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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGATgtgagtactctgccaatcgttccaagacttttgacgtcggtttctgttgtcagtcagcgctgattatctggaaatttgtataattttgtgctgcag

Basic information

species Physcomitrella patens
transcript PP1S295_30V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S295_30V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ30530 (Selaginella moellendorffii), 5'ss of exon 2
GTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGATgtgagtactctgccaatcgttccaagacttttgacgtcggtttctgttgtcagtcagcgctgattatctggaaatttgtataattttgtgctgcag
 | ||||| || ||||| ||||| || || || |||||||||||||| || ||||| ||||| ||| || |||||||| |||| |||||| ||||| | ||| |||     ||  ||| |||||   | | | ||| | |   |  ||                                       
ATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACGACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAGgtgag-attcttcca-----tcttagaattttgg-attgatctct-tcgcttgctag---------------------------------------

upper sequence: PP1S295_30V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ23006 (Selaginella moellendorffii), 5'ss of exon 2
GTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGATgtgagtactctgccaatcgttccaagacttttgacgtcggtttctgttgtcagtcagcgctgattatctggaaatttgtataattttgtgctgcag
 | ||||| || ||||| ||||| || || || ||||||||||||||||| ||||| ||||| ||| || |||||||| |||| |||||| ||||| | ||| |||    |   |  ||||| ||  | | | ||| | ||  |  ||                                       
ATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACCACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAGgtgag-attcttcca----tcttagaactttgga--ttgatctct-tcgtttgctag---------------------------------------

upper sequence: PP1S295_30V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ15891 (Selaginella moellendorffii), 5'ss of exon 2
GTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGATgtgagtactctgccaatcgttccaagacttttgacgtcggtttctgttgtcagtcagcgctgattatctggaaatttgtataattttgtgctgcag
 | |||||  || | ||| | || || || ||||||||||||||||| || |||||||| || |||||  | |||||| |||| |||||| ||||  | | |   | |  || |     | |   | ||  ||  | |  |  |||  |   ||| |                              
ATCCAACTCGTTAGAATACAAATCCGGGTGCCGGAGTATGGCTGGACAACGCAGAAAGTGTTCCATCTCCTCAATTTCTTTGTAAATGGAGgtgaaaagtttcatatttttttc-----tctcatcctc--ttgttttgattcgtcttcttcgatcag-----------------------------

upper sequence: PP1S295_30V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ33253 (Selaginella moellendorffii), 5'ss of exon 2
GTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGATgtgagtactctgccaatcgttccaaga-cttttgacgtcggtttctgttg-tcagtcagcgctgattatctggaaatttgtataattttgtgctgcag
 | |||||  || | ||| | || || || ||||||||||||||||| || |||||||| || |||||  | |||||| |||| |||||| ||||  | | |     |  |||    | | | |    | | ||  | ||  ||  ||||                                       
ATCCAACTCGTTAGAATACAAATCCGGGTGCCGGAGTATGGCTGGACAACGCAGAAAGTGTTCCATCTCCTCAATTTCTTTGTAAATGGAGgtgaaaagtttcattttttttctctcatcctcttgttttgattcgtcttcctcgatcag---------------------------------------

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|100414507|gb|BY992807.1|BY992807
EST:     CTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGAT                         TGCGCGCTTCGGTTTTCTGCTTCCGCGAGGATGTGCAGGCATTATCTCCTG
genomic: CTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGATgtgagtactc ... tgtgctgcagTGCGCGCTTCGGTTTTCTGCTTCCGCGAGGATGTGCAGGCATTATCTCCTG
EST: gi|162260165|gb|FC436300.1|FC436300
EST:     CTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGAT                         TGCGCGCTTCGGTTTTCTGCTTCCGCGAGGATGTGCAGGCATTATCTCCTG
genomic: CTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGATgtgagtactc ... tgtgctgcagTGCGCGCTTCGGTTTTCTGCTTCCGCGAGGATGTGCAGGCATTATCTCCTG
EST: gi|208385598|gb|DC937143.1|DC937143
EST:     CTGGACCACTCANAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGAT                         TGCGCGCTTCGGTTTTCTGCTTCCGCGAGGATGTGCAGGCATTATCTCCTG
genomic: CTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGATgtgagtactc ... tgtgctgcagTGCGCGCTTCGGTTTTCTGCTTCCGCGAGGATGTGCAGGCATTATCTCCTG
EST: gi|162278111|gb|FC453930.1|FC453930
EST:     CTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGAT                         TGCGCGCTTCGGTTTTCTGCTTCCGCGAGGATGTGCAGGCATTATCTCCTG
genomic: CTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGATgtgagtactc ... tgtgctgcagTGCGCGCTTCGGTTTTCTGCTTCCGCGAGGATGTGCAGGCATTATCTCCTG
EST: gi|208377957|gb|DC910961.1|DC910961
EST:     CTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGAT                         TGCGCGCTTCGGTTTTCTGCTTCCGCGAGGATGTGCAGGCATTATCTCCTG
genomic: CTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGATgtgagtactc ... tgtgctgcagTGCGCGCTTCGGTTTTCTGCTTCCGCGAGGATGTGCAGGCATTATCTCCTG
EST: gi|208374777|gb|DC932046.1|DC932046
EST:     CTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGAT                         TGCGCGCTTCGGTTTTCTGCTTCCGCGAGGATGTGCAGGCATTATCTCCTG
genomic: CTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGATgtgagtactc ... tgtgctgcagTGCGCGCTTCGGTTTTCTGCTTCCGCGAGGATGTGCAGGCATTATCTCCTG
EST: gi|162278110|gb|FC453929.1|FC453929
EST:     CTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGAT                         TGCGCGCTTCGGTTTTCTGCTTCCGCGAGGATGTGCAGGCATTATCTCCTG
genomic: CTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGATgtgagtactc ... tgtgctgcagTGCGCGCTTCGGTTTTCTGCTTCCGCGAGGATGTGCAGGCATTATCTCCTG
EST: gi|208349948|gb|DC913656.1|DC913656
EST:     CTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGAT                         TGCGCGCTTCGGTTTTCTGCTTCCGCGAGGATGTGCAGGCATTATCTCCTG
genomic: CTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGATgtgagtactc ... tgtgctgcagTGCGCGCTTCGGTTTTCTGCTTCCGCGAGGATGTGCAGGCATTATCTCCTG
EST: gi|208390738|gb|DC937894.1|DC937894
EST:     CTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGAT                         TGCGCGCTTCGGTTTTCTGCTTCCGCGAGGATGTGCAGGCATTATCTCCTG
genomic: CTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGATgtgagtactc ... tgtgctgcagTGCGCGCTTCGGTTTTCTGCTTCCGCGAGGATGTGCAGGCATTATCTCCTG
EST: gi|100364489|gb|BY984629.1|BY984629
EST:     CTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGAT                         TGCGCGCTTCGGTTTTCTGCTTCCGCGAGGATGTGCAGGCATTATCTCCTG
genomic: CTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGATgtgagtactc ... tgtgctgcagTGCGCGCTTCGGTTTTCTGCTTCCGCGAGGATGTGCAGGCATTATCTCCTG
EST: gi|162260166|gb|FC436301.1|FC436301
EST:     CTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGAT                         TGCGCGCTTCGGTTTTCTGCTTCCGCGAGGATGTGCAGGCATTATCTCCTG
genomic: CTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGATgtgagtactc ... tgtgctgcagTGCGCGCTTCGGTTTTCTGCTTCCGCGAGGATGTGCAGGCATTATCTCCTG
EST: gi|18361916|gb|BJ193983.1|BJ193983
EST:     CTGGACCACTCAGAAAGCCTTTCATCTGTTGAATTTCATTGTTAATGGAT                         TGCGCGCTTCGGTTTTCTGCTTCCGCGAGGATGTGCAGGCATTATCTCCTG
genomic: CTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGATgtgagtactc ... tgtgctgcagTGCGCGCTTCGGTTTTCTGCTTCCGCGAGGATGTGCAGGCATTATCTCCTG
EST: gi|208386340|gb|DC932836.1|DC932836
EST:     CTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGAT                         TGCGCGCTTCGGTTTTCTGCTTCCGCGAGGATGTGCAGGCATTATCTCCTG
genomic: CTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGATgtgagtactc ... tgtgctgcagTGCGCGCTTCGGTTTTCTGCTTCCGCGAGGATGTGCAGGCATTATCTCCTG
EST: gi|208387111|gb|DC941283.1|DC941283
EST:     CTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGAT                         TGCGCGCTTCGGTTTTCTGCTTCCGCGAGGATGTGCAGGCATTATCTCCTG
genomic: CTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGATgtgagtactc ... tgtgctgcagTGCGCGCTTCGGTTTTCTGCTTCCGCGAGGATGTGCAGGCATTATCTCCTG

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: 32 (upstream exon), 33 (downstream exon)
Score: 15

GTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGATgtgagtactc ... tgtgctgcagTGCGCGCTTCGGTTTTCTGCTTCCGCGAGGATGTGCAGGCATTATCTCCTGAG




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