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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggtctgctctgaagagattcggggtttcaatcaagcgaatgagcttgaagtaggtttcgctctgtttgcttcaaacgaaacattgctgtgcttgtgcagGATTGGATTGACATTGACTTTGGAATAGCTGAAGGGGTGGATTTCATTGCCATCTCTTTCGTCAAGACTTCTGAGGTCATTAAGCATTTGAAGAGCTACA

Basic information

species Physcomitrella patens
transcript PP1S70_15V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S70_15V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os07g08340.2 (Oryza sativa), 3'ss of exon 4
-gggtctgctctgaagagattcggggtttcaatcaagcgaatgagcttgaagtaggtttcgctctgtttgcttcaaacgaaacattgctgtgcttgtgcagGATTGGATTGACATTGACTTTGGAATAGCTGAAGGGGTGGATTTCATTGCCATCTCTTTCGTCAAGACTTCTGAGGTCATTAAGCATTTGAAGAGCTACA
   |||  |  |  |    || |     |  ||   |    | | |    |||   | | | |  |      | |  |  |    ||     ||| ||||||||||| ||||||| |||||||||||  ||||||| || ||||| |||||  | || || |||||  || | || || ||||| ||| |||| ||||| |
aaagtccaccatccatttcttagaaagctttatgtggactgtta-ccaagagttattgttgttgagaaatgatgattcttatttctgtgcaacttctgcagGATTGGCTTGACATAGACTTTGGAATTTCTGAAGGCGTAGATTTTATTGCAGTTTCGTTTGTCAAATCTGCAGAAGTAATTAACCATCTGAAAAGCTATA

upper sequence: PP1S70_15V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G078200_T01 (Zea mays), 3'ss of exon 4
gggtctgctctgaagagattcggggtttcaatcaagcgaatgagcttgaagtaggtttcgctctgtttgc---ttcaaacgaaac--attgctgtgcttgtgcagGATTGGATTGACATTGACTTTGGAATAGCTGAAGGGGTGGATTTCATTGCCATCTCTTTCGTCAAGACTTCTGAGGTCATTAAGCATTTGAAGAGCTACA
    || |||| | | | | |    || ||| ||| |  || |  |   |   | |   ||  |  ||||   |  |||  | ||  ||  |      | ||||||||||||||||||| || |||||||| |||||||| || |||||||| ||| | || || |||||| || |||| || ||||| ||||||||||| ||||
--tccttctcttatgtgttgcaaa-ttgcaaccaatc--attatataataaaggttcgtgcattacttgcagataaaaattatacttatgacctaaactttgcagGATTGGATTGACATAGATTTTGGAATTGCTGAAGGTGTTGATTTCATCGCCGTGTCATTTGTCAAGTCTGCTGAAGTAATTAATCATTTGAAGAGTTACA

upper sequence: PP1S70_15V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G066290_T01 (Zea mays), 3'ss of exon 3
gggtctgctctgaagagattcggggtttcaatcaagcgaatgagcttgaagtaggtttcgctctgt--ttgcttcaaacgaaacattgctgtg----cttgtgcagGATTGGATTGACATTGACTTTGGAATAGCTGAAGGGGTGGATTTCATTGCCATCTCTTTCGTCAAGACTTCTGAGGTCATTAAGCATTTGAAGAGCTACA
    ||||     |||| |     |||   |  ||  ||||    | | ||| |   |   | | |  |  |             ||  ||||    ||||||||||||||| ||||||| |||||||| || || ||||| || |||||||| ||  | || || |||||| || | || || |||| ||| ||||| |||||||
----ctgccaactagagttgtatagttgtga--aatggaatcttatagtagtggacattaatatataataacaatggtgctccttttcttgtgacaacttgtgcagGATTGGCTTGACATAGACTTTGGGATTGCCGAAGGTGTAGATTTCATCGCTGTTTCATTTGTCAAGTCTGCAGAAGTAATTAGGCACTTGAAAAGCTACA

upper sequence: PP1S70_15V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT3G22960.1 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------------------------------------------------------------------gggtctgctct--gaagagattcggg---gtttcaatcaagcgaatga-gcttgaagtaggtttcgctctgtttgcttcaaacgaaacattgctgtgcttgtgcagGATTGGATTGACATTGACTTTGGAATAGCTGAAGGGGTGGATTTCATTGCCATCTCTTTCGTCAAGACTTCTGAGGTCATTAAGCATTTGAAGAGCTACA
                                                                                         ||   || |  |||   |   | |    | | |   || |  ||||  | ||| | |       |||  ||| |    |    | |     | |   | | ||||| ||| | || ||||| |||||||| |||||||| ||||||||||||||  | || || |||||| |  |||| |||||||| ||  | || || ||  
gtttgtaattttgtatcttccctttaagctttgaattatgattcactttacttggtaaatttgggagggatcaaagcaatggtgaagatgtacacttttggaaactagatgagtccatgttagcaaaacagatgatacctgagggaaaacatactc-attttcactgatgatacctcaattctttatattcagGACTGGTTGGATATTGATTTTGGAATTGCTGAAGGTGTGGATTTCATTGCTGTATCGTTTGTCAAGTCGGCTGAAGTCATTAATCACCTTAAAAGTTATC

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|162170580|gb|FC347076.1|FC347076
EST:     GGCGGCTGGTCCGAGAGCGCAATGCCATGCTTCCCACTATCTCATCCAAG                         GATTGGATTGACATTGACTTTGGAATAGCTGAAGGGGTGGATTTCATTGCC
genomic: GGCGGCTGGTCCGAGAGCGCAATGCCATGCTTCCCACTATCTCATCCAAGgtgagtctga ... gcttgtgcagGATTGGATTGACATTGACTTTGGAATAGCTGAAGGGGTGGATTTCATTGCC
EST: gi|162275555|gb|FC451297.1|FC451297
EST:     GGCGGCTGGTCCGAGAGCGCAATGCCATGCTTCCCACTATCTCATCCAAG                         GATTGGATTGACATTGACTTTGGAATAGCTGAAGGGGTGGATTTCATTGCC
genomic: GGCGGCTGGTCCGAGAGCGCAATGCCATGCTTCCCACTATCTCATCCAAGgtgagtctga ... gcttgtgcagGATTGGATTGACATTGACTTTGGAATAGCTGAAGGGGTGGATTTCATTGCC
EST: gi|67718910|gb|BJ969169.1|BJ969169
EST:     GGCGGCTGGTCCGAGAGCGCAATGCCATGCTTCCCACTATCTCATCCAAG                         GATTGGATTGACATTGACTTTGGAATANCTGAAGGGGTGGATTTCATTGCC
genomic: GGCGGCTGGTCCGAGAGCGCAATGCCATGCTTCCCACTATCTCATCCAAGgtgagtctga ... gcttgtgcagGATTGGATTGACATTGACTTTGGAATAGCTGAAGGGGTGGATTTCATTGCC
EST: gi|162259749|gb|FC436547.1|FC436547
EST:     GGCGGCTGGTCCGAGAGCGCAATGCCATGCTTCCCACTATCTCATCCAAG                         GATTGGATTGACATTGACTTTGGAATAGCTGAAGGGGTGGATTTCATTGCC
genomic: GGCGGCTGGTCCGAGAGCGCAATGCCATGCTTCCCACTATCTCATCCAAGgtgagtctga ... gcttgtgcagGATTGGATTGACATTGACTTTGGAATAGCTGAAGGGGTGGATTTCATTGCC
EST: gi|162172704|gb|FC348085.1|FC348085
EST:     GGCGGCTGGTCCGAGAGCGCAATGCCATGCTTCCCACTATCTCATCCAAG                         GATTGGATTGACATTGACTTTGGAATAGCTGAAGGGGTGGATTTCATTGCC
genomic: GGCGGCTGGTCCGAGAGCGCAATGCCATGCTTCCCACTATCTCATCCAAGgtgagtctga ... gcttgtgcagGATTGGATTGACATTGACTTTGGAATAGCTGAAGGGGTGGATTTCATTGCC
EST: gi|162181332|gb|FC357075.1|FC357075
EST:     GGCGGCTGGTCCGAGAGCGCAATGCCATGCTTCCCACTATCTCATCCAAG                         GATTGGATTGACATTGACTTTGGAATAGCTGAAGGGGTGGATTTCATTGCC
genomic: GGCGGCTGGTCCGAGAGCGCAATGCCATGCTTCCCACTATCTCATCCAAGgtgagtctga ... gcttgtgcagGATTGGATTGACATTGACTTTGGAATAGCTGAAGGGGTGGATTTCATTGCC
EST: gi|162151423|gb|FC326928.1|FC326928
EST:     GGCGGCTGGTCCGAGAGCGCAATGCCATGCTTCCCACTATCTCATCCAAG                         GATTGGATTGACATTGACTTTGGAATAGCTGAAGGGGTGGATTTCATTGCC
genomic: GGCGGCTGGTCCGAGAGCGCAATGCCATGCTTCCCACTATCTCATCCAAGgtgagtctga ... gcttgtgcagGATTGGATTGACATTGACTTTGGAATAGCTGAAGGGGTGGATTTCATTGCC
EST: gi|162165719|gb|FC341199.1|FC341199
EST:     GGCGGCTGGTCCGAGAGCGCAATGCCATGCTTCCCACTATCTCATCCAAG                         GATTGGATTGACATTGACTTTGGAATAGCTGAAGGGGTGGATTTCATTGCC
genomic: GGCGGCTGGTCCGAGAGCGCAATGCCATGCTTCCCACTATCTCATCCAAGgtgagtctga ... gcttgtgcagGATTGGATTGACATTGACTTTGGAATAGCTGAAGGGGTGGATTTCATTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaagtaggtttcgctctgtttgcttcaaacgaaacattgctgtgcttgtgcagGATTGGATTGACATTGACTTTGGAATAGCTGAAGGGGTGGATTTCATTGCCATCTCTTTCGTCAAGACTTCTGAGGTCATTAAGCATTTGAAGAGCTACA
                                 aaacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gggtctgctctgaagagattcggggtttcaatcaagcgaatgagcttgaagtaggtttcgctctgtttgcttcaaacgaaacattgctgtgcttgtgcagGATTGGATTGACATTGACTTTGGAATAGCTGAAGGGGTGGATTTCATTGCCATCTCTTTCGTCAAGACTTCTGAGGTCATTAAGCATTTGAAGAGCTACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttca