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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgaccttgatatggaatgttcattgtgagttattgattacctagacttctagaatactgtgctaaagtgaagtgctttatattgtgattgggatcgcagGTACGTTGATGTCATATTACAGCTTATTGAGAAGGCTGGTGATTTTGTTAGTGATGATATATGGTACCGAGTGGTTCAATTTGTTACCAACAATGATGAT

Basic information

species Physcomitrella patens
transcript PP1S26_36V6.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S26_36V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 12
----ttgaccttgatatggaatgttcattgtgagttattgattacctagacttctagaatactg-tgctaaagtgaagtgctttatattgtgattgggatcgcagGTACGTTGATGTCATATTACAGCTTATTGAGAAGGCTGGTGATTTTGTTAGTGATGATATATGGTACCGAGTGGTTCAATTTGTTACCAACAATGATGAT
     ||| ||   | | | ||  | | | | || ||    |   ||||  || |   | | || || |       | |   | |  || |  ||        ||||| || ||||| ||  | ||||| || || || || || |||||||| ||||||||||||||||| |||||||| |||||||| ||||||||||| |||
agttctgaactacctgtaggatagtaactct-agctagcattggactagttttatgtgaaattgatgatttccaccaatatctaacttttttttt----ctatagGTATGTCGATGTTATTCTGCAGCTGATAGACAAAGCAGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTCACCAACAATGAAGAT

upper sequence: PP1S26_36V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 13
ttgaccttgatatggaatgttcattgtgagttat-tgattacctagacttctagaatactgtgctaaagtgaagtgctttatat-tgtgattgggatc---gcagGTACGTTGATGTCATATTACAGCTTATTGAGAAGGCTGGTGATTTTGTTAGTGATGATATATGGTACCGAGTGGTTCAATTTGTTACCAACAATGATGAT
   ||     ||   ||| |   |||| |||| | ||   |  |  | || |  |||   ||   |   |  |||  ||  ||| | ||||| | ||    | ||||| |||||||| ||  | || ||||| || || ||||| |||||||| ||||||||||||||||| |||||||| ||||||||||| ||||| || || 
--aacaactgtagcaaat-tgtgttgtcagttctgtgtgcattttaatttatgcaatttcgt--caccattgagtttttgctatatctgatttgtatttgtgtagGTATGTTGATGTTATTCTTCAACTTATAGACAAAGCTGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTTACGAACAACGAAGAC

upper sequence: PP1S26_36V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 12
------ttgaccttgatatggaatgttcattgtgagttattgattacctagacttctagaatactgtgctaaagtgaagtgct-ttatattgtgattgggatcgcagGTACGTTGATGTCATATTACAGCTTATTGAGAAGGCTGGTGATTTTGTTAGTGATGATATATGGTACCGAGTGGTTCAATTTGTTACCAACAATGATGAT
         |  |   ||   ||  |||  | |||  | ||||| |     |||| | |  |  |||  ||  ||  | || | | || |  |   |   ||  |||||| |||||||| ||  | ||  | ||||| ||||| ||||||||||| |||||||| |||||||  || |||||||| |||||||| |||||||| || 
tcaccccatatttcagtacaaaaaattccct-tgatatcttgatca---gaacttattgt-tgatgtaatat-gtatactgatatcatgtcatcccttttat-acagGTATGTTGATGTGATTCTTCAATTAATTGACAAGGCCGGTGATTTTGTCAGTGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGAC

upper sequence: PP1S26_36V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 12
-------ttgaccttgatatggaatgt-tcattgtgagttattgattacctagacttctagaatactgtgctaaagtgaagtgctttatattgtgattgggatcgcagGTACGTTGATGTCATATTACAGCTTATTGAGAAGGCTGGTGATTTTGTTAGTGATGATATATGGTACCGAGTGGTTCAATTTGTTACCAACAATGATGAT
          |  |   ||   ||  |  | |||  | ||  | |  || ||   |  |    || | || || | |||  |     ||    |   |   ||  |||||| ||||| || ||  | ||  | ||||| ||||| || ||||||||||| ||||| |||||||  || |||||||| |||||||| |||||||| || 
gtcacgccatatttcagtacaaaaaatacccttgatatttgatcagaactta--ttgttgatttaatatg-tacactgatat----catgccatcccttttat-acagGTATGTTGACGTGATTCTTCAATTAATTGACAAGGCCGGAGATTTTGTTAGCGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGAC

upper sequence: PP1S26_36V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: AT5G22770.2 (Arabidopsis thaliana), 3'ss of exon 13
-----------------------------------------ttgaccttgatatggaatgttcattgtgagttattgattaccta-gacttctagaatactgtgctaaagtgaagtgctttatattgt-gattggga---tcgcagGTACGTTGATGTCATATTACAGCTTATTGAGAAGGCTGGTGATTTTGTTAGTGATGATATATGGTACCGAGTGGTTCAATTTGTTACCAACAATGATGAT
                                         |  ||    || |||       |   ||  ||||  |||   |  ||| | ||||    ||     || | || || || |   |||  |||  ||   |  |||||| |||||||| ||  | ||| | || || |||||||| ||||||||||| ||||| |||||||  || |||||||| ||||| || || ||||| || 
gtgaggataactcgatacgaagtatatgtacacttcattcatgcacacaaatttggttacagtaacatgcattatccatttggtgtgacctttagatccttgc----aaatcaactggttaaagatgttaattttgatgttttcagGTATGTTGATGTGATCCTTCAGTTGATCGACAAGGCTGGGGATTTTGTTAGCGATGACATATGGTTTCGTGTGGTTCAGTTTGTAACAAATAATGAAGAC

upper sequence: PP1S26_36V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: EFJ34224 (Selaginella moellendorffii), 3'ss of exon 12
ttgaccttgatatggaatgttcattgtgagttattgattacctagacttctagaatactgtgctaaagtgaagtgctttatattgtgattgggatcgcagGTACGTTGATGTCATATTACAGCTTATTGAGAAGGCTGGTGATTTTGTTAGTGATGATATATGGTACCGAGTGGTTCAATTTGTTACCAACAATGATGAT
                                          | ||  |||  |  | | |      ||            |||||  || || |   |||||||| ||||| || ||||||||||||||||||||||| ||||| ||||| ||||| || |||||| |||| || |||||||| || ||||||||||||
---------------------------------------gtattgatatctgaagaaatctctccctgttgctaataaggaattgt--tttggct---agGTACGTGGATGTTATCTTACAGCTTATTGAGAAGGCTGGAGATTTCGTTAGCGATGACATTTGGTACAGAGTAGTCCAATTTGTGACAAACAATGATGAT

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|100415547|gb|BY992895.1|BY992895
EST:     GCTTTGAAAGCTGCCATTCTGTCTGAGAAGTTCGCTCCAGATTTGTCTTG                         GTACGTTGATGTCATATTACAGCTTATTGAGAAGGCTGGTGATTTTGTTAG
genomic: GCTTTGAAAGCTGCCATTCTGTCTGAGAAGTTCGCTCCAGATTTGTCTTGgtactctcct ... gggatcgcagGTACGTTGATGTCATATTACAGCTTATTGAGAAGGCTGGTGATTTTGTTAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttctagaatactgtgctaaagtgaagtgctttatattgtgattgggatcgcagGTACGTTGATGTCATATTACAGCTTATTGAGAAGGCTGGTGATTTTGTTAGTGATGATATATGGTACCGAGTGGTTCAATTTGTTACCAACAATGATGAT
               tgctaaa  putative branch site (score: 2)
                               tttatattgtgatt  TA-rich tract