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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaactgagtttgcatgatattttctacgttggacgtggtaaatattgaacttcttttcagttagcagtcggaatttgagtatgtttcgagaggttggttaattcggtgtttgcacatattgttctttctgtggtgcagATGTGGATCGCGAAATCAGAGTACGACGAGTCAGGTCCATCAATTGTGCATAGGAAGTGTTTCTAG

Basic information

species Physcomitrella patens
transcript PP1S372_48V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S372_48V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os03g50885.1 (Oryza sativa), 3'ss of exon 3
gtaaactgagtttgcatgatattttctacgttggacgtggtaaatattgaacttcttttcagttagcagtcggaatttgagtatgtttcgagaggttggttaattcggtgtttgcacatattgttctttctgtggtgcagATGTGGATCGCGAAATCAGAGTACGACGAGTCAGGTCCATCAATTGTGCATAGGAAGTGTTTCTAG----------------------------------
                                       ||||||||  || | |         |||| |       || || |   ||  ||  ||| | ||||   || || || || |||  ||| | ||  ||||||||||||| || ||  | |||||||||||||| || ||||| |||||||| ||||| || |||||                                   
---------------------------------------gtaaatatacaaatgc---------agcaatgtag---tgtgtttacctcatgaacttgatcaatt---tgcttaca-atgttg--cttgccgt--tgcagATGTGGATTGCCAAGGCTGAGTACGACGAGTCTGGCCCATCCATTGTGCACAGGAAATGCTTCTAATTCTTCGGACCCAAGAATGCTAAGCCAAGAGGAG

upper sequence: PP1S372_48V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA19G00850.1 (Glycine max), 3'ss of exon 3
gtaaactgagtttgcatgatattttctacgttggacgtggtaaatattgaacttcttttcagttagcagtcggaatttgagtatgtttcgagaggttggttaattcggtgtttgcacatattgttctttctgtggtgcagATGTGGATCGCGAAATCAGAGTACGACGAGTCAGGTCCATCAATTGTGCATAGGAAGTGTTTCTAG----------------------------------
                                            | ||    ||||||    | |  | |      || | |||   |    | | | | ||||           ||| | |||   ||     |||||||||||||| |||||  |||||||||||||||| || ||||||||||| ||||| ||||| |||||                                   
-----------------------------------------gtctgtttctgttctttaatatgactaattaactattaactattgctttgaatgcttgctaatg--------atacaaactgtcgcttg---agtgcagATGTGGATTGCGAAGGCAGAGTACGACGAGTCTGGACCATCAATTGTTCATAGAAAGTGCTTCTAAATTGTTTGGTTGATAGGGTTATTGAAGAAAAAGA

upper sequence: PP1S372_48V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA05G09290.3 (Glycine max), 3'ss of exon 4
gtaaactgagtttgcatgatattttctacgttggacgtggtaaatattgaacttcttttcagttagcagtcggaatttgagtatgtttcgagaggttggttaattcggtgtttgcacatattgttctttctgtggtgcagATGTGGATCGCGAAATCAGAGTACGACGAGTCAGGTCCATCAATTGTGCATAGGAAGTGTTTCTAG----------------------------------
                                               |    |||| |||  |||  | |    | |  | |||   |    | | | | ||||           ||| ||| |   ||     |||||||||||||| |||||  |||||||||||||||| || ||||||||||| ||||| ||||| |||||                                   
----------------------------------------------gtatgtttctgttct-ttaata-tgattaatgaactattgctttgaatgcttgctaatg--------atacaaattatcgcttg---agtgcagATGTGGATTGCGAAGGCAGAGTACGACGAGTCTGGACCATCAATTGTTCATAGAAAGTGCTTCTAAATTGTTTGAGCAATAGGGTTATTGAAGAAAAAGA

upper sequence: PP1S372_48V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA18G52780.1 (Glycine max), 3'ss of exon 3
gtaaactgagtttgcatgatattttctacgttggacgtggtaaatattgaacttcttttcagttagcagtcggaatttgagtatgtttcgagaggttggttaattcggtgtttgca--catattgttctttctgtggtgcagATGTGGATCGCGAAATCAGAGTACGACGAGTCAGGTCCATCAATTGTGCATAGGAAGTGTTTCTAG
                                |   ||  |     || |   | ||| | | |     | ||||| | |   ||||  ||||   |   |  |||  || |   |   | |   || | | |   |||||||||||||| || ||  |||| || |||||||| ||||||||||||||||| || ||||| ||||| 
--------------------------------gtttgttctcttcctttattctttttcctgcttc---ttggaatgttatgttgttgtgagatagtacattcttctatgataataatgacacacttttgttttgagtgcagATGTGGATTGCAAAGGCAGAATATGACGAGTCTGGTCCATCAATTGTGCACAGAAAGTGCTTCTAA

upper sequence: PP1S372_48V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA13G41060.1 (Glycine max), 3'ss of exon 3
gtaaactgagtttgcatgatattttctacgttggacgtggtaaatat-tgaacttcttttcagttagcagtcggaatttgagtatgtttcgagaggttggttaattcggtgtttgcacatattgttctttctgtggtgcagATGTGGATCGCGAAATCAGAGTACGACGAGTCAGGTCCATCAATTGTGCATAGGAAGTGTTTCTAG
                                     |  |  || | || ||| |   |            |   |||   |||| |       || ||   |||   || |    ||  ||||| ||   |   ||||||||||||| |||||  |||||||||| ||||| ||||| |||||||| || ||||| || || |  
-------------------------------------tcatgcatttgtgcactccccctagaaattagaatgttgttttgatatggtcaatttagtagggatatt-aatgatgaggcac-ttgtttttg--gaaatgcagATGTGGATTGCGAAGGCAGAGTACGATGAGTCCGGTCCTTCAATTGTACACAGGAAATGCTTTTGA

upper sequence: PP1S372_48V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA02G10170.1 (Glycine max), 3'ss of exon 4
gtaaactgagtttgcatgatattttctacgttggacgtggtaaatattgaacttcttttcagttagcagtcggaatttgagtatgtttcgagag--gttggttaattc----ggtgtttgcacatattgttctttctgtggtgcagATGTGGATCGCGAAATCAGAGTACGACGAGTCAGGTCCATCAATTGTGCATAGGAAGTGTTTCTAG----------------------------------
                                       ||   |  |   | | ||||    |     | ||||| | |   | |   ||||    ||  |  || |      |  |  |||  | |||| |||     |||||||||||||| || ||  |||| || ||||| || ||||||||||||||||| || ||||| |||||                                   
---------------------------------------gtttgttctcttcattttttttcctgcttcttggaatgttatgttatcgtgagatacattcttctatgctaataataatgacacgaactgttgttttga--gtgcagATGTGGATTGCAAAGGCAGAATATGACGAATCTGGTCCATCAATTGTGCACAGAAAGTGCTTCTAAACTGTTTCGATAGATAGGGTTATTGAAGGGAAAG

upper sequence: PP1S372_48V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA15G04360.1 (Glycine max), 3'ss of exon 3
gtaaactgagtttgcatgatattttctacgttggacgtggtaaatattgaacttcttttcagttagcagtc-ggaatttgagtatgtttcgag-aggttggttaattcggtgtttgcacatattgttctttctgtggtgcagATGTGGATCGCGAAATCAGAGTACGACGAGTCAGGTCCATCAATTGTGCATAGGAAGTGTTTCTAG----------------------------------
                                           ||  | |      |||  |  | ||  |  |||| |   | || |  |   |  || ||        || |   |   ||  |  |||  |   ||||||||||||| |||||  ||||||| || ||||| ||||| |||||||| || ||||| || || ||                                   
------------------------------------------catcctcatgcaaatttgggcaaacaccctagaatgttgttttgatatggttaatttagtagggatattgatgataaggatcttatttttggaaatgcagATGTGGATTGCGAAGGCAGAGTATGATGAGTCTGGTCCTTCAATTGTACACAGGAAATGCTTTTAAATGCAGCAGAATGGCTTGGTGTAGGTACAGCGTC

upper sequence: PP1S372_48V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv13s0019g01240.t01 (Vitis vinifera), 3'ss of exon 3
gtaaactgagtttgcatgatattttctacgttggacgtggtaaatattgaacttcttttcagttagcagtcggaatttgagtatgtttcgagaggttggttaa-ttcggt-gtttgcacatattgttctttctgtg-gtgcagATGTGGATCGCGAAATCAGAGTACGACGAGTCAGGTCCATCAATTGTGCATAGGAAGTGTTTCTAG----------------------------------
                                               |   ||||||||| |  |  | |    || || | ||| ||| |   ||   | |  || | | ||||     |   || | || | || |||||||||||||| || ||  | ||||| || ||||| || |||||||| ||||||||||| ||||||||                                   
----------------------------------------------gtttgcttcttttctgcaaagattt---atatgtgaatgattctaaccgtgaatcatctttgatagtttctgattggagtgcattttttgagtgcagATGTGGATAGCAAAGGCGGAGTATGATGAGTCTGGGCCATCAATCGTGCATAGGAAATGTTTCTAATTGTTCAAGAATAGGATCATGGAAGAAAGGAAGC

upper sequence: PP1S372_48V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ35077 (Selaginella moellendorffii), 3'ss of exon 3
gtaaactgagtttgcatgatattttctacgttggacgtggtaaatattgaacttcttttcagttagcagtcggaatttgagtatgtttcgagaggttggttaattcggtgtttgcacatattgttctttctgtggtgcagATGTGGATCGCGAAATCAGAGTACGACGAGTCAGGTCCATCAATTGTGCATAGGAAGTGTTTCTAG
                                                                        | |    |  ||  ||      |||  |    || |   |||    | || |||||| |  |   ||||||||||| || || || |||||||| ||||| |||||||| |||||||| || ||||| ||||||
------------------------------------------------------------------------gtaccacaacattcttttgctcgtttttcttatcagc-cttgtttttctttttcttttttcg---cagATGTGGATTGCAAAGTCCGAGTACGATGAGTCGGGTCCATCGATTGTGCACAGAAAGTGCTTCTAG

upper sequence: PP1S372_48V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 3
gtaaactgagtttgcatgatattttctacgttggacgtggtaaatattgaacttcttttcagttagcagtcggaatttgagtatgtttcgagaggttggttaattcggtgtttgcacatattgttctttctgtggtgcagATGTGGATCGCGAAATCAGAGTACGACGAGTCAGGTCCATCAATTGTGCATAGGAAGTGTTTCTAG
                                                                        | |    |  ||  ||      |||  |    || |   |||    | || || ||  | |   |||||||||||| || || || |||||||| ||||| |||||||| |||||||| || ||||| ||||||
------------------------------------------------------------------------gtaccacaacattcttttgctcgtttttcttatcagc-cttgt---ttttctttttcgtttctcgcagATGTGGATTGCAAAGTCCGAGTACGATGAGTCGGGTCCATCGATTGTGCACAGAAAGTGCTTCTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcgagaggttggttaattcggtgtttgcacatattgttctttctgtggtgcagATGTGGATCGCGAAATCAGAGTACGACGAGTCAGGTCCATCAATTGTGCATAGGAAGTGTTTCTAG
            ggttaat  putative branch site (score: 4)
                                   ttgttctttct  putative PPT
                                atattgtt  TA-rich tract