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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtggatagcctcaacctttggataaggttaacctacggttttaggtttggagtcacttggctcgctatttgcttggaattgatgacgattttggttgtagGTGGAGCTCGGAGGTGGTGGCGGAGGAATTGGTAATAAGAACTTCAATGGGGGTGGCGACGGAGGTGACGATGATGGTGATGATGACGACTACTTTGGTG

Basic information

species Physcomitrella patens
transcript PP1S4_62V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S4_62V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA15G05240.1 (Glycine max), 3'ss of exon 1
gtggatagcctcaacctttggataaggttaacct-acggttttaggtttggagtcacttggctcgctatttgcttggaattga---tgacgattttggtt-gtagGTGGAGCTCGGAGGTGGTGGCGGAGGAATTGGTAATAAGAACTTCAATGGGGGTGGCGACGGAGGTGACGATGATGGTGATGATGACGACTACTTTGGTG
    ||  | ||      |   |   | | || | ||    | |  |   || ||| |||  | | || |   | | |||  |   | | | ||||  || | || | ||  | || || ||||| ||||  ||||| || || | |    |||| ||||| || |||||||| |||||||| ||||||||||| ||||||| ||
---aatgacatcgtgtagtccttgtagctgacttcacttagtgaaataaagattcatttg--ttgttagtatttggaaatccattttcatgcttttaatttgcagCTAGACATTGGGGGAGGTGGAGGAGACATTGGAAAGAAAATCAATCATGGTGGTGGTGATGGAGGTGATGATGATGGGGATGATGACGATTACTTTGATG

upper sequence: PP1S4_62V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT5G24690.1 (Arabidopsis thaliana), 3'ss of exon 1
gtggatagcctcaacctttg-gataaggttaacctacggttttaggtttggagtcacttggctcgc-tatttgcttggaattg-atgacgattttggttgtagGTGGAGCTCGGAGGTGGTGGCGGAGGAATTGGTAATAAGAACTTCAATGGGGGTGGCGACGGAGGTGACGATGATGGTGATGATGACGACTACTTTGGTG
  | ||    ||  |||| | |||||   |   |   |  | ||  |||| |   |   |    |  ||  |   || | ||  ||  |   |||  ||  || | |     ||||| || || |||   ||||| || |  | |   ||||| |||||||| |||||||||||| ||||||||||||| || ||||||| ||
--gaatgatatcttccttggagataacagtttgcagtgaatctat-tttgcaccgatcagaaaagagtagctttgtgaatttttatttcatgtttcattacagATTGCAACTGGAGGAGGGGGTGGAAACATTGGAAAGAGTATCAATAATGGTGGTGGCGATGGAGGTGACGATAATGGTGATGATGATGATTACTTTGATG

upper sequence: PP1S4_62V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv12s0034g01370.t01 (Vitis vinifera), 3'ss of exon 1
--gtggatagcctcaacctttggataaggttaacctacggttttaggtttggagtcacttggctcgctatttgcttggaattgatgacgattttggttgtagGTGGAGCTCGGAGGTGGTGGCGGAGGAATTGGTAATAAGAACTTCAATGGGGGTGGCGACGGAGGTGACGATGATGGTGATGATGACGACTACTTTGGTG
  || ||      || | |||   |   | ||  ||     |||   |||  | | |||| |    ||       ||   || |         |  ||| ||   |   | || |||||||| ||||  || || || |  | |   ||||| ||||| || |||||||| ||||||||||||||||| || |||||||  |
gagtagactttaccatcttttcatttgtgctattctgtttatttccattta-acttacttagaatcctgagcaagtgatttttacttttgaaata-ttgcagACTGCTATTGGTGGTGGTGGTGGAGACATCGGAAAGAGAATCAATAATGGTGGTGGTGATGGAGGTGATGATGATGGTGATGATGATGATTACTTTGACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggagtcacttggctcgctatttgcttggaattgatgacgattttggttgtagGTGGAGCTCGGAGGTGGTGGCGGAGGAATTGGTAATAAGAACTTCAATGGGGGTGGCGACGGAGGTGACGATGATGGTGATGATGACGACTACTTTGGTG
                               aattgat  putative branch site (score: 4)
                               aattgat  TA-rich tract