTTTCACGTGCGGACTACAATTCTGCCATCTGAGAAAGACATGCCTGG
genomic: GCTACCGGAATCTCCACCGTTCCAGGTTCAGGGTTCGGCCAGAAAGAGGGgtacgttttc ... tgttgctcagGACCTTTCACGTGCGGACTACAATTCTGCCATCTGAGAAAGACATGCCTGG
EST: gi|162185273|gb|FC361783.1|FC361783
EST:     GCTACCGGAATCTCCACCGTTCCAGGTTCAGGGTTCGGCCAGAAAGAGGG                         GACCTTTCACGTGCGGACTACAATTCTGCCATCTGAGAAAGACATGCCTGG
genomic: GCTACCGGAATCTCCACCGTTCCAGGTTCAGGGTTCGGCCAGAAAGAGGGgtacgttttc ... tgttgctcagGACCTTTCACGTGCGGACTACAATTCTGCCATCTGAGAAAGACATGCCTGG
EST: gi|208350104|gb|DC921908.1|DC921908
EST:     GCTACCGGAATCTCCACCGTTCCAGGTTCAGGGTTCGGCCAGAAAGAGGG                         GACCTTTCACGTGCGGACTACAATTCTGCCATCTGAGAAAGACATGCCTGG
genomic: GCTACCGGAATCTCCACCGTTCCAGGTTCAGGGTTCGGCCAGAAAGAGGGgtacgttttc ... tgttgctcagGACCTTTCACGTGCGGACTACAATTCTGCCATCTGAGAAAGACATGCCTGG
EST: gi|37842040|gb|BJ600048.1|BJ600048
EST:     GCTACCGGAATCTCCACCGTTCCAGGTTCAGGGTTCGGCCAGAAAGAGGG                         GACCTTTCACGTGCGGACTACAATTCTGCCATCTGAGAAAGACATGCCTGG
genomic: GCTACCGGAATCTCCACCGTTCCAGGTTCAGGGTTCGGCCAGAAAGAGGGgtacgttttc ... tgttgctcagGACCTTTCACGTGCGGACTACAATTCTGCCATCTGAGAAAGACATGCCTGG
EST: gi|67692166|gb|BJ952399.1|BJ952399
EST:     GCTACCGGAATCTCCACCGTTCCAGGTTCAGGGTTCGGCCAGAAAGAGGG                         GACCTTTCACGTGCGGACTACAATTCTGCCATCTGAGAAAGACATGCCTGG
genomic: GCTACCGGAATCTCCACCGTTCCAGGTTCAGGGTTCGGCCAGAAAGAGGGgtacgttttc ... tgttgctcagGACCTTTCACGTGCGGACTACAATTCTGCCATCTGAGAAAGACATGCCTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAAGCAGGGAAAGCCCCCGATGTTTTCTACTGCCTGAGGCTTCTTGAGGCTACCGGAATCTCCACCGTTCCAGGTTCAGGGTTCGGCCAGAAAGAGGGgtacgttttcttgaagtcgaccttatactgcatcatgtattggcgcatatttctgaaagtctatttagctatacattactttgtgttgtttttttgaaac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG