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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATGCGTGAAGCGCATTGAGGAGGATGAGAATGGTCAAAAGCATTGCACTGGCCAGTATTTCGACTATTGGGGCTGCATTGATCAATGTgtaagtggttctaccatttccatcttcattttgtacagtgtctgtacaatgcataagtctctttcacatgatttaagctttaagacattgaatgaagcaa...

Basic information

species Physcomitrella patens
transcript PP1S491_11V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S491_11V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT1G15120.1 (Arabidopsis thaliana), 5'ss of exon 4
GCATGCGTGAAGCGCATTGAGGAGGATGAGAATGGTCAAAAGCATTGCACTGGCCAGTATTTCGACTATTGGGGCTGCATTGATCAATGTgtaagtggttctaccatttccatcttcattttgtacagtgtctgtacaatgcataagtctct-ttcacatgatttaagctttaagacattgaatgaagcaa
||||| || ||| | ||  | |  |||||   ||| || ||||||||||||||||||||||| ||||| |||   ||||||||  |||||||||||   |  |    |   || ||  | ||  |   | |   ||   |  | |  |   |  | | ||||  |  | |||  ||  || |         
GCATGTGTCAAGAGAATCCAAGGTGATGATTCTGGCCACAAGCATTGCACTGGCCAGTATTTTGACTACTGGCAATGCATTGACAAATGTgtaagttacttgaattatgttattttgctgtttcatcatatg-atatcttctaaagtttgatactgagatgaaattggattttggatcttcag--------

upper sequence: PP1S491_11V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT1G15120.2 (Arabidopsis thaliana), 5'ss of exon 5
GCATGCGTGAAGCGCATTGAGGAGGATGAGAATGGTCAAAAGCATTGCACTGGCCAGTATTTCGACTATTGGGGCTGCATTGATCAATGTgtaagtggttctaccatttccatcttcattttgtacagtgtctgtacaatgcataagtctctttcacatgatttaagctttaagacattgaatgaagcaa
||||| || ||| | ||  | |  |||||   ||| || ||||||||||||||||||||||| ||||| |||   ||||||||  |||||||||||   |  |    |   || ||  | ||  |   | |   ||   |  | |                                             
GCATGTGTCAAGAGAATCCAAGGTGATGATTCTGGCCACAAGCATTGCACTGGCCAGTATTTTGACTACTGGCAATGCATTGACAAATGTgtaagttacttgaattatgttattttgctgtttcatcatatg-atatcttctaaag--------------------------------------------
















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|208397291|gb|DC920645.1|DC920645
EST:     AGCATTGCACTGGCCAGTATTTCGACTATTGGGGCTGCATTGATCAATGT                         GCCGCACCAAAGCTCTTCCGCAAGATAGTATGAGAATGGCTCATTAGTGTC
genomic: AGCATTGCACTGGCCAGTATTTCGACTATTGGGGCTGCATTGATCAATGTgtaagtggtt ... gtactgtcagGCCGCACCAAAGCTCTTCCGCAAGATAGTATGAGAATGGCTCATTAGTGTC
EST: gi|37838829|gb|BJ596837.1|BJ596837
EST:     AGCATTGCACTGGCCAGTATTTCGACTATTGGGGCTGCATTGATCAATGT                         GCCGCACCAAAGCTCTTCCGCAAGATAGTATGAGAATGGCTCATTAGTGTC
genomic: AGCATTGCACTGGCCAGTATTTCGACTATTGGGGCTGCATTGATCAATGTgtaagtggtt ... gtactgtcagGCCGCACCAAAGCTCTTCCGCAAGATAGTATGAGAATGGCTCATTAGTGTC
EST: gi|208376115|gb|DC906774.1|DC906774
EST:     AGCATTGCACTGGCCAGTATTTCGACTATTGGGGCTGCATTGATCAATGT                         GCCGCACCAAAGCTCTTCCGCAAGATAGTATGAGAATGGCTCATTAGTGTC
genomic: AGCATTGCACTGGCCAGTATTTCGACTATTGGGGCTGCATTGATCAATGTgtaagtggtt ... gtactgtcagGCCGCACCAAAGCTCTTCCGCAAGATAGTATGAGAATGGCTCATTAGTGTC
EST: gi|7147932|gb|AW509854.1|AW509854
EST:     AGCATTGCACTGGCCAGTATTTCGACTATTGGGGCTGCATTGATCAATGT                         GCCGCACCAAAGCTCTTCCGCAAGATAGTATGAGAATGGCTCATTAGTGTC
genomic: AGCATTGCACTGGCCAGTATTTCGACTATTGGGGCTGCATTGATCAATGTgtaagtggtt ... gtactgtcagGCCGCACCAAAGCTCTTCCGCAAGATAGTATGAGAATGGCTCATTAGTGTC
EST: gi|18360940|gb|BJ193004.1|BJ193004
EST:     AGCATTGCACTGGCCAGTATTTCGACTATTGGGGCTGCATTGATCAATGT                         GCCGCACCAAAGCTCTTCCGCAAGATAGTATGAGAATGGCTCATTAGTGTC
genomic: AGCATTGCACTGGCCAGTATTTCGACTATTGGGGCTGCATTGATCAATGTgtaagtggtt ... gtactgtcagGCCGCACCAAAGCTCTTCCGCAAGATAGTATGAGAATGGCTCATTAGTGTC
EST: gi|162229029|gb|FC405064.1|FC405064
EST:     AGCATTGCACTGGCCAGTATTTCGACTATTGGGGCTGCATTGATCAATGT                         GCCGCACCAAAGCTCTTCCGCAAGATAGTATGAGAATGGCTCATTAGTGTC
genomic: AGCATTGCACTGGCCAGTATTTCGACTATTGGGGCTGCATTGATCAATGTgtaagtggtt ... gtactgtcagGCCGCACCAAAGCTCTTCCGCAAGATAGTATGAGAATGGCTCATTAGTGTC

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: 19 (upstream exon), 20 (downstream exon)
Score: 2

GCATGCGTGAAGCGCATTGAGGAGGATGAGAATGGTCAAAAGCATTGCACTGGCCAGTATTTCGACTATTGGGGCTGCATTGATCAATGTgtaagtggtt ... gtactgtcagGCCGCACCAAAGCTCTTCCGCAAGATAGTATGAGAATGGCTCATTAGTGTCATAGTTTCTGTGTAAATCTGCTGAAGAGATGCTGTAGACAACCCATTTG




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