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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATCAAAGAGTCCGACACCGGGCTGGCAGTGCCTAGTCAGTGGGATCTCGTATCAGATAAGCAGATGATGCAAGAGGAACAACCATTGCAGgttagttaatcccagccaggttgtcaaacttctcgacatgatctcgtgcatttcttactcgtatttagcagacgggtggtaataacttaatttattaattgtggcag

Basic information

species Physcomitrella patens
transcript PP1S152_13V6.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S152_13V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os02g54340.1 (Oryza sativa), 5'ss of exon 3
GAATCAAAGAGTCCGACACCGGGCTGGCAGTGCCTAGTCAGTGGGATCTCGTATCAGATAAGCAGATGATGCAAGAGGAACAACCATTGCAGgttagttaatc--ccagccaggttgtcaaacttctcgacatgatctcgtgcatttcttact--cgtatttagcagacgggtggtaataacttaatttattaattgtggcag-----------------------------------------------
| || || ||||| ||||| |||||||||   || || || |||||||| |||||||||||||||||||||||||| || |||||  |||| ||   |   |   ||         | | | |||||   | || | |  |   ||| |  ||  | || ||     | |     |||  |||||  ||      | | |                                                  
GGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAAgtatatcgcttaacctatttccccgcctaccttcttc-cttgttttaatagttttgtgcctagcatacttcatgcatgatgcctaaggacttagatttcctgctttagttttatgtcttctgtgattttactgacaagatattttcctccttttgaag

upper sequence: PP1S152_13V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os06g09290.2 (Oryza sativa), 5'ss of exon 3
GAATCAAAGAGTCCGACACCGGGCTGGCAGTGCCTAGTCAGTGGGATCTCGTATCAGATAAGCAGATGATGCAAGAGGAACAACCATTGCAGgttagttaatcccagccaggttgtcaaacttctcgacatgatctcgtgcattt-cttactcgtatt-tagcagacgggtggtaataacttaatttattaattgtggcag------
|||| |||||||| ||||| ||  ||||    ||||| |||||||| || ||||| ||||||||||||||||| ||||| |||||  ||||||| |  |  |    |      |  |  |||| | |   | ||  | | ||  | | ||||   | | |  |    |  |  | ||  |||    || |||  ||           
GAATTAAAGAGTCTGACACTGGATTGGCTCCACCTAGCCAGTGGGACCTTGTATCCGATAAGCAGATGATGCAGGAGGAGCAACCCCTGCAGgtaa--tgcttgacgttcacctaactgactttttggttttattgcattcaaatgcatactgtcaatattccctgtgcttcctcatgccttctactaataagcgtccttctgcaag

upper sequence: PP1S152_13V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G110185_T01 (Zea mays), 5'ss of exon 3
GAATCAAAGAGTCCGACACCGGGCTGGCAGTGCCTAGTCAGTGGGATCTCGTATCAGATAAGCAGATGATGCAAGAGGAACAACCATTGCAGgttagttaatcccagccaggttgtcaaacttctcgacatgatctcgtgcatttcttactcgtatttagcagacgggtggtaataacttaatttattaattgtggcag-----------------------------
| || || ||||| || || ||||||||    ||||| ||||||||| | || ||||||||||||||||||||||| |||||||| || || ||   |||| |  | || | |  |       ||     || | |      |||     |  || ||||        |  |  |   || | || |||  |||| |||                             
GGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAAgtatattaa-ctgaacctgat-attgtgtcacttagt-tgtttttacagctttgagcatgatagttaggcacaaaatctttttggtttcagtt-ttacatgtgccagcgcactataacttctctctctttctgcag

upper sequence: PP1S152_13V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G181359_T01 (Zea mays), 5'ss of exon 3
GAATCAAAGAGTCCGACACCGGGCTGGCAGTGCCTAGTCAGTGGGATCTCGTATCAGATAAGCAGATGATGCAAGAGGAACAACCATTGCAGgt-tagttaatcccagccaggttgtcaaacttctcgacatgatctcgtgcatttcttactcgt-atttagca-----gacgggtggtaataacttaatttatt--aattgtggcag--------------------------------------
| || || ||||| || || ||| ||||    ||||| ||||||||| | || |||||||| |||||||||||||| |||||||| || || || || | |||  |    |  ||||   |||||      |   ||  | ||  | | | |  | |  || ||     ||  | |||||  ||  |  ||  ||  |||| |    |                                      
GTATAAAGGAGTCTGATACAGGGTTGGCTCCACCTAGCCAGTGGGATTTGGTTTCAGATAAACAGATGATGCAAGAAGAACAACCGTTACAAgtatattaaatgaccctgatattgtgttacttcgtagattttacttttacagctttgagttatgacctaccatgcatgatagttggtagaaatctttttggtttcaattttacatgtgctagtgcattaataacttctctttctctttctgcag

upper sequence: PP1S152_13V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EFJ13722 (Selaginella moellendorffii), 5'ss of exon 3
GAATCAAAGAGTCCGACACCGGGCTGGCAGTGCCTAGTCAGTGGGATCTCGTATCAGATAAGCAGATGATGCAAGAGGAACAACCATTGCAGgttagttaatcccagccaggttgtcaaacttctcgacatgatctcgtgcatttcttactcgtatttagcagacgggtggtaataacttaatttattaattgtggcag
| ||||| ||||||||||| || || ||||  ||||| ||||||||||| || || |||||||| ||||||||||| || || ||| |||| || ||| |            || |   |  ||| |   |  |||  |   | || |  | |  ||| | ||                                    
GGATCAAGGAGTCCGACACTGGTCTAGCAGCTCCTAGCCAGTGGGATCTGGTGTCTGATAAGCAAATGATGCAAGAAGAGCAGCCACTGCAAgtaagtgagatttt-----tttcttcgatctcttgcttt--tcttttttctctcatgtttggttttggtag------------------------------------

upper sequence: PP1S152_13V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EFJ29161 (Selaginella moellendorffii), 5'ss of exon 3
GAATCAAAGAGTCCGACACCGGGCTGGCAGTGCCTAGTCAGTGGGATCTCGTATCAGATAAGCAGATGATGCAAGAGGAACAACCATTGCAGgttagttaatcccagccaggttgtcaaacttctcgacatgatctcgtgcatttcttac---tcgtatttagcagacgggtggtaataacttaatttattaattgtggcag
| ||||| ||||||||||| || || ||||  ||||| ||||||||||| || || |||||||| ||||||||||| || || ||| |||| || ||             ||     | | || |      |||||  ||| ||||| |    | |  ||| | ||                                    
GGATCAAGGAGTCCGACACTGGTCTAGCAGCTCCTAGCCAGTGGGATCTGGTGTCTGATAAGCAAATGATGCAAGAAGAGCAGCCACTGCAAgtaag-------------gg-----agatttttttcttcgatctattgcttttctcatgttttggttttggtag------------------------------------

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|208399150|gb|DC912407.1|DC912407
EST:     GGGATCTCGTATCAGATAAGCAGATGATGCAAGAGGAACAACCATTGCAG                         GTTGCCAGGTGTACAAAGATAATCAACGCCAATACGGATGACTCCAAATAC
genomic: GGGATCTCGTATCAGATAAGCAGATGATGCAAGAGGAACAACCATTGCAGgttagttaat ... attgtggcagGTTGCCAGGTGTACAAAGATAATCAACGCCAATACGGATGACTCCAAATAC
EST: gi|162256308|gb|FC432318.1|FC432318
EST:     GGGATCTCGTATCAGATAAGCAGATGATGCAAGAGGAACAACCATTGCAG                         GTTGCCAGGTGTACAAAGATAATCAACGCCAATACGGATGACTCCAAATAC
genomic: GGGATCTCGTATCAGATAAGCAGATGATGCAAGAGGAACAACCATTGCAGgttagttaat ... attgtggcagGTTGCCAGGTGTACAAAGATAATCAACGCCAATACGGATGACTCCAAATAC
EST: gi|162257097|gb|FC432557.1|FC432557
EST:     GGGATCTCGTATCAGATAAGCAGATGATGCAAGAGGAACAACCATTGCAG                         GTTGCCAGGTGTACAAAGATAATCAACGCCAATACGGATGACTCCAAATAC
genomic: GGGATCTCGTATCAGATAAGCAGATGATGCAAGAGGAACAACCATTGCAGgttagttaat ... attgtggcagGTTGCCAGGTGTACAAAGATAATCAACGCCAATACGGATGACTCCAAATAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAATCAAAGAGTCCGACACCGGGCTGGCAGTGCCTAGTCAGTGGGATCTCGTATCAGATAAGCAGATGATGCAAGAGGAACAACCATTGCAGgttagttaatcccagccaggttgtcaaacttctcgacatgatctcgtgcatttcttactcgtatttagcagacgggtggtaataacttaatttattaattgtggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA