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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAATAGGAGAACGTCAATTGGCTACAGCGGGTTGGCTGGCAGTCATGCCTGTATTCGAACCACATTGGCAAATCTGCATGGCGGGTGGTTTGTCCACAGgtctgctcattactatttcagaagactccgcattccagcaaaaactcttaagtgtggaggctaagcgtcttgatttagaatgtgatcgctggaaattatc...

Basic information

species Physcomitrella patens
transcript PP1S9_51V6.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S9_51V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: LOC_Os02g17650.1 (Oryza sativa), 5'ss of exon 5
---TCAATAGGAGAACGTCAATTGGCTACAGCGGGTTGGCTGGCAGTCATGCCTGTATTCGAACCACATTGGCAAATCTGCATGGCGGGTGGTTTGTCCACAGgtctgctcattactat-ttcagaagactccgcattccagcaaaaactcttaagtgtggaggctaagcgtcttgatttagaatgtgatcgc-tggaaattatc-
      |    | | |   |||   ||   || |||||||| || |   | ||| | || ||||| ||||||||||| |||||||| ||||| || ||||||||| ||    |   | | ||    | |||   ||       |   | | ||   | |     |||   || || |||     |  ||| ||         |   
GATGTCACGTCAAAGCAGAAATCAACT---GCTGGTTGGCTTGCTGCTTTTCCTTTCTTTGAACCTCATTGGCAAATATGCATGGCTGGTGGCTTATCCACAGgtttgtatttctttgtatttgataaactgaacagagagatatttaatttttctttttac--ctactggttttcattctaggta-gatggcacatgtgccactg

upper sequence: PP1S9_51V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GRMZM2G009785_T03 (Zea mays), 5'ss of exon 5
TCAATAGGAGAAC--GTCAATTGGCTACAGCGGGTTGGCTGGCAGTCATGCCTGTATTCGAACCACATTGGCAAATCTGCATGGCGGGTGGTTTGTCCACAGgtctgctcattactatttcagaagactccgcat-tccagcaaaaactcttaagtgtggaggctaagcgtcttgatttagaatgtgatcgctgg-aaattatc-
   ||   | | |    || ||| | ||||| |||||||| ||||   | ||| | || ||||| ||||||||||| ||||||||  |||| |||||||||||| ||    |    |   ||||| | |    || |  |   | |   ||    |    |   |     |  | |   ||    |   | |||     ||    
--GATGTCAAATCTAAGCAGTTGTCCACAGctggttggcttgcagcttttcctttctttgaacctcattggcaaatttgcatggctagtggcttgtccacaggtttgtctttgtgca---cagaaaaataaagatatttactgagagacctgctattcataaatttgttcttgttagacagcccatatccactgttgcgttgctg

upper sequence: PP1S9_51V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GRMZM2G009785_T02 (Zea mays), 5'ss of exon 5
TCAATAGGAGAACGTCAATTGGCTACAGCGGGTTGGCTGGCAGTCATGCCTGTATTCGAACCAC--ATTGGCAAATCTGCATGGCGGGTGGTTTGTCCACAGgtctgctcattactatttcagaagactccgcattccagcaa-aaactcttaagtgtggaggctaagcgtcttgatttagaatgtgatcgctggaaattatc----
||||     |   | ||| || | | |    | | ||||| |||   ||     | |     |    | ||   || |  |      |  ||| |||||||| |       || |   ||       ||  | |   ||     ||| |   | |  | | ||||   |  |     || |  | ||  | | | ||| ||      
TCAAACTACG--TGCCAAATGTCCAAAC--AGCTCGCTGGGAGTACAGCACTCGTCCAGTTTATGGGTGGGGTGATGTCAAATCTAAGCAGTT-GTCCACAGCTGgttggcttgcagcttttcctttctttgaacctcattggcaaatttgcatggctagtggcttgtc--cacaggtttgtctttgtgcacagaaaaataaagata

upper sequence: PP1S9_51V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA04G08750.1 (Glycine max), 5'ss of exon 6
-TCAATAGGAGAACGTCAATTGGCTACAGCGGGTTGGCTGGCAGTCATGCCTGTATTCGAACCACATTGGCAAATCTGCATGGCGGGTGGTTTGTCCACAGgtctgctcattactatttcagaagactccgcattccagcaaaaactcttaagtgtggaggctaagcgtcttgatttagaatgtgatcgctggaaattatc--------
     | |    ||| ||   | |||| || || ||||| ||||   | ||||| || ||||||||||||||||| |||||||| |||||  |||| |||||| |  ||  ||||  |||||   | |    |||| | |    | |      | | | ||   || ||| ||  ||   |||| ||  ||| |    | |        
GATGTTGGTTCTACG-CAGAAGTCTACTGCTGGGTGGCTTGCAGCTTTTCCTGTTTTTGAACCACATTGGCAAATATGCATGGCTGGTGGACTGTCAACAGgtattttc--tacttgttcagct-attggctattcgatcttttattt----attttgtggtctagtgtcctg-cttgttatgttatgtctgaactgaaacatgataat

upper sequence: PP1S9_51V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA06G08850.1 (Glycine max), 5'ss of exon 5
-TCAATAGGAGAACGTCAATTGGCTACAGCGGGTTGGCTGGCAGTCATGCCTGTATTCGAACCACATTGGCAAATCTGCATGGCGGGTGGTTTGTCCACAGgtctgctcattactatttcagaagactccgcattccagcaaaaactcttaagtgtggaggctaagcgtcttgatttagaatgtgatcgctggaaattatc--------
     | |    ||| ||   | |||| || || ||||| ||||   | ||||| || ||||||||||||||||| |||||||| |||||  |||| |||||  |  ||  ||||  |||||   | |    |||  | |    | |      | | | ||   || |||   | ||   |||| ||  ||| ||   | |        
GATGTTGGTTCCACG-CAGAAGTCTACTGCTGGGTGGCTTGCAGCTTTTCCTGTTTTTGAACCACATTGGCAAATATGCATGGCTGGTGGACTGTCAACAGgcattttc--tacttgttcagct-attggctatttgatcttttattt----attttgtggtctagtgtccc-acttgttatgttatgtctgaaatgaaacatgataat

upper sequence: PP1S9_51V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: Vv04s0008g03600.t01 (Vitis vinifera), 5'ss of exon 5
TCAATAGGAGAAC--GTCAATTGGCTACAGCGGGTTGGCTGGCAGTCATGCCTGTATTCGAACCACATTGGCAAATCTGCATGGCGGGTGGTTTGTCCACAGgt-ctgctca-ttactatttcagaag-actccgcattccagc-aaaaactcttaagtgtggaggctaagcgtcttgatttagaatgtgatcgctggaaattatc
  |||    |  |    ||   | | ||||| || ||||| ||||   | |||||||| ||||| ||||||||||| ||||||||||| ||  | || ||||||  |||| | |  | ||||   |||   |   || |  |       | | ||  |  |  |  ||||   | ||   ||||       ||      ||||   
--AATGTTGGGTCTAAACAGAAGTCCACAGCTGGCTGGCTTGCAGCTTTTCCTGTATTTGAACCCCATTGGCAAATATGCATGGCGGGAGGACTCTCAACAGgtattgcttaatctccattttgcaagtggtttacacttgatttgtttaattttttgctttcattctaa---tttttgcttagttaactgtcatgttgaattgc-

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|100353188|gb|BY945650.1|BY945650
EST:     TGTATTCGAACCACATTGGCAAATCTGCATGGCGGGTGGTTTGTCCACAG                         GCTGGATTGAGTGGGGTGATCGACGCTTTGAGTTTGAGGATGCTCCTTCAT
genomic: TGTATTCGAACCACATTGGCAAATCTGCATGGCGGGTGGTTTGTCCACAGgtctgctcat ... aattgtgcagGCTGGATTGAGTGGGGTGATCGACGCTTTGAGTTTGAGGATGCTCCTTCAT