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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaaatctcgtccaagacaactctgtgctccaggaatcattttgtccagaatgttcagtccaacgaagacgatgggttcaattattgacgtcgagaactttcgacggtgcagGTGATTGCGCTGGACATCAGCAAGGAGTGGTATGACATTGGAGCGCCGGTAATTCAAAAGGCGGGCGTTGCTCACAAGATCGACTTCCGGGACGGACCTG

Basic information

species Physcomitrella patens
transcript PP1S16_28V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S16_28V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os06g06980.3 (Oryza sativa), 3'ss of exon 2
gtgaaatctcgtccaagacaactctgtgctccaggaatcattt-tgtccagaatgttcagtccaacgaagacgatgggttcaatt-attgacgtcgagaacttt--cgac-ggtgcagGTGATTGCGCTGGACATCAGCAAGGAGTGGTATGACATTGGAGCGCCGGTAATTCAAAAGGCGGGCGTTGCTCACAAGATCGACTTCCGGGACGGACCTG
                      || |     |   ||||     | ||    ||      ||   | |  |         ||||  ||||||||| |   || |    ||   ||||| |  | ||| ||||||||| |  ||||   || ||  | ||    |||   ||  | |||||||| || || |||||||||||||||||||| ||||| |
---------------------gtcagcaacacgcaaatcccccatctcttccatcgcagatctggcaagaa----atccccaatcgattgacgtccatccctctgctaactaatgcagATCTTGGCGATGGACATCAACCGGGAGAACTACGAGCTGGGGCTCCCGTCGATCGAGAAGGCGGGAGTGGCGCACAAGATCGACTTCCGGGAGGGACCCG

upper sequence: PP1S16_28V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT4G34050.2 (Arabidopsis thaliana), 3'ss of exon 1
gtgaaatctcgtccaagacaactctgtgctccaggaatcattttgtccagaatgttcagtccaacgaagacgatgggttcaattattgacgtcgagaactttcgacggtgcagGTGATTGCGCTGGACATCAGCAAGGAGTGGTATGACATTGGAGCGCCGGTAATTCAAAAGGCGGGCGTTGCTCACAAGATCGACTTCCGGGACGGACCTG--------------------------------
                                                                                ||||    | ||      ||||  |   | ||| |  | ||  ||||  ||| ||  |||   || ||  | ||    ||| | ||| | || || |||||||||||||||||||||||| |||| || ||||                                
--------------------------------------------------------------------------------aattg--aaagtttcatcctttttatcat-cagattctggctatggatgtcaacagagagaattacgaattgggtttaccgatcattgagaaagccggcgttgCTCACAAGATCGACTTCAGGGAAGGCCCTGCTCTTCCCGTTCTTGATGAAATCGTTGCTGAC

upper sequence: PP1S16_28V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT4G34050.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgaaatctcgtccaagacaactctgtgctccaggaatcattttgtccagaatgttcagtccaacgaaga----cgatgggttcaattattgac-gtcgagaactttcgacggtgcagGTGATTGCGCTGGACATCAGCAAGGAGTGGTATGACATTGGAGCGCCGGTAATTCAAAAGGCGGGCGTTGCTCACAAGATCGACTTCCGGGACGGACCTG
                                   ||||| | | | ||   |  || ||     |  |      |  |   |     |||||  ||      ||||  |   | ||| |  | ||  ||||  ||| ||  |||   || ||  | ||    ||| | ||| | || || |||||||||||||||||||||||| |||| || ||||
--------------------------------gtaaatcaatctcttcatcctcctctgttttttggtgggttttgtcgaacttgggaattgaaagtttcatcctttttatcat-cagATTCTGGCTATGGATGTCAACAGAGAGAATTACGAATTGGGTTTACCGATCATTGAGAAAGCCGGCGTTGCTCACAAGATCGACTTCAGGGAAGGCCCTG

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|208390036|gb|DC938091.1|DC938091
EST:     CAGGCTATTCGCTTCTTTGCACCGCCCTTGCATTACCGCCGGATGGCAAG                         GTGATTGCGCTGGACATCAGCAAGGAGTGGTATGACATTGGAGCGCCGGTA
genomic: CAGGCTATTCGCTTCTTTGCACCGCCCTTGCATTACCGCCGGATGGCAAGgtgaaatctc ... gacggtgcagGTGATTGCGCTGGACATCAGCAAGGAGTGGTATGACATTGGAGCGCCGGTA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtccaacgaagacgatgggttcaattattgacgtcgagaactttcgacggtgcagGTGATTGCGCTGGACATCAGCAAGGAGTGGTATGACATTGGAGCGCCGGTAATTCAAAAGGCGGGCGTTGCTCACAAGATCGACTTCCGGGACGGACCTG
                         tattgac  putative branch site (score: 2)
                   ttcaattatt  TA-rich tract