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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGTGCAATAGGAGCAAGGTTGACTGGAGCTGGTTGGGGTGGTTGTGTTGTTGCTCTGGTCAAGGAAGAGGAAGTGGATTCTTTCATCTCTGCCCTCAAGgtatgcatccccatctccccaccctgtgaacgataaaatcaacgggttcattgaaattggtgtgtatctccaactagtgggctcatcaatattagtgtttctggatgtccttgtgcag

Basic information

species Physcomitrella patens
transcript PP1S89_154V6.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S89_154V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA07G36610.1 (Glycine max), 5'ss of exon 12
CGGTGCAATAGGAGCAAGGTTGACTGGAGCTGGTTGGGGTGGTTGTGTTGTTGCTCTGGTCAAGGAAGAGGAAGTGGATTCTTTCATCTCTGCCCTCAAGgtatgcatccccatctccccaccctgtgaacgataaaatcaacgggttcattgaaattggtgtgtatctccaactagtgggctcatcaatattagtgtttctggatgtccttgtgcag
 |||||  | || |||||| | ||||||||||| ||||||||||||| ||||||| |||| || ||      |||       || |||  |    | ||||| ||       |||     |  || |||       ||| ||     || ||| |          || |  | |||    | |  |||||  |    |||    || ||| | |||||
TGGTGCTCTTGGGGCAAGGCTTACTGGAGCTGGATGGGGTGGTTGTGCTGTTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAGgtttgt-----tatcatattattct-tgacattcctaattaa-----tcgttggag---------atttggagctaacaagtt-gtcaatgctgaatttt----atatccat-tgcag

upper sequence: PP1S89_154V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA17G03990.1 (Glycine max), 5'ss of exon 12
CGGTGCAATAGGAGCAAGGTTGACTGGAGCTGGTTGGGGTGGTTGTGTTGTTGCTCTGGTCAAGGAAGAGGAAGTGGATTCTTTCATCTCTGCCCTCAAGgtatgcatccccatctccccaccctgtgaacgataaaatcaacgggttcattgaaattggtgtgtatctccaactagtgggctcatcaatattagtgtttctggatgtccttgtgcag
 |||||  | || |||||| | ||||||||||| ||||||||||||| ||||||| |||| || ||      |||       || |||  |    | ||||| |||   |  ||                   || | |  ||      | | || | | ||   || |  | |||    | |  |||||  |    |||    |  |||   |||||
TGGTGCTCTTGGGGCAAGGCTTACTGGAGCTGGATGGGGTGGTTGTGCTGTTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAGgtttgctatcatat-------------------tatatttgacattcctaattaa-tcgttggagatttggagctaacaagtt-gtcaatgctgaacttt----acatcca-atgcag

upper sequence: PP1S89_154V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: Vv05s0077g00690.t01 (Vitis vinifera), 5'ss of exon 12
CGGTGCAATAGGAGCAAGGTTGACTGGAGCTGGTTGGGGTGGTTGTGTTGTTGCTCTGGTCAAGGAAGAGGAAGTGGATTCTTTCATCTCTGCCCTCAAGgtatgcatccccatctccccaccctgtgaacgataaaatcaacgggttcattgaaattggtgtgtatctccaactagtgggctcatcaatattagtgtttctggatgtccttgtgcag
 || ||  | ||||||||| | ||||||||||| |||||||||||||  |||||  |||| || ||       ||       |||||        | ||||| ||  |||    ||||| |  |||         || || ||    ||  | | |   |   || | |   | |||     |||| | |    |  ||| |                
TGGAGCGCTTGGAGCAAGGCTTACTGGAGCTGGATGGGGTGGTTGTGCAGTTGCCTTGGTGAAAGAGAGCATTGTCCCACAATTCATTCTAAATTTGAAGgtctgtttccta--ctcccaaagctg--------gaattccactctctctcttacaaaagcaagtttttgacattagaca--tcatgattccatgcttttatcag-------------

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|162189012|gb|FC365130.1|FC365130
EST:     TTGCTCTGGTCAAGGAAGAGGAAGTGGATTCTTTCATCTCTGCCCTCAAG                         GAGACGTATTACAAACCTCTGCTGGAAAGAGGGAAGATCAAGGAGGAAGAT
genomic: TTGCTCTGGTCAAGGAAGAGGAAGTGGATTCTTTCATCTCTGCCCTCAAGgtatgcatcc ... ccttgtgcagGAGACGTATTACAAACCTCTGCTGGAAAGAGGGAAGATCAAGGAGGAAGAT
EST: gi|208388403|gb|DC957041.1|DC957041
EST:     TTGCTCTGGTCAAGGAAGAGGAAGTGGATTCTTTCATCTCTGCCCTCAAG                         GAGACGTATTACAAACCTCTGCTGGAAAGAGGGAAGATCAAGGAGGAAGAT
genomic: TTGCTCTGGTCAAGGAAGAGGAAGTGGATTCTTTCATCTCTGCCCTCAAGgtatgcatcc ... ccttgtgcagGAGACGTATTACAAACCTCTGCTGGAAAGAGGGAAGATCAAGGAGGAAGAT
EST: gi|162195375|gb|FC369310.1|FC369310
EST:     TTGCTCTGGTCAAGGAAGAGGAAGTGGATTCTTTCATCTCTGCCCTCAAG                         GAGACGTATTACAAACCTCTGCTGGAAAGAGGGAAGATCAAGGAGGAAGAT
genomic: TTGCTCTGGTCAAGGAAGAGGAAGTGGATTCTTTCATCTCTGCCCTCAAGgtatgcatcc ... ccttgtgcagGAGACGTATTACAAACCTCTGCTGGAAAGAGGGAAGATCAAGGAGGAAGAT
EST: gi|162272814|gb|FC448802.1|FC448802
EST:     TTGCTCTGGTCAAGGAAGAGGAAGTGGATTCTTTCATCTCTGCCCTCAAG                         GAGACGTATTACAAACCTCTGCTGGAAAGAGGGAAGATCAAGGAGGAAGAT
genomic: TTGCTCTGGTCAAGGAAGAGGAAGTGGATTCTTTCATCTCTGCCCTCAAGgtatgcatcc ... ccttgtgcagGAGACGTATTACAAACCTCTGCTGGAAAGAGGGAAGATCAAGGAGGAAGAT
EST: gi|208385544|gb|DC956700.1|DC956700
EST:     TTGCTCTGGTCAAGGAAGAGGAAGTGGATTCTTTCATCTCTGCCCTCAAG                         GAGACGTATTACAAACCTCTGCTGGAAAGAGGGAAGATCAAGGAGGAAGAT
genomic: TTGCTCTGGTCAAGGAAGAGGAAGTGGATTCTTTCATCTCTGCCCTCAAGgtatgcatcc ... ccttgtgcagGAGACGTATTACAAACCTCTGCTGGAAAGAGGGAAGATCAAGGAGGAAGAT
EST: gi|162195376|gb|FC369311.1|FC369311
EST:     TTGCTCTGGTCAAGGAAGAGGAAGTGGATTCTTTCATCTCTGCCCTCAAG                         GAGACGTATTACAAACCTCTGCTGGAAAGAGGGAAGATCAAGGAGGAAGAT
genomic: TTGCTCTGGTCAAGGAAGAGGAAGTGGATTCTTTCATCTCTGCCCTCAAGgtatgcatcc ... ccttgtgcagGAGACGTATTACAAACCTCTGCTGGAAAGAGGGAAGATCAAGGAGGAAGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGTGCAATAGGAGCAAGGTTGACTGGAGCTGGTTGGGGTGGTTGTGTTGTTGCTCTGGTCAAGGAAGAGGAAGTGGATTCTTTCATCTCTGCCCTCAAGgtatgcatccccatctccccaccctgtgaacgataaaatcaacgggttcattgaaattggtgtgtatctccaactagtgggctcatcaatattagtgtttctggatgtccttgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA