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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattccgacttgtcccctccatttattaacactctagcctttatttcctctattcagaattaaatcttgcatagtatttttttggttctgttcatttatgtactgttggctaaggtctgtgccataagtatgcataacctgggtgcattttacatttcatcagGTTCTGGCATCAAGACAACGAAGTGCGTTTCCACCTAATTTTGTGCACTCTTTAGATAGCTCTCACATGATGATGACAGCCCTTGCTTGTAGTAAAGCGG

Basic information

species Physcomitrella patens
transcript PP1S246_118V6.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S246_118V6.1 (Physcomitrella patens), 3'ss of exon 18
lower sequence: LOC_Os06g44230.1 (Oryza sativa), 3'ss of exon 16
gtaattccgacttgtcccctccatttattaacactctagcctttatttcctctattcagaattaaatcttgcatagtatttttttggttctgttcatttatgtactgttggctaaggtctgtgccataagtatgcataacctgggtgcattttacatttcatcagGTTCTGGCATCAAGACAACGAAGTGCGTTTCCACCTAATTTTGTGCACTCTTTAGATAGCTCTCACATGATGATGACAGCCCTTGCTTGTAGTAAAGCGG
                                                    ||   | ||  || |  || ||  |  |||||  ||||| ||| || || |||||  |  |||  ||  || || || |              | ||  || || | || |       ||||  ||| ||       || ||||| || ||||||||||||||| | ||||| || |||||||||||||| ||  |||| || |  || || |
---------------------------------------------------gtaagtaaaaccaatttctggat--tgatttttccgttct-ttctttcat-tactgc-gattaatatcgctgtcacaatt--------------tccagATTGCACTCCAGC-------GGCAA-AAGGCA-------GCTTTTCCCCCAAATTTTGTGCACTCTCTTGATAGTTCACACATGATGATGACTGCTATTGCATGCAAAAAGGCTG

upper sequence: PP1S246_118V6.1 (Physcomitrella patens), 3'ss of exon 18
lower sequence: GRMZM2G115564_T02 (Zea mays), 3'ss of exon 16
gtaattccgacttgtcccctccatttattaacactctagcctttatttcctctattcagaattaaatcttgcatagtatttttttggttctgttcatttatgtactgttggctaaggtctgtgccataagtatgcataacctgggtgcattttacatttcatcagGTTCTGGCATCAAGACAACGAAGTGCGTTTCCACCTAATTTTGTGCACTCTTTAGATAGCTCTCACATGATGATGACAGCCCTTGCTTGTAGTAAAGCGG
                                                                                   |  |||| | | ||||    ||  ||  ||      | | ||||   | |   |||        |||     ||||  |||| ||        ||| |||      || |||||||| ||||||||||||||  | ||||| || || ||||||||||||||  ||||||| |   |  | |
----------------------------------------------------------------------------------gtgagttcagct-atttcaaaacgttttcctgtttcttttcccattcttgtagctaattaattgacata----attt--tcagATTGCAATCCAAAGGCAAAAGGCAGCTTTTCCACCAAATTTTGTGCACTCACTGGATAGTTCACATATGATGATGACAGCGATTGCTTGCAAGGAGTCTG
















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|15327490|gb|BI488244.1|BI488244
EST:     AAACCTCTCTTCAAGTTTTGGCTCTTAGAAATACAGATGATAATCACCCG                         GTTCTGGCATCAAGACAACGAAGTGCGTTTCCACCTAATTTTGTGCACTCT
genomic: AAACCTCTCTTCAAGTTTTGGCTCTTAGAAATACAGATGATAATCACCCGgtaattccga ... atttcatcagGTTCTGGCATCAAGACAACGAAGTGCGTTTCCACCTAATTTTGTGCACTCT
EST: gi|162164596|gb|FC341891.1|FC341891
EST:     AAACCTCTCTTCAAGTTTTGGCTCTTAGAAATACAGATGATAATCACCCG                         GTTCTGGCATCAAGACAACGAAGTGCGTTTCCACCTAATTTTGTGCACTCT
genomic: AAACCTCTCTTCAAGTTTTGGCTCTTAGAAATACAGATGATAATCACCCGgtaattccga ... atttcatcagGTTCTGGCATCAAGACAACGAAGTGCGTTTCCACCTAATTTTGTGCACTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctaaggtctgtgccataagtatgcataacctgggtgcattttacatttcatcagGTTCTGGCATCAAGACAACGAAGTGCGTTTCCACCTAATTTTGTGCACTCTTTAGATAGCTCTCACATGATGATGACAGCCCTTGCTTGTAGTAAAGCGG
                       gcataac  putative branch site (score: 3)
                                              tttcatc  putative PPT
                                      attttacatttcat  TA-rich tract