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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttttattgtgcaacagatagctcattctgatccatgggtgaataagagaactcgtacgattttctaacaatgagtacatgaaaacgtggatgcaacagGTATTGTGAATGTTTTGCCTCAGGTACATATTGTGAGGGTTGCAATTGTGTAAACTGTTGCAACAATGTTGAGAATGAAATCGTTCGTCAGGAAGCAGTG

Basic information

species Physcomitrella patens
transcript PP1S9_436V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S9_436V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA09G32420.1 (Glycine max), 3'ss of exon 5
gcttttattgtgcaacagatagctcattctgatccatggg---tgaataagagaactcgtacgattttctaaca-atgagtacatgaaaacgtggatgcaacagGTATTGTGAATGTTTTGCCTCAGGTACATATTGTGAGGGTTGCAATTGTGTAAACTGTTGCAACAATGTTGAGAATGAAATCGTTCGTCAGGAAGCAGTG
  |  | |  |    ||  |   |   |   |   | ||    |   |     ||||  |    |  | || || |  | |   |||||   |   |  | ||||||||||||||||||||| ||||| | ||||||||| |||||||| |||||||| |||| |||||||||||| |||||    | | | |  ||||| || 
-ttactgtcttctgtcattttttttccttcaacagagggcattttgttgttgcaacttattgtttgctgtatcacactaatttttgaaa---tattttgagcagGTATTGTGAATGTTTTGCATCAGGAATATATTGTGATGGTTGCAACTGTGTAAATTGTTTCAACAATGTTGAAAATGAGGCTGCTAGACGAGAAGCTGTT

upper sequence: PP1S9_436V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA07G09380.1 (Glycine max), 3'ss of exon 1
gcttttattgtgcaacagatagctcattctgatccatgggtgaataagagaact----cgtacgattttctaacaatgagtacatgaaaacgtggatgcaacagGTATTGTGAATGTTTTGCCTCAGGTACATATTGTGAGGGTTGCAATTGTGTAAACTGTTGCAACAATGTTGAGAATGAAATCGTTCGTCAGGAAGCAGTG
    ||| ||| |  |||     |  |||        | | | ||        |    | ||   ||| |||      | ||  |    |  |   |  | ||||||||| ||||||||||| ||||| | ||||||||| ||||| || |||||||| |||| |||||||||||| ||||||   | | | |  ||||| || 
---attactgt-cttcagtcgttttgttccttcaacagagggcattttgttgttgcaacttattgtttgctatatcaaactaatttttgaactatttcgagcagGTATTGCGAATGTTTTGCATCAGGAATATATTGTGATGGTTGTAACTGTGTAAATTGTTTCAACAATGTTGAAAATGAAGCTGCTAGACGAGAAGCTGTT

upper sequence: PP1S9_436V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA08G04180.1 (Glycine max), 3'ss of exon 2
gcttttattgtgcaacagatagctcattctgatccatgggtgaataagagaactcgtacgattttctaa---caatgagtacatgaaaacgtggatgc-----aacagGTATTGTGAATGTTTTGCCTCAGGTACATATTGTGAGGGTTGCAATTGTGTAAACTGTTGCAACAATGTTGAGAATGAAATCGTTCGTCAGGAAGCAGTG
         ||     | |||        |  ||  |||       |  |  ||  | |   ||  |     ||||| | |  | |        |||      | ||| ||||||||||||||||| || || | ||||||||| || ||||| |||||||| ||||| |||||||| || || |||   | | | |  |||||||| 
---------gtaagtgaaatactctgactttctctgtggtcattgtattgtgcttttgcaccttgttggatgcaatgtggagctaatgtttgaaatgtctttgagcagATATTGTGAATGTTTTGCTTCGGGAATATATTGTGACGGCTGCAACTGTGTAAATTGTTGTAACAATGTGGAAAACGAAGCTGCTAGACGAGAAGCAGTT

upper sequence: PP1S9_436V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT2G20110.2 (Arabidopsis thaliana), 3'ss of exon 2
gcttttattgtgcaacagatagctcatt--ctgatccatgggtgaataagagaactcgtacgattttctaacaatgagtacatgaaaacgtggatgcaacagGTATTGTGAATGTTTTGCCTCAGGTACATATTGTGAGGGTTGCAATTGTGTAAACTGTTGCAACAATGTTGAGAATGAAATCGTTCGTCAGGAAGCAGTG
   |   |    || || |    |   |  |  | |  |  ||   |  | | ||| || | ||| |  |   |  | |  |  |   | |   |  | ||||||||||||||||||||| || || || || ||||| |||||||| |||||||| |||| |||||| ||||| ||||||   |   | |   |||| || 
--gtaagtctctcatcataccatttgatgacaaaactctttgtttctttgtggacttgttc-attgtgaattgaacactgtacaatgtctttttttgatcagGTATTGTGAATGTTTTGCATCTGGCACTTACTGTGATGGTTGCAACTGTGTAAATTGTTTCAACAACGTTGAAAATGAACCTGCGAGACGACAAGCGGTT

upper sequence: PP1S9_436V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT4G29000.1 (Arabidopsis thaliana), 3'ss of exon 2
--gcttttattgtgcaacaga--tagctcattctgatccatgggtgaataagagaactcgtacgattttctaacaatgagtacatgaaaacgtggatgcaacagGTATTGTGAATGTTTTGCCTCAGGTACATATTGTGAGGGTTGCAATTGTGTAAACTGTTGCAACAATGTTGAGAATGAAATCGTTCGTCAGGAAGCAGTG
   ||||| || |||  ||    ||    | ||  |    ||  |   ||||   ||   |     ||  |||   ||  |   ||    |          |||||| |||||||| ||||| || || ||||||||||| ||||| || |||||||| |||| |||||||||||| ||||||   | | | |  ||||| |||
ttccttttcttctgctgcatgtctaagaaactcaaaagtctgattttttaagtttaccaatttttgttgttaattgtggatttctg----cactatcttgtcagGTACTGTGAATGCTTTGCATCCGGAACATATTGTGACGGTTGTAACTGTGTAAATTGTTTCAACAATGTTGATAATGAACCTGCTAGACGAGAAGCTGTG

upper sequence: PP1S9_436V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv11s0016g03680.t01 (Vitis vinifera), 3'ss of exon 2
-gcttttattgtgcaac----agatagctcattctgatccatgggtgaataagagaactcgtacgattttctaacaatgagtacatgaaaacgtggatgcaacagGTATTGTGAATGTTTTGCCTCAGGTACATATTGTGAGGGTTGCAATTGTGTAAACTGTTGCAACAATGTTGAGAATGAAATCGTTCGTCAGGAAGCAGTG
 | |||  ||    ||     | | |    ||    | |   |    | | | | | ||  ||     |   ||   ||| |     || | || | |    |||||||||||| |||||||| || || | ||||||||| || || || |||||||| |||  ||| |||||||| |||||    | | | |  ||||| || 
agttttatttcaataatttctatacaaagtatatgtaacttagttctagtgaaaaatcttatattgaatatgaa-gctgattctggtaatatgttggt----cagGTATTGTGAGTGTTTTGCATCTGGAATATATTGTGATGGGTGTAACTGTGTAAATTGTCACAATAATGTTGAAAATGAGGCTGCTAGGCGAGAAGCTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagagaactcgtacgattttctaacaatgagtacatgaaaacgtggatgcaacagGTATTGTGAATGTTTTGCCTCAGGTACATATTGTGAGGGTTGCAATTGTGTAAACTGTTGCAACAATGTTGAGAATGAAATCGTTCGTCAGGAAGCAGTG
                  ttctaac  putative branch site (score: 1)
               attttctaa  TA-rich tract