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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttgaatattggatgagtcggaataacgtagagccagaaatgacgtagtgactgttgaatttttatttctgtgggctgcgtctaaggtcggaattatctagttttctgccatggtcagagtgctggttttgcgctggtgttgatattgaccctaactgtatgcagGAAATCATGGGCGTATTCAACAGGAACTGTATGATCAGTTACTCTGCGTACCGGTGTATTTTTCCTATCTGGGCACTGGGTGAGTACCGGCAAAAATTGA

Basic information

species Physcomitrella patens
transcript PP1S33_211V6.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S33_211V6.1 (Physcomitrella patens), 3'ss of exon 17
lower sequence: Vv09s0054g01110.t01 (Vitis vinifera), 3'ss of exon 19
gtacttgaatattggatgagtcggaataacgtagagccagaaatgacgtagtgactgttgaatttttatttctgtgggctgcgtctaaggtcggaattatctagttttctgccatggtcagagtgctggttttgcgctggtgttgatattgaccctaactgtatgcagGAAATCATGGGCGTATTCAACAGGAACTGTATGATCAGTTACTCTGCGTACCGGTGTATTTTTCCTATCTGGGCACTGGGTGAGTACCGGCAAAAATTGA
                                                      ||| | |     |   | ||   ||||  ||  |  | ||||  |  | | |  || |||||  | || |   |||||     | |  |  | |||        ||  || |||||||||||||| || ||||||| ||||||||||||||| || ||||| || |||   ||||||||||| |||||||| || || |||||  |     || 
-----------------------------------------------------tctggttagaaaatgagtatgcatgctgattccca--ttggaacaactttgctgactcccatg-cctgaata--ggtttaa---tagcttcaacattt-------cttcatacagGAAATCATGGGAGTCTTCAACAAGAACTGTATGATCAGCTATTCTGCATATCGGAACATTTTTCCTATATGGGCACTTGGAGAATACCGATATCGGGTGC

upper sequence: PP1S33_211V6.1 (Physcomitrella patens), 3'ss of exon 17
lower sequence: Vv09s0018g00630.t01 (Vitis vinifera), 3'ss of exon 17
gtacttgaatattggatgagtcggaataacgtagagccagaaatgacgtagtgactgttgaatttttatttctgtgggctgcgtctaaggtcggaattatctagttttctgccatggtcagagtgctggttttgcgctggtgttgatattgaccctaactgtatgcagGAAATCATGGGCGTATTCAACAGGAACTGTATGATCAGTTACTCTGCGTACCGGTGTATTTTTCCTATCTGGGCACTGGGTGAGTACCGGCAAAAATTGA
                                                      ||| | |     |   | ||   ||||  ||  |  | | ||  |  | | |  || |||||  | || |   |||||     | || |  | |||        ||  || |||||||||||||| || ||||||| ||||||||||| ||| || ||||| || |||   ||||||||||| |||||||| || || ||||||       |  
-----------------------------------------------------tctggttagaaaatgagtatgcatgctgattccca--ttgcaacaactttgctgactcccatg-cctgaata--ggtttaa---tagtttcaacattt-------cttcatacagGAAATCATGGGAGTCTTCAACAAGAACTGTATGAGCAGCTATTCTGCATATCGGAACATTTTTCCTATATGGGCACTTGGCGAATACCGGTCTCGGGTAC

upper sequence: PP1S33_211V6.1 (Physcomitrella patens), 3'ss of exon 17
lower sequence: Vv09s0054g01090.t01 (Vitis vinifera), 3'ss of exon 18
gtacttgaatattggatgagtcggaataacgtagagccagaaatgacgtagtgactgttgaatttttatttctgtgggctgcgtctaaggtcggaattatctagttttctgccatggtcagagtgctggttttgcgctggtgttgatattgaccctaactgtatgcagGAAATCATGGGCGTATTCAACAGGAACTGTATGATCAGTTACTCTGCGTACCGGTGTATTTTTCCTATCTGGGCACTGGGTGAGTACCGGCAAAAATTGA
                                                      ||| | |     |     ||   ||||  ||  |  | | ||  |  |   |  || |||||     |    ||||||                |||| | |  ||  || |||||||||||||| || ||||||| ||||||||||||||| || ||| | || |||   ||||| ||||| ||||| || || || |||| |       |  
-----------------------------------------------------tctggttagaaaatgagcatgcatgctgattccca--ttgtaacaactttactgactcccatgcctgaa---ttggtttaatagc----------ttgaacatttcttcatacagGAAATCATGGGAGTCTTCAACAAGAACTGTATGATCAGCTATTCTACATATCGGAACATTTTCCCTATATGGGCTCTTGGAGAATACCAGTCTCGGGTAC

upper sequence: PP1S33_211V6.1 (Physcomitrella patens), 3'ss of exon 17
lower sequence: Vv09s0054g01180.t01 (Vitis vinifera), 3'ss of exon 13
gtacttgaatattggatgagtcggaataacgtagagccagaaatgacgtagtgactgttgaatttttatttctgtgggctgcgtctaaggtcggaattatctagttttctgccatggtcagagtgctggttttgcgctggtgttgatattgaccctaactgtatgcagGAAATCATGGGCGTATTCAACAGGAACTGTATGATCAGTTACTCTGCGTACCGGTGTATTTTTCCTATCTGGGCACTGGGTGAGTACCGGCAAAAATTGA
                                                   ||  |    |||   |||  |||| |  | |        | | ||  |  | | |  || |||||  | || |    ||||     | |  |  | |||        ||  || |||||||||||||| || ||||||| |||||||||||  ||||| ||||| || |||   ||||||||||| ||||| || || || ||||||       |  
-------------------------------------------------tctggttagaaaatgagtatgcctgttgattccc------attgcaacaactttgctgactcccatg-cctgaata--agtttaa---tagcttcaacattt-------cttcatacagGAAATCATGGGAGTCTTCAACAAGAACTGTATGAATAGTTATTCTGCATATCGGAACATTTTTCCTATATGGGCTCTTGGAGAATACCGGTCTCGGGTAC

upper sequence: PP1S33_211V6.1 (Physcomitrella patens), 3'ss of exon 17
lower sequence: Vv09s0054g01550.t01 (Vitis vinifera), 3'ss of exon 17
gtacttgaatattggatgagtcggaataacgtagagccagaaatgacgtagtgactgttgaatttttatttctgtgggctgcgtctaaggtcggaattatctagttttctgccatggtcagagtgctggttttgcgctggtgttgatattgaccctaactgtatgcagGAAATCATGGGCGTATTCAACAGGAACTGTATGATCAGTTACTCTGCGTACCGGTGTATTTTTCCTATCTGGGCACTGGGTGAGTACCGGCAAAAATTGA
                                                      ||| | |     |     ||   |||   ||  |  | | ||  |  | | |  || |||||  | || |   |||||     | |  |  | |||        ||  || |||||||||||||| || ||||||| ||||||||||||||  || ||||| || |||   ||||| ||||| ||||| || || ||  |||||       |  
-----------------------------------------------------tctggttagaaaatgagcatgcatgctcattccca--ttgcaacaactttgctggctcccatg-cctgaata--ggtttaa---tagcttcaacattt-------cttcatacagGAAATCATGGGAGTCTTCAACAAGAACTGTATGATCAACTATTCTGCATATCGGAACATTTTCCCTATATGGGCTCTTGGAGAACACCGGTCTCGGGTAC

upper sequence: PP1S33_211V6.1 (Physcomitrella patens), 3'ss of exon 17
lower sequence: Vv11s0065g00640.t01 (Vitis vinifera), 3'ss of exon 18
gtacttgaatattggatgagtcggaataacgtagagccagaaatgacgtagtgactgttgaatttttatttctgtgggctgcgtctaaggtcggaattatctagttttctgccatggtcaga-gtgctggttttgcgctggtgttgatattgaccctaactgtatgcagGAAATCATGGGCGTATTCAACAGGAACTGTATGATCAGTTACTCTGCGTACCGGTGTATTTTTCCTATCTGGGCACTGGGTGAGTACCGGCAAAAATTGA
                                                                  ||        | |||  |  || |     |||     |  ||| | |||| ||  |    |     |    |  ||  |   | |    ||   ||  ||||||| |||||||| || ||||| |||||||||||||||| |||  |||| ||| |    || || || || ||||| |||||||| |||||        |  
------------------------------------------------------------------tagggaaa-agtctgaatgaaatggttccatttctgtggattcaggcatgctcttacactccaaagtcattcatgttctataacttgttct--ttgattgcagGAGATCATGGGGGTCTTCAATAGGAACTGTATGATCACTTATGCTGCATACAGAAACATCTTCCCCATTTGGGCTCTGGGTGAATACCGATGTCGGGTTC

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|67722337|gb|BJ972596.1|BJ972596
EST:     CTTCAGTACTTATTAATAAGCAAATGGAGTCTGGAGACTTCCCTCAAGAG                         GAAATCATGGGCGTATTCAACAGGAACTGTATGATCAGTTACTCTGCGTAC
genomic: CTTCAGTACTTATTAATAAGCAAATGGAGTCTGGAGACTTCCCTCAAGAGgtacttgaat ... ctgtatgcagGAAATCATGGGCGTATTCAACAGGAACTGTATGATCAGTTACTCTGCGTAC
EST: gi|208359001|gb|DC957749.1|DC957749
EST:     CTTCAGTACTTATTAATAAGCAAATGGAGTCNGGAGACTTCCCTCAAGAG                         GAAATCATGGGCGTATTCAACAGGAACTGTATGATCAGTTACTCTGCGTAC
genomic: CTTCAGTACTTATTAATAAGCAAATGGAGTCTGGAGACTTCCCTCAAGAGgtacttgaat ... ctgtatgcagGAAATCATGGGCGTATTCAACAGGAACTGTATGATCAGTTACTCTGCGTAC
EST: gi|162252971|gb|FC429032.1|FC429032
EST:     CTTCAGTACTTATTAATAAGCAAATGGAGTCTGGAGACTTCCCTCAAGAG                         GAAATCATGGGCGTATTCAACAGGAACTGTATGATCAGTTACTCTGCGTAC
genomic: CTTCAGTACTTATTAATAAGCAAATGGAGTCTGGAGACTTCCCTCAAGAGgtacttgaat ... ctgtatgcagGAAATCATGGGCGTATTCAACAGGAACTGTATGATCAGTTACTCTGCGTAC
EST: gi|67725482|gb|BJ975741.1|BJ975741
EST:     CTTCAGTACTTATTAATAAGCAAATGGAGTCTGGAGACTTCCCTCAAGAG                         GAAATCATGGGCGTATTCAACAGGAACTGTATGATCAGTTACTCTGCGTAC
genomic: CTTCAGTACTTATTAATAAGCAAATGGAGTCTGGAGACTTCCCTCAAGAGgtacttgaat ... ctgtatgcagGAAATCATGGGCGTATTCAACAGGAACTGTATGATCAGTTACTCTGCGTAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 12 (upstream exon), 24 (downstream exon)
Score: 1

TGGGAGAGAAATCCCGAGCCTTTGCATAGAGCAGCTTCAGTACTTATTAATAAGCAAATGGAGTCTGGAGACTTCCCTCAAGAGgtacttgaat ... ctgtatgcagGAAATCATGGGCGTATTCAACAGGAACTGTATGATCAGTTACTCTGCGTACCGGTGTATTTTTCCTATCTGGGCACTGGGTGAGTACCGGCAAAAATTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggtcagagtgctggttttgcgctggtgttgatattgaccctaactgtatgcagGAAATCATGGGCGTATTCAACAGGAACTGTATGATCAGTTACTCTGCGTACCGGTGTATTTTTCCTATCTGGGCACTGGGTGAGTACCGGCAAAAATTGA
                                       ccctaac  putative branch site (score: 1)
                             ttgatatt  TA-rich tract