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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaagcccccctccaggaacaccttgcagaacacctttgtgtctttacttctgagggttgcaggatatcgcggtgttgctgcgggtttacatgagcgaatattacgaatgacggtatttaagcaagttgataagaaaatggttgtgcgatgcagGTGGGTAGTGGCACAGAGTGTGTTCTACCACTTATACAACCAAGTGTCATACATGTCATTGGACAAAATCTCCCCACTCACATTCAGCGTTGGCAACACG

Basic information

species Physcomitrella patens
transcript PP1S18_317V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S18_317V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os07g33954.1 (Oryza sativa), 3'ss of exon 3
gtgaagcccccctccaggaacaccttgcagaacacctttgtgtctttacttctgagggttgcaggatatcgcggtgttgctgcgggtttacatgagcgaatattacg-aatgacggtatttaagcaagttgataagaaaatggttgtg-cgatgcagGTGGGTAGTGGCACAGAGTGTGTTCTACCACTTATACAACCAAGTGTCATACATGTCATTGGACAAAATCTCCCCACTCACATTCAGCGTTGGCAACACG
                                                           || | || |     |   |       | ||  ||||   | | ||  |  || |      | |  || || |  | | |  |   ||||    || |||||||| | ||| |||||||||||||||||||| |||||||||||||| ||||||||||||||| | ||||| ||||| ||||||||| | |||||||| 
-------------------------------------------------------attctgaaagagaaataagaagtatcaaaagatttgatgat--atttttgtgtgataatccagctgattcatgtggccatggatttctctgtggttttgtagGTGGGTGGCGGCGCAGAGTGTGTTCTACCACTTGTACAACCAAGTGTCCTACATGTCATTGGACGAGATCTCACCACTGACATTCAGCATCGGCAACACC

upper sequence: PP1S18_317V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os08g08840.2 (Oryza sativa), 3'ss of exon 4
gtgaagcccccctccaggaacaccttgcagaacacctttgtgtctttacttctgagggttgcaggatatcgcggtgttgctgcgggtttacatgagcgaatattacgaatgacggtatttaagcaagttgataagaaaatggttgtgcgatgcagGTGGGTAGTGGCACAGAGTGTGTTCTACCACTTATACAACCAAGTGTCATACATGTCATTGGACAAAATCTCCCCACTCACATTCAGCGTTGGCAACACG
                                        | | ||   ||    |  || ||  |||   | | ||   ||| |    || ||||   || |||    |||   || ||||         |  |   ||| |||     || |||||||| |  |||||||| || |||||||||||||||||||| ||||| ||||||||  ||||  | || || ||| | ||||| ||| ||||||| |||
----------------------------------------tatattgtatttgatgatttacaacatactacagcgta--tgcagcaacacttgagt--attttat---tgatattacttaaat-------tttggggatg-ttgaatattgtagGTGGGTTGCTGCACAGAGCGTTTTCTACCACTTATACAACCAGGTGTCTTACATGTCTCTGGATGAGATTTCTCCATTGACATTTAGCATTGGCAATACG

upper sequence: PP1S18_317V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 4
gtgaagcccccctccaggaacaccttgcagaacacctttgtgtctttacttctgagggttgc-aggatatcgcggtgttgctgcgggtttacatgagcgaatattacgaatgacggtatttaagcaagttgataagaaaatggttgtgcgatgcagGTGGGTAGTGGCACAGAGTGTGTTCTACCACTTATACAACCAAGTGTCATACATGTCATTGGACAAAATCTCCCCACTCACATTCAGCGTTGGCAACACG
                                             ||| ||  ||  | ||  ||||| |   | |  || |      ||| || | ||| | | | | ||   | |||||   | | |   | |       ||||     |  |||||| | |  |||||||| ||||||||||||||||| ||||| ||||| ||||||||  | ||  | || || ||| | ||||||||| ||||||| || 
-------------------------------------------tattattttggattgatgttaggatctaatgatagtgata-----ttatatca-cgactgt-atgtatactgatattttccctaatgtgtta-----ctgttgaatt-tatagGTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACCAGGTGTCCTACATGTCTCTCGATCAGATTTCTCCATTGACATTCAGCATTGGCAATACA

upper sequence: PP1S18_317V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G009223_T01 (Zea mays), 3'ss of exon 3
gtgaagcccccctccaggaacaccttgcagaacacctttgtgtctttacttctgagggttgcaggatatcgcggtgttgctgcgg-gtttacatgagcgaatattacgaatgacggtatttaagcaagttgataagaaaatggttgtgcgatgcagGTGGGTAGTGGCACAGAGTGTGTTCTACCACTTATACAACCAAGTGTCATACATGTCATTGGACAAAATCTCCCCACTCACATTCAGCGTTGGCAACACG
                                                      ||  | |       |  || | || | | |    | |    || |     | ||  || |   ||| |||    ||  |  |    ||   ||| |  |||||||||| | ||| ||||| |||||||||||| | |||||||| ||||| ||||||||  ||||| | ||||| || ||||| |||  | | |||||||| 
-----------------------------------------------------cagaatcgattaccgtttcgatatttccgtgataatcaatccagagctgggttcgtgtggctaaattaaag--gcttcctctgtgcgtgtgcgtg-ggcgcagGTGGGTGGCGGCGCAGAGCGTGTTCTACCACCTGTACAACCAGGTGTCCTACATGTCCCTGGACGAGATCTCGCCCCTCACCTTCTCCATCGGCAACACC

upper sequence: PP1S18_317V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA15G11270.1 (Glycine max), 3'ss of exon 3
gtgaagcccccctccaggaacaccttgcagaacacctttgtgtctttacttctgagggttgcaggatatcgcggtgttgctgcgggtttacatg---agcgaatattacgaatgacggtatttaagcaagttgataagaaaatggttgtgcgatgcagGTGGGTAGTGGCACAGAGTGTGTTCTACCACTTATACAACCAAGTGTCATACATGTCATTGGACAAAATCTCCCCACTCACATTCAGCGTTGGCAACACG
                                                           | |||  | |     | || || |    |||       | | ||  ||| |  |  |  |||  ||    ||| |  |    ||  |  ||   | |||||||||||  || |||||||| ||||||||||| ||||| ||||| |||||||||||  | ||  | || || ||  | ||||||||| |||| ||||| 
---------------------------------------------------------aattcagtctttttttcttttccttcttccttaaccacccacccaaccttatgtctccctttataaaatgttgttaactaatggattttgatgtt-tacagGTGGGTAGCTGCCCAGAGTGTCTTCTACCACTTGTACAATCAAGTCTCATACATGTCTCTTGATCAGATTTCTCCCTTAACATTCAGCATTGGAAACACA

upper sequence: PP1S18_317V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA13G27680.1 (Glycine max), 3'ss of exon 3
gtgaagcccccctccaggaacaccttgcagaacacctttgtgtctttacttctgagggttgcaggatatcgcggtgtt-gctgcgggtttacatgagcgaatattacgaatgacggtatttaagcaa-gttgataagaaaatggttgtgcgat--gcagGTGGGTAGTGGCACAGAGTGTGTTCTACCACTTATACAACCAAGTGTCATACATGTCATTGGACAAAATCTCCCCACTCACATTCAGCGTTGGCAACACG
  | |  | |  |     ||    || | |      ||||  |   | |  |  | | || |    | | | | | ||   | |  |||     |    | ||        ||   | ||||   || |||| |||  ||  | || ||   |  | ||||||||||  ||||||||||| || |||||||| ||||| ||||| |||||||||||  | ||  | || || ||  | ||||| ||| |||| ||||| 
--gtaagcacatttttttaattttttactgttagtttttgaattggttcaac--aagatttcttattgttgtgctttttatttcatgttgttgggccaaattaacttagtggattctgtttatcaaatgttgttaactaatggattttgatgtttgtagGTGGGTAGCTGCACAGAGTGTCTTTTACCACTTGTACAATCAAGTCTCATACATGTCTCTTGATCAGATTTCTCCCTTAACATTTAGCATTGGAAACACA

upper sequence: PP1S18_317V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT5G54800.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgaagcccccctccaggaacaccttgcagaacacctttgtgtctttacttctgagggttgcaggatatcgcggtgttgctgcgggtttacatgagcgaatattacgaatgacggtatttaag--caagttgataagaaaatggttgtgcgatgcagGTGGGTAGTGGCACAGAGTGTGTTCTACCACTTATACAACCAAGTGTCATACATGTCATTGGACAAAATCTCCCCACTCACATTCAGCGTTGGCAACACG
                                                   || |  |||  || ||      || ||  |  | | |||    |  ||||    |  ||     |||   |   ||  ||  |    ||     | |||     |||||||| || || |||||||||||||| ||| | |||||||||||||| |||||||| || ||| ||||||| ||  | || || || ||||| ||||| 
---------------------------------------------------ctaaacgtttaagaatccttgagtcttttta-gtgattagggcaatgaatccatcccattcacttatccgattccacatttttctttaatcaaatttgc-----agGTGGGTGGTTGCGCAGAGTGTGTTCTATCACCTCTACAACCAAGTGTCTTACATGTCTTTAGACCAAATCTCTCCCTTGACGTTTAGTGTTGGTAACACC

upper sequence: PP1S18_317V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT1G61800.1 (Arabidopsis thaliana), 3'ss of exon 3
-------gtgaagcccccctccaggaac----accttgcagaacacctttgtgtctttacttctgagggttgca---ggatatcgcggtgttgctgcgggtttacatgagcgaatattacgaatgacggtatttaagcaagttgataagaaaatggttgtgcgatgcagGTGGGTAGTGGCACAGAGTGTGTTCTACCACTTATACAACCAAGTGTCATACATGTCATTGGACAAAATCTCCCCACTCACATTCAGCGTTGGCAACACG
        | ||  ||   || |  | |    |   |     |    ||   | ||  |  ||  | |  |      ||||       | |||||   | |       | |  |   ||  |  ||   ||  | |    |||| |       |  |||    |   ||||||||||||||||| |||||||| ||||| || ||||| || || |||||||||||||| ||| | || || ||  | || |||||  | || || |||
gtatgatctaaaaaccaaatcaataatctttaattgtttgttaagttttatagactccaactcaaatgactatgagtggattggtatatattgctttagttcccttctaacttaagatataa--gattctaacttaatgtgttgtttttgtttt--ttgaatca-atagGTGGGTAGTGGCACAAAGTGTGTTTTACCATTTGTACAATCAGGTCTCATACATGTCATTAGACCAGATTTCGCCGTTAACTTTCAGTATCGGTAATACG

upper sequence: PP1S18_317V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT4G03950.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgaagcccccctccaggaacaccttgcagaacacctttgtgtctttacttctgagggttgcaggatatcgcggtgttgctgcgggtttacatgagcgaatattacgaatgacggtatttaagcaagttgataagaaaatggttgtgcgatgcagGTGGGTAGTGGCACAGAGTGTGTTCTACCACTTATACAACCAAGTGTCATACATGTCATTGGACAAAATCTCCCCACTCACATTCAGCGTTGGCAACACG
                                         || | || |  ||    ||| |  |||     | |          ||   |  ||   || | |    |       | ||||  | |||||   ||| || |||    || |||||||||||||||||| ||||| |||||||| || || || ||||| ||||||||                                              
-----------------------------------------gtttatattgatg----ttgtacaatacaaaagagacaaaaaaaattcgaagaagttgatttaaaacct-------tgtaaggtatttgattctaaa-tgtttg---aattcagGTGGGTAGTGGCACATAGTGTTTTCTACCATTTGTATAATCAAGTCTCATACAT----------------------------------------------

upper sequence: PP1S18_317V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ37591 (Selaginella moellendorffii), 3'ss of exon 3
gtgaagcccccctccaggaacaccttgcagaacacctttgtgtctttacttctgagggttgcaggatatcgcggtgttgctgcgggtttacatgagcgaatattacgaatgacggtatttaagcaagttgataagaaaatggttgtgcgatgcagGTGGGTAGTGGCACAGAGTGTGTTCTACCACTTATACAACCAAGTGTCATACATGTCATTGGACAAAATCTCCCCACTCACATTCAGCGTTGGCAACACG
                                                                                             |  || |||||| | | |   |   | | |||  |       ||   |  |     ||||||||||||  |||| ||||| |||||||| ||| | ||||||||||| ||||||||||| |||||  |||| || || |||||||||||| |||| ||||| 
---------------------------------------------------------------------------------------------gtacgtatattaggca-gcgagcggtgacgcatctc------aactcgtctcactaatgcagGTGGGTCATGGCCCAGAGCGTGTTCTATCACCTCTACAACCAAGTCTCATACATGTCCTTGGATGAAATATCTCCTCTCACATTCAGCATTGGGAACACC

upper sequence: PP1S18_317V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ15095 (Selaginella moellendorffii), 3'ss of exon 3
gtgaagcccccctccaggaacaccttgcagaacacctttgtgtctttacttctgagggttgcaggatatcgcggtgttgctgcgggtttacatgagcgaatattacgaatgacggtatttaagcaagttgataagaaaatggttgtgcgatgcagGTGGGTAGTGGCACAGAGTGTGTTCTACCACTTATACAACCAAGTGTCATACATGTCATTGGACAAAATCTCCCCACTCACATTCAGCGTTGGCAACACG
                                                                                     || | | |  ||      |  |  ||||  |   |       |   |  | |||||  |       |||||||||| ||||| ||||| || ||||||||| | ||||| || ||||||||||||||  ||||  | ||||| || ||||| |||||| |||| ||||||
-------------------------------------------------------------------------------------gtatgcttt-gcctcctctctgcgtgaccctgactc------tccgtttgcaaatgact------cgcagGTGGGTTGTGGCCCAGAGCGTCTTCTACCACCTCTACAATCAGGTGTCATACATGTCCCTGGATGAGATCTCGCCCCTCACCTTCAGCATTGGGAACACG

upper sequence: PP1S18_317V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ37594 (Selaginella moellendorffii), 3'ss of exon 3
gtgaagcccccctccaggaacaccttgcagaacacctttgtgtctttacttctgagggttgcaggatatcgcggtgttgctgcgggtttacatgagcgaatattacgaatgacggtatttaagcaagttgataagaaaatggttgtgcgatgcagGTGGGTAGTGGCACAGAGTGTGTTCTACCACTTATACAACCAAGTGTCATACATGTCATTGGACAAAATCTCCCCACTCACATTCAGCGTTGGCAACACG
                                                                                     || | | |   |   |  |      |  |    | |  |   |   |  | |||||  |       |||||||||| ||||| ||||| || ||||||||| | ||||| || ||||||||||||||  ||||  | ||||| || ||||| |||||| |||| ||||||
-------------------------------------------------------------------------------------gtatgctttgcctcctcctctctgcg-tgaccctgactc---tccgtttgcaaatgact------cgcagGTGGGTTGTGGCCCAGAGCGTCTTCTACCACCTCTACAATCAGGTGTCATACATGTCCCTGGATGAGATCTCGCCCCTCACCTTCAGCATTGGGAACACG

upper sequence: PP1S18_317V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ15098 (Selaginella moellendorffii), 3'ss of exon 3
gtgaagcccccctccaggaacaccttgcagaacacctttgtgtctttacttctgagggttgcaggatatcgcggtgttgctgcgggtttacatgagcgaatattacgaatgacggtatttaagcaagttgataagaaaatggttgtgcgatgcagGTGGGTAGTGGCACAGAGTGTGTTCTACCACTTATACAACCAAGTGTCATACATGTCATTGGACAAAATCTCCCCACTCACATTCAGCGTTGGCAACACG
                                                                                                       ||||  |    |      ||  |  || ||    | |       | ||||||||||||  |||| ||||| |||||||| ||| | ||||||||||| ||||||||||| |||||  |||| || || |||||||||||| |||| ||||| 
------------------------------------------------------------------------------------------------------gtacgtgtattagggagcgagtga--tggtatctca-tctcaactcaatgcagGTGGGTCATGGCCCAGAGCGTGTTCTATCACCTCTACAACCAAGTCTCATACATGTCCTTGGATGAAATATCTCCGCTCACATTCAGCATTGGGAACACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattacgaatgacggtatttaagcaagttgataagaaaatggttgtgcgatgcagGTGGGTAGTGGCACAGAGTGTGTTCTACCACTTATACAACCAAGTGTCATACATGTCATTGGACAAAATCTCCCCACTCACATTCAGCGTTGGCAACACG
                         agttgat  putative branch site (score: 5)
                              ataagaaaat  TA-rich tract