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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGGAGTGCTCTATCGGATCCATATCTGTCTTTTGCTGCTGGAATGAACGGTTTAGCAGGCCCTCTGCACGGGCTTGCAAATCAGgtcagtctcataactttgaaaaatgttctctaatatcatgatataataagcgaaggttttgtgatcagtgacagattgatatggatatgggggctttgtt...

Basic information

species Physcomitrella patens
transcript PP1S37_33V6.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S37_33V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: AT3G60100.1 (Arabidopsis thaliana), 5'ss of exon 13
GTTGGGAGTGCTCTATCGGATCCATATCTGTCTTTTGCTGCTGGAATGAACGGTTTAGCAGGCCCTCTGCACGGGCTTGCAAATCAGgtcagtctcataactttgaaaaatgtt------ctctaatatcatgatataataagcgaaggttttgtgatcagtgacagatt---gatatggatatgggggctttgtt--------------------------
||||||||||| || || ||||||||||| || |||||||||| | |||| |||||||| || || || || ||  | || ||||||||     | ||| | || |  | | ||       || ||| |     | ||   | |      | |  |||         |||       |  |  |||   |||  |                           
GTTGGGAGTGCACTTTCAGATCCATATCTTTCATTTGCTGCTGCATTGAATGGTTTAGCTGGGCCACTCCATGGTTTGGCTAATCAGgta---tttatatccttaatgagtcttatattgttcgaatctacaagtgtatataacttgaactctaagattgactcttaattataagcttaaacttggaatcttactctgttttttttcgttgtcttgttgtag
















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|162176172|gb|FC351914.1|FC351914
EST:     CTGCTGGAATGAACGGTTTAGCAGGCCCTCTGCACGGGCTTGCAAATCAG                         GAAGTGCTGCGCTGGATTCAGCAAGTGGTAGATGAAATTGGTAGTGAAGTC
genomic: CTGCTGGAATGAACGGTTTAGCAGGCCCTCTGCACGGGCTTGCAAATCAGgtcagtctca ... gatgttgcagGAAGTGCTGCGCTGGATTCAGCAAGTGGTAGATGAAATTGGTAGTGAAGTC
EST: gi|162165708|gb|FC340889.1|FC340889
EST:     GCACGGGCTTGCAAATCAG                         GAAGTGCTGCGCTGGATTCAGCAAGTGGTAGATGAAATTGGTAGTGAAGTC
genomic: GCACGGGCTTGCAAATCAGgtcagtctca ... gatgttgcagGAAGTGCTGCGCTGGATTCAGCAAGTGGTAGATGAAATTGGTAGTGAAGTC
EST: gi|208386538|gb|DC952747.1|DC952747
EST:     CTGCTGGAATGAACGGTTTAGCAGGCCCTCTGCACGGGCTTGCAAATCAG                         GAAGTGCTGCGCTGGATTCAGCAAGTGGTAGATGAAATTGGTAGTGAAGTC
genomic: CTGCTGGAATGAACGGTTTAGCAGGCCCTCTGCACGGGCTTGCAAATCAGgtcagtctca ... gatgttgcagGAAGTGCTGCGCTGGATTCAGCAAGTGGTAGATGAAATTGGTAGTGAAGTC
EST: gi|67697462|gb|BJ957695.1|BJ957695
EST:     CTGCTGGAATGAACGGTTTAGCAGGCCCTCTGCACGGGCTTGCAAATCAG                         GAAGTGCTGCGCTGGATTCAGCAAGTGGTAGATGAAATTGGTAGTGAAGTC
genomic: CTGCTGGAATGAACGGTTTAGCAGGCCCTCTGCACGGGCTTGCAAATCAGgtcagtctca ... gatgttgcagGAAGTGCTGCGCTGGATTCAGCAAGTGGTAGATGAAATTGGTAGTGAAGTC
EST: gi|37823157|gb|BJ581223.1|BJ581223
EST:     CGGGCTTGCAAATCAG                         GAAGTGCTGCGCTGGATTCAGCAAGTGGTAGATGAAATTGGTAGTGAAGTC
genomic: CGGGCTTGCAAATCAGgtcagtctca ... gatgttgcagGAAGTGCTGCGCTGGATTCAGCAAGTGGTAGATGAAATTGGTAGTGAAGTC
EST: gi|208388659|gb|DC953435.1|DC953435
EST:     CTGCTGGAATGAACGGTTTAGCAGGCCCTCTGCACGGGCTTGCAAATCAG                         GAAGTGCTGCGCTGGATTCAGCAAGTGGTAGATGAAATTGGTAGTGAAGTC
genomic: CTGCTGGAATGAACGGTTTAGCAGGCCCTCTGCACGGGCTTGCAAATCAGgtcagtctca ... gatgttgcagGAAGTGCTGCGCTGGATTCAGCAAGTGGTAGATGAAATTGGTAGTGAAGTC
EST: gi|208363044|gb|DC957985.1|DC957985
EST:     CTGCTGGAATGAACGGTTTAGCAGGCCCTCTGCACGGGCTTGCAAATCAG                         GAAGTGCTGCGCTGGATTCAGCAAGTGGTAGATGAAATTGGTAGTGAAGTC
genomic: CTGCTGGAATGAACGGTTTAGCAGGCCCTCTGCACGGGCTTGCAAATCAGgtcagtctca ... gatgttgcagGAAGTGCTGCGCTGGATTCAGCAAGTGGTAGATGAAATTGGTAGTGAAGTC
EST: gi|37835509|gb|BJ593521.1|BJ593521
EST:     GGCTTGCAAATCAG                         GAAGTGCTGCGCTGGATTCAGCAAGTGGTAGATGAAATTGGTAGTGAAGTC
genomic: GGCTTGCAAATCAGgtcagtctca ... gatgttgcagGAAGTGCTGCGCTGGATTCAGCAAGTGGTAGATGAAATTGGTAGTGAAGTC
EST: gi|162152561|gb|FC328839.1|FC328839
EST:     CTGCTGGAATGAACGGTTTAGCAGGCCCTCTGCACGGGCTTGCAAATCAG                         GAAGTGCTGCGCTGGATTCAGCAAGTGGTAGATGAAATTGGTAGTGAAGTC
genomic: CTGCTGGAATGAACGGTTTAGCAGGCCCTCTGCACGGGCTTGCAAATCAGgtcagtctca ... gatgttgcagGAAGTGCTGCGCTGGATTCAGCAAGTGGTAGATGAAATTGGTAGTGAAGTC
EST: gi|67724660|gb|BJ974919.1|BJ974919
EST:     CTGCTGGAATGAACGGTTTAGCAGGCCCTCTGCACGGGCTTGCAAATCAG                         GAAGTGCTGCGCTGGATTCAGCAAGTGGTAGATGAAATTGGTAGTGAAGTC
genomic: CTGCTGGAATGAACGGTTTAGCAGGCCCTCTGCACGGGCTTGCAAATCAGgtcagtctca ... gatgttgcagGAAGTGCTGCGCTGGATTCAGCAAGTGGTAGATGAAATTGGTAGTGAAGTC
EST: gi|162194037|gb|FC370212.1|FC370212
EST:     CTGCTGGAATGAACGGTTTAGCAGGCCCTCTGCACGGGCTTGCAAATCAG                         GAAGTGCTGCGCTGGATTCAGCAAGTGGTAGATGAAATTGGTAGTGAAGTC
genomic: CTGCTGGAATGAACGGTTTAGCAGGCCCTCTGCACGGGCTTGCAAATCAGgtcagtctca ... gatgttgcagGAAGTGCTGCGCTGGATTCAGCAAGTGGTAGATGAAATTGGTAGTGAAGTC
EST: gi|208356950|gb|DC922286.1|DC922286
EST:     CTGCTGGAATGAACGGTTTAGCAGGCCCTCTGCACGGGCTTGCAAATCAG                         GAAGTGCTGCGCTGGATTCAGCAAGTGGTAGATGAAATTGGTAGTGAAGTC
genomic: CTGCTGGAATGAACGGTTTAGCAGGCCCTCTGCACGGGCTTGCAAATCAGgtcagtctca ... gatgttgcagGAAGTGCTGCGCTGGATTCAGCAAGTGGTAGATGAAATTGGTAGTGAAGTC
EST: gi|162234310|gb|FC409848.1|FC409848
EST:     CTGCTGGAATGAACGGTTTAGCAGGCCCTCTGCACGGGCTTGCAAATCAG                         GAAGTGCTGCGCTGGATTCAGCAAGTGGTAGATGAAATTGGTAGTGAAGTC
genomic: CTGCTGGAATGAACGGTTTAGCAGGCCCTCTGCACGGGCTTGCAAATCAGgtcagtctca ... gatgttgcagGAAGTGCTGCGCTGGATTCAGCAAGTGGTAGATGAAATTGGTAGTGAAGTC
EST: gi|37825198|gb|BJ583264.1|BJ583264
EST:     GGAATGAACGGTTTAGCAGGCCNTCTGCACGGGCTTGCAAATCAG                         GAAGTGCTGCGCTGGATTCAGCAAGTGGTAGATGAAATTGGTAGTGAAGTC
genomic: GGAATGAACGGTTTAGCAGGCCCTCTGCACGGGCTTGCAAATCAGgtcagtctca ... gatgttgcagGAAGTGCTGCGCTGGATTCAGCAAGTGGTAGATGAAATTGGTAGTGAAGTC
EST: gi|162202112|gb|FC378033.1|FC378033
EST:     CTGCTGGAATGAACGGTTTAGCAGGCCCTCTGCACGGGCTTGCAAATCAG                         GAAGTGCTGCGCTGGATTCAGCAAGTGGTAGATGAAATTGGTAGTGAAGTC
genomic: CTGCTGGAATGAACGGTTTAGCAGGCCCTCTGCACGGGCTTGCAAATCAGgtcagtctca ... gatgttgcagGAAGTGCTGCGCTGGATTCAGCAAGTGGTAGATGAAATTGGTAGTGAAGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGGGAGTGCTCTATCGGATCCATATCTGTCTTTTGCTGCTGGAATGAACGGTTTAGCAGGCCCTCTGCACGGGCTTGCAAATCAGgtcagtctcataactttgaaaaatgttctctaatatcatgatataataagcgaaggttttgtgatcagtgacagattgatatggatatgggggctttgtt

- - - - - - - - - - - - - - - - - - -  GCTGGA