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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGGAAATTGCTGTGACTCGATTGCTACTTAAGTCCTACTATGACATTGTGCGGAAGAATATTCAAGACTTAGTACCGAAAGCTATCATGCATTTCCTGgtttgtagttttctcacttatatcttgctgaagatgttgcttcaattcattggacttactgtcataggtttactaggaggcagcaatacatttgttggtctatgaataagtttacatgtttccttggtcgaattttcaacctgatgactgttttcttgatataacag

Basic information

species Physcomitrella patens
transcript PP1S187_100V6.2
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S187_100V6.2 (Physcomitrella patens), 5'ss of exon 19
lower sequence: AT4G33650.1 (Arabidopsis thaliana), 5'ss of exon 17
TCTGGAAATTGCTGTGACTCGATTGCTACTTAAGTCCTACTATGACATTGTGCGGAAGAATATTCAAGACTTAGTACCGAAAGCTATCATGCATTTCCTGgtttgtagttttctcacttatatcttgctgaagatgttgcttcaa-ttcattggacttactgtcataggtttactaggaggcagcaatacatttgttggtctatgaataagtttacatgtttccttggtcgaattttcaacctgatgactgttttcttgatataacag
  | || |||    | ||     || |||| |  || ||||||||||||||  ||||||||||| | ||||  ||||| ||||| ||||||||||||||||   |||   |  || |||    |  | |        |   ||||  |  |  ||  ||   |||      || | |   ||  |  |  | ||||   |                                                                    
AGTTGAGATTCAGATAACAAAGCTGTTACTAAGATCATACTATGACATTGTAAGGAAGAATATTGAGGACTCGGTACCAAAAGCAATCATGCATTTCCTGgcaagtaccctcatccctttccccaagtttcttgcagtatctcaaacttgtacgatatatcatcaccttgatatttgattgcc-ctttgaaattgtctttt-------------------------------------------------------------------

upper sequence: PP1S187_100V6.2 (Physcomitrella patens), 5'ss of exon 19
lower sequence: AT2G14120.3 (Arabidopsis thaliana), 5'ss of exon 18
TCTGGAAATTGCTGTGACTCGATTGCTACTTAAGTCCTACTATGACATTGTGCGGAAGAATATTCAAGACTTAGTACCGAAAGCTATCATGCATTTCCTGgtttgtagttttctcacttatatcttgctgaagatgttgcttcaattcattggacttactgtcataggtt-tactaggaggcagcaatacatttgttggtctatgaataagtttacatgtttccttggtcgaattttcaacctgatgactgttttcttgatataacag
  | || ||||   | ||     |  || | || |||||||||||||||||  |||||||| |  | ||||| || || ||||| ||||||||||| |||||| ||   || | | ||| ||   | ||||   | | ||   |   |||    ||||  ||||| | |   |||  | |   |       |||||  |   |  ||||| | ||    |     |  | |    |  |||                           
AGTTGAGATTGAGATAACAAAGCTATTATTGAAATCCTACTATGACATTGTAAGGAAGAATGTCGAGGACTTGGTCCCAAAAGCAATCATGCATTTTCTGgttagtg--ttccactcttctagtcttctgattgtctagccaaa---cat----cttatggtcattgatgacacttagtgtgggtcgattctttgtgaggggactaataactctat---tccatataattgtgaataaaacacag-----------------------
















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|37828396|gb|BJ586408.1|BJ586408
EST:     TGCGGAAGAATATTCAAGACTTAGTACCGAAAGCTATCATGCATTTCCTG                         GTCAACCACGTGAAAAGGGAACTTCATACTGTATTTATCAGAAAGTTGTAC
genomic: TGCGGAAGAATATTCAAGACTTAGTACCGAAAGCTATCATGCATTTCCTGgtttgtagtt ... gatataacagGTCAACCACGTGAAAAGGGAACTTCATACTGTATTTATCAGAAAGTTGTAC
EST: gi|162202221|gb|FC377570.1|FC377570
EST:     TGCGGAAGAATATTCAAGACTTAGTACCGAAAGCTATCATGCATTTCCTG                         GTCAACCACGTGAAAAGGGAACTTCATACTGTATTTATCAGAAAGTTGTAC
genomic: TGCGGAAGAATATTCAAGACTTAGTACCGAAAGCTATCATGCATTTCCTGgtttgtagtt ... gatataacagGTCAACCACGTGAAAAGGGAACTTCATACTGTATTTATCAGAAAGTTGTAC
EST: gi|37836254|gb|BJ594262.1|BJ594262
EST:     TGCGGAAGAATATTCAAGACTTAGTACCGAAAGCTATCATGCATTTCCTG                         GTCAACCACGTGAAAAGGGAACTTCATACTGTATTTATCAGAAAGTTGTAC
genomic: TGCGGAAGAATATTCAAGACTTAGTACCGAAAGCTATCATGCATTTCCTGgtttgtagtt ... gatataacagGTCAACCACGTGAAAAGGGAACTTCATACTGTATTTATCAGAAAGTTGTAC
EST: gi|18336786|gb|BJ168809.1|BJ168809
EST:     TGCGGAAGAATATTCAAGACTTAGTACCGAAAGCTATCATGCATTTCCTG                         GTCAACCACGTGAAAAGGGAACTTCATACTGTATTTATCAGAAAGTTGTAC
genomic: TGCGGAAGAATATTCAAGACTTAGTACCGAAAGCTATCATGCATTTCCTGgtttgtagtt ... gatataacagGTCAACCACGTGAAAAGGGAACTTCATACTGTATTTATCAGAAAGTTGTAC
EST: gi|162257800|gb|FC433998.1|FC433998
EST:     TGCGGAAGAATATTCAAGACTTAGTACCGAAAGCTATCATGCATTTCCTG                         GTCAACCACGTGAAAAGGGAACTTCATACTGTATTTATCAGAAAGTTGTAC
genomic: TGCGGAAGAATATTCAAGACTTAGTACCGAAAGCTATCATGCATTTCCTGgtttgtagtt ... gatataacagGTCAACCACGTGAAAAGGGAACTTCATACTGTATTTATCAGAAAGTTGTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTGGAAATTGCTGTGACTCGATTGCTACTTAAGTCCTACTATGACATTGTGCGGAAGAATATTCAAGACTTAGTACCGAAAGCTATCATGCATTTCCTGgtttgtagttttctcacttatatcttgctgaagatgttgcttcaattcattggacttactgtcataggtttactaggaggcagcaatacatttgttggtctatgaataagtttacatgtttccttggtcgaattttcaacctgatgactgttttcttgatataacag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA