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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATTGCACCGGAAAAGATTGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATGgtgcgttcatttaatcgacggtcgcatctttttaatgattgcacgttactttttcgtgtgacggaaacgtgtagcaactggtgttacgtatactggaaaaactaccaactcattgaaatccaatcattcttaccaatcgtataattggttggtggtgaattgcacag

Basic information

species Physcomitrella patens
transcript PP1S12_178V6.2
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S12_178V6.2 (Physcomitrella patens), 5'ss of exon 21
lower sequence: LOC_Os11g04980.1 (Oryza sativa), 5'ss of exon 19
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATTGCACCGGAAAAGATTGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATGgtgcgttcatttaatcgacggtcgcatctttttaatgattgcacgttactttttcgtgtgacggaaacgtgtagcaactggtgttacgtatactggaaaaactaccaactcattgaaatccaatcattcttaccaatcgtataattggttggtggtgaattgcacag
||||||||||||||||||||||||||||||||||| || || || |||||||||||  | |||  |    |   ||||||| ||||||| ||  ||||||||      ||   ||  | | ||  || ||     | ||| |    || || ||  |   | | | |     |||   || | ||   |  |                                                                           
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgta-----at---attcatgatcttatatt---ggttattacgtactaattatt--taccatgtatattctaagccgttgat-ttgaatgcag--------------------------------------------------------------------------

upper sequence: PP1S12_178V6.2 (Physcomitrella patens), 5'ss of exon 21
lower sequence: LOC_Os12g04990.3 (Oryza sativa), 5'ss of exon 18
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATTGCACCGGAAAAGATTGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATGgtgcgttcatttaatcgacggtcgcatctttttaatgattgcacgttactttttcgtgtgacggaaacgtgtagcaactggtgttacgtatactggaaaaactaccaactcattgaaatccaatcattcttaccaatcgtataattggttggtggtgaattgcacag
||||||||||||||||||||||||||||||||||| || || || |||||||||||  | |||  |    |   ||||||| ||||||  ||  ||||||||               |   ||   || || || || ||  |   |||   |   | || |  | | ||     | ||| || | || || | |                                                                        
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATGgta--------------atattcatgtccttatactggttata-actaccaata-atttgccatatatgttcta-agctgttgattcggatgcag------------------------------------------------------------------------

upper sequence: PP1S12_178V6.2 (Physcomitrella patens), 5'ss of exon 21
lower sequence: GRMZM2G059381_T01 (Zea mays), 5'ss of exon 19
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATTGCACCGGAAAAGATTGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATGgtg-cgttcat---ttaatcgacggtcgcatctttttaatgattgcacgttactttttcgtgtgacggaaacgtgtagcaactggtgttacgtatactggaaaaactaccaactcattgaaatccaatcattcttaccaatcgtataattggttggtggtgaattgcacag
||||||||||||||||||||||||||||||||||| || || || |||||||||||  | |||  |    |   ||| ||| | || || ||  ||||||||    |||||   || |||   | |   | |   ||  ||            || ||  | ||   | |                                                                                                     
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATATATGgtaatattcatgctttcatctgagctgaaagcaccttcgtgtacatcttaaggttgttgatctggatgcag----------------------------------------------------------------------------------------------------

upper sequence: PP1S12_178V6.2 (Physcomitrella patens), 5'ss of exon 21
lower sequence: GRMZM2G176546_T01 (Zea mays), 5'ss of exon 10
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATTGCACCGGAAAAGATTGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATGgtgcgttcatttaatcgacggtcgcatctttttaatgattgcacgttactttttcgtgtgacggaaacgtgtagcaactggtgttacgtatactggaaaaactaccaactcattgaaatccaatcattcttaccaatcgtataattggttggtggtgaattgcacag
||||||||||||||||||||||||||||||||||| || || || |||||||| ||  | |||       |   ||| ||| | || |||||  ||||||||    |   | | ||   | | ||      |  ||||      ||||       |  ||    |||  | | |   | | ||                                                                                    
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaatatttatgattctgtgttggc------tatatgaccatcagttatggccaagcatgttctaaatctcttgtttcggttgcag---------------------------------------------------------------------------------

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|162234487|gb|FC409518.1|FC409518
EST:     TGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATG                         GCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACA
genomic: TGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATGgtgcgttcat ... aattgcacagGCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACA
EST: gi|37847723|gb|BJ605731.1|BJ605731
EST:     TGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCATTGTTTCGTATATG                         GCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACA
genomic: TGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATGgtgcgttcat ... aattgcacagGCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACA
EST: gi|162231381|gb|FC406804.1|FC406804
EST:     TGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATG                         GCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACA
genomic: TGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATGgtgcgttcat ... aattgcacagGCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACA
EST: gi|162272001|gb|FC448419.1|FC448419
EST:     TGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATG                         GCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACA
genomic: TGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATGgtgcgttcat ... aattgcacagGCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACA
EST: gi|162272000|gb|FC448418.1|FC448418
EST:     TGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATG                         GCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACA
genomic: TGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATGgtgcgttcat ... aattgcacagGCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACA
EST: gi|162159914|gb|FC336167.1|FC336167
EST:     TGAGAACATTTTTCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATG                         GCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACA
genomic: TGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATGgtgcgttcat ... aattgcacagGCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACA
EST: gi|37846424|gb|BJ604432.1|BJ604432
EST:     TGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATG                         GCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACA
genomic: TGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATGgtgcgttcat ... aattgcacagGCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACA
EST: gi|162192790|gb|FC369628.1|FC369628
EST:     TGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATG                         GCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACA
genomic: TGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATGgtgcgttcat ... aattgcacagGCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACA

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

AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATTGCACCGGAAAAGATTGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATGgtgcgttcat ... aattgcacagGCGATAGTTTCAACGCCAACCTCGTAGCAGTTGCTGTTATTGATCCAGACACTCTACCTGCCTGGGCTAAATCAAGGGGTATTAAG




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