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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccacggcatgtgtcagtgtgtacaactcggttcactcggtctgatgccacgatgctctggtaccttaacttaagaaactgcgtgggttattttcggcagAGCTACAATCGGTCAAGGCTATGGTTTAACAGAGACTTGTGCTGGTGGGACATTCACCGAATGGGATGATCGCTCCGTTCGTCGTGCGGGGCCTCCGACA

Basic information

species Physcomitrella patens
transcript PP1S15_17V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S15_17V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os05g25310.2 (Oryza sativa), 3'ss of exon 7
---tccacggcatgtgtcagtgtgtacaactcggttcactcggtctgatgccacgatgctctggtaccttaacttaagaaactgcgtgggttattttcggcagAGCTACAATCGGTCAAGGCTATGGTTTAACAGAGACTTGTGCTGGTGGGACATTCACCGAATGGGATGATCGCTCCGTTCGTCGTGCGGGGCCTCCGACA
   | || |   | ||  |   |||   |   | |||  |   |   ||| | |     | || |       |||| | |  |  |       | | | |||| |   || | |||||||||||||| || ||||||||||||||||| |   | ||  | |||||||||||       ||  | ||||  || || ||    
gagtacatgcactatgctataatgtg--atgagcttccttttattgtatgtcgctgcatt-tgtttttggttcttatgcagttttgaattacctgtgctgcagTGTACCAGTAGGTCAAGGCTATGGATTGACAGAGACTTGTGCTGGAGCAGCCTTTTCTGAATGGGATGACACAAGTGTGGGCCGTGTTGGTCCACCCCTT

upper sequence: PP1S15_17V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA14G23710.1 (Glycine max), 3'ss of exon 6
tccacggcatgtgtcagtgtgtacaactcgg-----ttcactcggtctgatgccacgatgctctggtaccttaacttaagaaactgcgtgggttattttcg-gcagAGCTACAATCGGTCAAGGCTATGGTTTAACAGAGACTTGTGCTGGTGGGACATTCACCGAATGGGATGATCGCTCCGTTCGTCGTGCGGGGCCTCCGACA
   |  | |  | | | ||  |   ||||       ||  ||   |    |    || | |  |  |   |||   |  ||   |   |   ||||  ||    || ||| ||||||||||||| |||||| | ||||||||||||||||||||||||||| | ||    ||||||   || ||| | ||||  || || ||    
---aaaggaaatattactggcttttactcaagtgctttttcttttttgatttttgcgtttcctttattatttattctgtga---tttataatttatggtcatatagTGCTCCAATCGGTCAAGGATATGGTCTCACAGAGACTTGTGCTGGTGGGACATTCTCTGATGTTGATGATACATCTGTTGGCCGTGTTGGACCACCTCTT

upper sequence: PP1S15_17V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA13G03280.1 (Glycine max), 3'ss of exon 6
tccacggcatgtgtc-agtgtgtacaactcggttcactcggtctgatgccacgatgctctggtaccttaacttaagaaactgcgtgggttattttcg---gcagAGCTACAATCGGTCAAGGCTATGGTTTAACAGAGACTTGTGCTGGTGGGACATTCACCGAATGGGATGATCGCTCCGTTCGTCGTGCGGGGCCTCCGACA
   | |  || | || ||  | |||      | |   ||  | |        |    ||   ||   |   |   |  | |   |   ||||  ||     ||| ||| ||||||||||||| |||||| | ||||||||||||||||||||||||||| | ||    ||||||   || ||  | ||||  || || ||    
---aggaaatatttctagcttttactgtagtgctttttcttttttgctttttgcgtttcctttattattcttgctgtcatt-tataatttatggtcatattcagTGCTCCAATCGGTCAAGGATATGGTCTTACAGAGACTTGTGCTGGTGGGACATTCTCTGATGTTGATGATACATCTGTCGGCCGTGTTGGACCACCTCTT

upper sequence: PP1S15_17V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA06G11860.1 (Glycine max), 3'ss of exon 6
tccacggcatgtgtcagtgtgtacaactcggttcactcggtctgatgccacgatgctctgg--taccttaacttaagaaactgcgtg---ggttattttcggcagAGCTACAATCGGTCAAGGCTATGGTTTAACAGAGACTTGTGCTGGTGGGACATTCACCGAATGGGATGATCGCTCCGTTCGTCGTGCGGGGCCTCCGACA
      | || ||||    | ||  |     ||     | | || |     |||   |||   || |||   |     |  |   |    |||| |  |   ||| ||| |||| |||||||| |||||| ||||||||||||||||||||||| ||||| | || |  || |||   || ||| | ||||  ||||| ||    
----tagaat-tgtctagctttatcatgtactttttctgttttgctttacagatttcctgtattatcttttttctgtcacatttatatttggttttcattttcagTGCTCCAATAGGTCAAGGATATGGTCTAACAGAGACTTGTGCTGGTGGGTCATTCTCTGATTTTGACGATACATCTGTTGGACGTGTTGGGCCACCTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgccacgatgctctggtaccttaacttaagaaactgcgtgggttattttcggcagAGCTACAATCGGTCAAGGCTATGGTTTAACAGAGACTTGTGCTGGTGGGACATTCACCGAATGGGATGATCGCTCCGTTCGTCGTGCGGGGCCTCCGACA
                  ccttaac  putative branch site (score: 3)
                                          ttattttc  putative PPT
                    ttaacttaa  TA-rich tract