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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttgagattcaatgatacatggttcgtaagaattcctgtacaatgagtaaaaattgattctccttcaatgtagtttggatttcttgatgtctgtactgccttctatttttcatgcagGTCAATCCACAAAACGCACCTCAGGTGGTTGGGCAATTGCTTGATGATGATTGCCCTGAGGACTTCATTAAGGGTTTGATCTTATCCGTCCGCTCACTGC

Basic information

species Physcomitrella patens
transcript PP1S452_30V6.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 21
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 21
gtaatttgagattcaatgatacatggttcgtaagaattcctgtacaatgagtaaaaattgattctccttcaatgtagtttggatttcttgatgtctgtactgccttctatttttcatgcagGTCAATCCACAAAACGCACCTCAGGTGGTTGGGCAATTGCTTGATGATGATTGCCCTGAGGACTTCATTAAGGGTTTGATCTTATCCGTCCGCTCACTGC
                         ||  | ||   ||||  | || ||       | |        |   ||||  | || ||||    |||  | |  | | || ||||      | |||| || ||   ||| || ||    || ||||| ||  | ||||||||||| |||||||| || |||||||||||||||||  | || ||||| || || |
-------------------------gtatgcaactcttccaattcagtgttattggagtatcatcattctcatgtgctatgtattta--aatgcttattttcctttatatt------gtagGTGAACCCTGGAAATGCTCCATTAGTTGTTGGACAGCTACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCC

upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 21
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 21
gtaatttgagattcaatgatacatggttcgtaagaattcctgtacaatgagtaaaaattgattctccttcaatgtagtttggatttcttgatgtctgtactgccttctatttttcatgcagGTCAATCCACAAAACGCACCTCAGGTGGTTGGGCAATTGCTTGATGATGATTGCCCTGAGGACTTCATTAAGGGTTTGATCTTATCCGTCCGCTCACTGC
                         ||  | ||   ||||  | || ||       | |        |   ||||  | || ||||    |  |   || |  | | ||| ||    | |||| || ||   ||| || ||    || ||||| ||  | ||||||||||| |||||||| || |||||||||||||||||  | || ||||| || || |
-------------------------gtatgcaactcttccaattcagtgttattggagtatcatcattctcatgtgctatgtattt----aaattcttattttcctttatatt----gtagGTGAACCCTGGAAATGCTCCATTAGTTGTTGGACAGCTACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCC

upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 21
lower sequence: GRMZM2G111355_T01 (Zea mays), 3'ss of exon 1
gtaatttgagattcaatgatacatggttcgtaagaattcctgtacaatgagtaaaaattgattctccttcaatgtagtttggatttcttgatgtctgtactgccttctatttttcatgcagGTCAATCCACAAAACGCACCTCAGGTGGTTGGGCAATTGCTTGATGATGATTGCCCTGAGGACTTCATTAAGGGTTTGATCTTATCCGTCCGCTCACTGC
           ||||        | ||  ||    | || |||  |||  ||         |  | | |||   ||| |||  | |    |||  |  | |   || | || ||  | ||||| |||||    || || ||   ||| || |||||||| ||||||||||| |||||||| || || || |||||||||||| | || || || || || |
----------gttcagaaggtagttgtgtgtttcgactc-tgt-taattcgtgcg------tcgttcctcataataggttgagtatgagaatggtta-attcttttttcttgtt--tccagGTGAATCCCGGGAATGCTCCATTGGTAGTGGGGCAATTACTTGATGATGAATGCCCTGAAGATTTTATCAAGGGTTTGATCCTCTCTGTTCGTTCTCTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcaatgtagtttggatttcttgatgtctgtactgccttctatttttcatgcagGTCAATCCACAAAACGCACCTCAGGTGGTTGGGCAATTGCTTGATGATGATTGCCCTGAGGACTTCATTAAGGGTTTGATCTTATCCGTCCGCTCACTGC
                   tcttgat  putative branch site (score: 4)
                                 ctgccttctatttttc  putative PPT
                                      ttctattttt  TA-rich tract