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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagttgcatccttcctttgtcatcaagtttcagtatttgctttctttgaaatgggcattttactttgttatattatttttgctctttcttgactgcgtgcagtcttcgactgtggacttctccttgtctgtactaagcttcacctttgtggcatttcgtgcagATATTACCCACCCAATTCCTGATCTTACAGGATATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAG

Basic information

species Physcomitrella patens
transcript PP1S425_12V6.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA18G48280.1 (Glycine max), 3'ss of exon 10
gtcagttgcatccttcctttgtcatcaagtttcagtatttgctttctttgaaatgggcattttactttgttatattatttttgctctttcttgactgcgtgcagtcttcgactgtggacttctccttgtctgtactaagcttcacctttgtggcatttcgtgcagATATTACCCACCCAATTCCTGATCTTACAGGATATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAG-
                                                                   || |  | |||| |||    || |   ||        || |  | | || |||     ||  ||| ||| |  ||    ||  ||   ||  || |||||||||| || |||| |||||||||||||||||||||||| || || || || ||| | ||  | |||||  | ||||| ||| 
-------------------------------------------------------------------tgatgaaatattattgaatcttatcagcta-------tcatgcattatgcactctcaatt--ctg-actga--ttatttttcttgaacttctgtacagaTATTACGCATCCAACTCCTGATCTTACAGGATATATTACTGAGGGACAGATATATATCGACAGACAGTTGTATAACAGGCAGG

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA09G38110.1 (Glycine max), 3'ss of exon 10
gtcagttgcatccttcctttgtcatcaagtttcagtatttgctttctttgaaatgggcattttactttgttatattatttttgctctttcttgactgcgtgcagtcttcgactgtggacttctccttgtctgtactaagcttcacctttgtggcatttcgtgcagATATTACCCACCCAATTCCTGATCTTACAGGATATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAG
                                                                   || |  | |||| |||    || |   ||        || |  |   || |||     ||  ||| ||| |  ||    ||  ||   ||  || |||||||||| || |||| |||||||||||||||||||||||| || || || || ||| ||||  |||||||  | ||||| |||
------------------------------------------------------------------gtgatgaaatattattgaatcttatcagcta-------tcatgcataatgcactctcaatt--ctg-actga--ttgtttttcttgaacttctgtacagATATTACACATCCAACTCCTGATCTTACAGGATATATTACTGAGGGACAGATATATATTGACAGGCAGTTGTATAACAGGCAG

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 11
gtcagttgcatccttcctttgtcatcaagtttcagtatttgctttctttgaaatgggcattttactttgttatattatttttgctctttcttgactgcgtgcagtcttcgactgtgg-acttctccttgtctgtactaagcttcacctttgtggcatttcgtgcagATATTACCCACCCAATTCCTGATCTTACAGGATATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAG
                                                                                       |  |  | |        |  ||  || |    | |     | |    ||| |         || ||   ||  || |||||||||| ||||||| ||||||||| ||||||||||| || || || || || ||  | ||  ||||| |  | || ||||||
--------------------------------------------------------------------------------------gtaatgaaatatagaagttaatcagctatcttgcataatggttttaacactgaatgattatattttgaacttctgtacagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAG

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA10G42940.3 (Glycine max), 3'ss of exon 10
gtcagttgcatccttcctttgtcatcaagtttcagtatttgctttctttgaaatgggcattttactttgttatattatttttgctctttcttgactgcgtgcagtcttcgactgt---ggacttctccttgtctgtactaagcttcacctttgtggcatttcgtgcagATATTACCCACCCAATTCCTGATCTTACAGGATATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAG
                                                                                       |  |  | |        || ||  || |   | |       || |    ||| |         || ||   ||  || |||||||||| ||||||| ||||||||| ||||||||||| || || || || || ||  | ||  ||||| |  | || ||||||
--------------------------------------------------------------------------------------gtaatgaaatatacaagttcatcagctatcttgcatgatggtttcttaacactgaatgattatattttgaacttctgtacagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAG

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|208363000|gb|DC946897.1|DC946897
EST:     CCGTAAAGGATCTATTACTCAGATTCCTATTCTAACTATGCCGAATGATG                         ATATTACCCACCCAATTCCTGATCTTACAGGATATATTACGGAAGGTCAAA
genomic: CCGTAAAGGATCTATTACTCAGATTCCTATTCTAACTATGCCGAATGATGgtcagttgca ... tttcgtgcagATATTACCCACCCAATTCCTGATCTTACAGGATATATTACGGAAGGTCAAA
EST: gi|162186055|gb|FC361883.1|FC361883
EST:     TTCTAACTATGCCGAATGATG                         ATATTACCCACCCAATTCCTGATCTTACAGGATATATTACGGAAGGTCAAA
genomic: TTCTAACTATGCCGAATGATGgtcagttgca ... tttcgtgcagATATTACCCACCCAATTCCTGATCTTACAGGATATATTACGGAAGGTCAAA
EST: gi|37828436|gb|BJ586448.1|BJ586448
EST:     CGTAAAGGATCTATTACTCAGATTCCTATTCTAACTATGCCGAATGATG                         ATATTACCCACCCAATTCNTGATCTTACAGGATATATTACGGAAGGTCAAA
genomic: CGTAAAGGATCTATTACTCAGATTCCTATTCTAACTATGCCGAATGATGgtcagttgca ... tttcgtgcagATATTACCCACCCAATTCCTGATCTTACAGGATATATTACGGAAGGTCAAA
EST: gi|18334455|gb|BJ166472.1|BJ166472
EST:     CTATGCCGAATGATG                         ATATTACCCACCCAATTCCTGATCTTACAGGATATATTACGGAAGGTCAAA
genomic: CTATGCCGAATGATGgtcagttgca ... tttcgtgcagATATTACCCACCCAATTCCTGATCTTACAGGATATATTACGGAAGGTCAAA
EST: gi|37844824|gb|BJ602832.1|BJ602832
EST:     CCGTAAAGGATCTATTACTCAGATTCCTATTCTAACTATGCCGAATGATG                         ATATTACCCACCCAATTCCTGATCTTACAGGATATATTACGGAAGGTCAAA
genomic: CCGTAAAGGATCTATTACTCAGATTCCTATTCTAACTATGCCGAATGATGgtcagttgca ... tttcgtgcagATATTACCCACCCAATTCCTGATCTTACAGGATATATTACGGAAGGTCAAA
EST: gi|37848287|gb|BJ606295.1|BJ606295
EST:     CCGTAAAGGATCTATTACTCAGATTCCTATTCTAACTATGCCGAATGATG                         ATATTACCCACCCAATTCNTGATCTTACAGGATATATTACGGAAGGTCAAA
genomic: CCGTAAAGGATCTATTACTCAGATTCCTATTCTAACTATGCCGAATGATGgtcagttgca ... tttcgtgcagATATTACCCACCCAATTCCTGATCTTACAGGATATATTACGGAAGGTCAAA
EST: gi|18339737|gb|BJ171764.1|BJ171764
EST:     CGTAAAGGATCTATTACTCAGATTCCTATTCTAACTATGCCGAATGATG                         ATATTACCCACCCAATTCCTGATCTTACAGGATATATTACGGAAGGTCAAA
genomic: CGTAAAGGATCTATTACTCAGATTCCTATTCTAACTATGCCGAATGATGgtcagttgca ... tttcgtgcagATATTACCCACCCAATTCCTGATCTTACAGGATATATTACGGAAGGTCAAA
EST: gi|162158554|gb|FC334557.1|FC334557
EST:     CCGTAAAGGATCTATTACTCAGATTCCTATTCTAACTATGCCGAATGATG                         ATATTACCCACCCAATTCCTGATCTTACAGGATATATTACGGAAGGTCAAA
genomic: CCGTAAAGGATCTATTACTCAGATTCCTATTCTAACTATGCCGAATGATGgtcagttgca ... tttcgtgcagATATTACCCACCCAATTCCTGATCTTACAGGATATATTACGGAAGGTCAAA
EST: gi|67700014|gb|BJ960247.1|BJ960247
EST:     CCGTAAAGGATCTATTACTCAGATTCCTATTCTAACTATGCCGAATGATG                         ATATTACCCACCCAATTCCTGATCTTACAGGATATATTACGGAAGGTCAAA
genomic: CCGTAAAGGATCTATTACTCAGATTCCTATTCTAACTATGCCGAATGATGgtcagttgca ... tttcgtgcagATATTACCCACCCAATTCCTGATCTTACAGGATATATTACGGAAGGTCAAA
EST: gi|162191294|gb|FC366868.1|FC366868
EST:     CCGTAAAGGATCTATTACTCAGATTCCTATACTAACTATGCCGAATGATG                         ATATTACCCACCCAATTCCTGATCTTACAGGATATATTACGGAAGGTCAAA
genomic: CCGTAAAGGATCTATTACTCAGATTCCTATTCTAACTATGCCGAATGATGgtcagttgca ... tttcgtgcagATATTACCCACCCAATTCCTGATCTTACAGGATATATTACGGAAGGTCAAA
EST: gi|162185240|gb|FC361750.1|FC361750
EST:     CCGTAAAGGATCTATTACTCAGATTCCTATTCTAACTATGCCGAATGATG                         ATATTACCCACCCAATTCCTGATCTTACAGGATATATTACGGAAGGTCAAA
genomic: CCGTAAAGGATCTATTACTCAGATTCCTATTCTAACTATGCCGAATGATGgtcagttgca ... tttcgtgcagATATTACCCACCCAATTCCTGATCTTACAGGATATATTACGGAAGGTCAAA

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: 26 (upstream exon), 11 (downstream exon)
Score: 2

ATGTATACTGATCTGGCCACCATTTATGAACGTGCTGGACGAATCGAAGGCCGTAAAGGATCTATTACTCAGATTCCTATTCTAACTATGCCGAATGATGgtcagttgca ... tttcgtgcagATATTACCCACCCAATTCCTGATCTTACAGGATATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAG




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