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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGAAAGTGCGAACATTTCAGATTATCGTCATGCAGGGTCTAGTGGGATCATTGCCATGGACGGCTATGGTTTTTTTCACAATGTGGTTGGAGCTTATTGgtgagactacacatgacctgttaatatcccttagccaaatactgtcgtgaatgaactttctaatgacatcgtattcttatgccacttatggatattgtctaggcgctatccatgttgcttacactcctaaactttctttcttgaatatctcgatctgaatcagaacctcacgagctgtctcag

Basic information

species Physcomitrella patens
transcript PP1S55_231V6.3
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S55_231V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: LOC_Os03g59450.1 (Oryza sativa), 5'ss of exon 3
ATGAAAGTGCGAACATTTCAGATTATCGTCATGCAGGGTCTAGTGGGATCATTGCCATGGACGGCTATGGTTTTTTTCACAATGTGGTTGGAGCTTATTGgtgagactacacatgacctgttaatatcccttagccaaatactgtcgtgaatgaactttctaatgacatcgtattcttatgccacttatggatattgtctaggcgctatccatgttgcttacactcctaaactttctttcttgaatatctcgatctgaatcagaacctcacgagctgtctcag
|||||||||||||||||||| || || ||| |||||||  |||| || |||||||||||||| ||| | ||||| |||||||||||||| ||||| ||||||  |   | | ||   |  || |||           |||| |    ||||   | || ||  |  | || ||      || ||||  || |  || ||                                                                                    
ATGAAAGTGCGAACATTTCAAATCATTGTCTTGCAGGGCATAGTTGGCTCATTGCCATGGACTGCTGTAGTTTTCTTCACAATGTGGTTTGAGCTCATTGgtatgcaaatatatagac-atttatac----------aatatt----tgaaattatttcct--tcccgtcataagacattgacactcttgaactttatcag----------------------------------------------------------------------------------
















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|208367766|gb|DC944012.1|DC944012
EST:     ATTGCCATGGACGGCTATGGNNNNNNNCACAATGTGGTTGGAGCTTATTG                         GTTTTGGACACAAAGCTGCAGCAAGCCTAATGAGCCTATTCTCCGCTGGCT
genomic: ATTGCCATGGACGGCTATGGTTTTTTTCACAATGTGGTTGGAGCTTATTGgtgagactac ... gctgtctcagGTTTTGGACACAAAGCTGCAGCAAGCCTAATGAGCCTATTCTCCGCTGGCT
EST: gi|37821142|gb|BJ579208.1|BJ579208
EST:     ATTGCCATGGACGGCTATGGNNNNNNNCACAATGTGGTTGGAGCTTATTG                         GTTTTGGACACAAAGCTGCAGCAAGCNTAATGAGCCTATTCTCCGCTGGCT
genomic: ATTGCCATGGACGGCTATGGTTTTTTTCACAATGTGGTTGGAGCTTATTGgtgagactac ... gctgtctcagGTTTTGGACACAAAGCTGCAGCAAGCCTAATGAGCCTATTCTCCGCTGGCT
EST: gi|162158998|gb|FC334013.1|FC334013
EST:     ATTGCCATGGACGGCTATGGNNNNNNNCACAATGTGGTTGGAGCTTATTG                         GTTTTGGACACAAAGCTGCAGCAAGCCTAATGAGCCTATTCTCCGCTGGCT
genomic: ATTGCCATGGACGGCTATGGTTTTTTTCACAATGTGGTTGGAGCTTATTGgtgagactac ... gctgtctcagGTTTTGGACACAAAGCTGCAGCAAGCCTAATGAGCCTATTCTCCGCTGGCT
EST: gi|162176157|gb|FC351093.1|FC351093
EST:     CACAATGTGGTTGGAGCTTATTG                         GTTTTGGACACAAAGCTGCAGCAAGCCTAATGAGCCTATTCTCCGCTGGCT
genomic: CACAATGTGGTTGGAGCTTATTGgtgagactac ... gctgtctcagGTTTTGGACACAAAGCTGCAGCAAGCCTAATGAGCCTATTCTCCGCTGGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGAAAGTGCGAACATTTCAGATTATCGTCATGCAGGGTCTAGTGGGATCATTGCCATGGACGGCTATGGTTTTTTTCACAATGTGGTTGGAGCTTATTGgtgagactacacatgacctgttaatatcccttagccaaatactgtcgtgaatgaactttctaatgacatcgtattcttatgccacttatggatattgtctaggcgctatccatgttgcttacactcctaaactttctttcttgaatatctcgatctgaatcagaacctcacgagctgtctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT