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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcgcgatctgctttgagggtgtggaatcaagtatcgtccattcttagttgcttctggataatcggagtcatgcactgactgggttcgatgatttggcagATGATGTGGCGGCTCAATTTCCTGGTCTTCTTTAGCTGCATTGTACTGAACAATGACTACATGCTCTACTACATCTGTCCAATGCACACTCTCTTCACTC

Basic information

species Physcomitrella patens
transcript PP1S5_239V6.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S5_239V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os01g44040.2 (Oryza sativa), 3'ss of exon 7
-------ttcgcgatctgctttgagggtgtggaatcaagtatcgtc-cat-tcttagttgcttctggataatcggagtcatgcactgactgggttcgatgatttggcagATGATGTGGCGGCTCAATTTCCTGGTCTTCTTTAGCTGCATTGTACTGAACAATGACTACATGCTCTACTACATCTGTCCAATGCACACTCTCTTCACTC
       |  |   | |      |   |||   ||    ||   |   || | ||  || | |     ||||    |   | |||||||         |  |   ||||||||||||| | || |||||  | ||    ||  |||||||||| ||  ||||||| ||||||||||| ||||| || |||||||||||| | || ||||
gtgccattctgatctttaaccccaatctgttctatatgatactttagtatgttttcatttccttgatttaatgcatggtttacactgac-aaccatatttctaatgcagATGATGTGGAGACTTAATTTTTTTGTGGCTTTCTGCTGCATTGTCCTTGACAATGATTACATGCTCTATTACATATGCCCAATGCACACTTTGTTTACTC

upper sequence: PP1S5_239V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G020721_T01 (Zea mays), 3'ss of exon 7
ttcgcgatctgctttgagggtgtggaatcaagtatcgtccattcttagttgcttctggataatcggagtcatgcactgactgggttcgatgatttggcagATGATGTGGCGGCTCAATTTCCTGGTCTTCTTTAGCTGCATTGTACTGAACAATGACTACATGCTCTACTACATCTGTCCAATGCACACTCTCTTCACTC
                     ||| |       | |  ||| | ||   || ||||  | | | |   |  |   || ||  ||||  |   ||   |||||||||||||| ||||||||| | ||  | ||  |||||||||| ||||||||||| || |  ||||| || || ||||| |||||||| || ||||| |
---------------------gtgcatctttacacc--ccactgttc-ctgattctctacactagagttttt---ctaacatggtttcacc-ttcaacagATGATGTGGCGCCTCAATTTCTTTGTTATATTCTGCTGCATTGTCCTGAACAATGATTATACACTCTATTATATTTGTCCTATGCACACCCTTTTCACCC

upper sequence: PP1S5_239V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA05G25780.1 (Glycine max), 3'ss of exon 8
------------------ttcgcgatctgctttgagg-gtgtggaatcaagtatc-gtccattcttagttgcttctggataatcggagtcatgcactgactgggttcgatgatttggcagATGATGTGGCGGCTCAATTTCCTGGTCTTCTTTAGCTGCATTGTACTGAACAATGACTACATGCTCTACTACATCTGTCCAATGCACACTCTCTTCACTC
                  ||    | |   ||||       | |  || | | ||  ||| ||    ||| ||  |     ||       || | || ||| | |   ||   ||| ||||||||||||||||| |||||  | ||   |||  | || ||||| || ||||||||||| ||||||||||| || || ||||||||||| || |||||| 
gtaatagagtccttgaccttaaataccatttttgctttactttgtgtccactgtctatccttttcctgttactctttttgcataaacaatatac-ctaactcgttaaaattccttg-cagATGATGTGGCGGCTTAATTTTTTTGTGGCCTTCTGTTGTATTGTGCTTAACAATGACTATATGCTCTACTATATATGCCCAATGCACACGCTTTTCACTT

upper sequence: PP1S5_239V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA08G08730.1 (Glycine max), 3'ss of exon 8
---------------ttcgcgatctgctttgagg-gtgtggaatcaagtatc-gtccattcttagttgcttctggataatcggagtcatgcactgactgggttcgatgatttggcagATGATGTGGCGGCTCAATTTCCTGGTCTTCTTTAGCTGCATTGTACTGAACAATGACTACATGCTCTACTACATCTGTCCAATGCACACTCTCTTCACTC
                |      |   ||||       ||| ||| | | ||  ||| ||     || ||  |     ||   |   ||  ||  |    |||  |   | | |||||||||||||||||| |||||  | ||   |||  | || ||||| || ||||||||||| ||||||||||| || || ||||||||||| || |||||| 
gtaagagtcattgaccttaaataccattttgctttacttggtatccattgtctatccttttcctattactctttttgcat--aaacaatatacctaactcgttaaaatttcttgcagATGATGTGGCGGCTTAATTTTTTTGTGGCCTTCTGTTGTATTGTGCTTAACAATGACTATATGCTCTACTATATATGCCCAATGCACACGCTTTTCACTT

upper sequence: PP1S5_239V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT1G29890.1 (Arabidopsis thaliana), 3'ss of exon 6
-------------ttcgcgatctgctttgagggtgtgg--aatcaagtatcgtccattcttagttgcttctggataatcggagtcatgcactgactgggttcgatgatttgg--cagATGATGTGGCGGCTCAATTTCCTGGTCTTCTTTAGCTGCATTGTACTGAACAATGACTACATGCTCTACTACATCTGTCCAATGCACACTCTCTTCACTC
             ||  |||||  | | |   ||   |   | || ||   || | ||   ||     | ||  |        ||| |   |   ||    |  | | ||    ||||||||||||||||| || ||  | ||    ||| | |||||| | || ||||||||||| ||||| |||||||||||||||||||||||||| ||||| |
gtcagatcaactattttcgatcaccatagtttgttcagtttaccatgtgatgttcttttagagagcactatgtctttcaaagctcaagatttttatgaaagcttttacttaatccagATGATGTGGCGGCTTAACTTTTTTGTGGCGTTTTGTTGCATTATTCTCAACAATGACTATATGCTGTACTACATCTGTCCAATGCACACTCTATTCACGC

upper sequence: PP1S5_239V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT2G34410.1 (Arabidopsis thaliana), 3'ss of exon 7
----ttcgcgatctgctttgagggtgtgga--atcaagtatcgtcc--attcttagttgcttctggataatcggagtcatgcactgactgggttcgatgatttggcagATGATGTGGCGGCTCAATTTCCTGGTCTTCTTTAGCTGCATTGTACTGAACAATGACTACATGCTCTACTACATCTGTCCAATGCACACTCTCTTCACTC
    ||     |   |  | |    || ||  || |  |||  | |  |     |  |  || |  || |    ||     || |||     ||   |  ||   |||||||||||||| || || ||  | ||    |||||||||||| | || || ||||| || ||||| |||||||||||||||||||||||||| |||||||
gtcatttcaattgcacagttaattagttgaccatgatatatgcttctaagggacatgttgttttcaatgactcaagatgctca-tgaaaacttttacttcttc--cagATGATGTGGCGTCTTAACTTATTTGTGGCGTTTAGCTGCATTATTCTCAATAATGATTATATGCTGTACTACATCTGTCCAATGCACACTCTGTTCACTC

upper sequence: PP1S5_239V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT3G06550.2 (Arabidopsis thaliana), 3'ss of exon 7
ttcgcgatctgctttgagggtgtggaatcaagtatcgtccattcttagttgcttctggataatcggagtcatgcactgactgggttcgatgatttggcagATGATGTGGCGGCTCAATTTCCTGGTCTTCTTTAGCTGCATTGTACTGAACAATGACTACATGCTCTACTACATCTGTCCAATGCACACTCTCTTCACTC
                   ||   ||   | ||     |   | ||   |  || | |    ||     | || | |       |    |   |   ||||||||||||||||| |||||||||||| | ||   |||||| || || |||||    |||||||| ||||||||||| |||||||||||||| || ||||
-------------------gta-agagctatgtcctcccggcttttttcttatttttggctgtcacctacttgaaattctaacatattcttggtctacagATGATGTGGCGGCTAAATTTCCTGGTCATATTCTCCTGCATCGTCCTCAACAACAGTTACATGCTATACTACATCTGCCCAATGCACACTCTGTTTACTC

upper sequence: PP1S5_239V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT5G46340.1 (Arabidopsis thaliana), 3'ss of exon 8
ttcgcgatctgctttgagggtgtggaatcaagtatcgtccattcttagttgcttctggataatcggagtcatgcactgactgggttcgatgatttggcagATGATGTGGCGGCTCAATTTCCTGGTCTTCTTTAGCTGCATTGTACTGAACAATGACTACATGCTCTACTACATCTGTCCAATGCACACTCTCTTCACTC
              |||     |  | || |  |    |  |  | | ||| | || ||||||| |   |||  |    || |||||     | | ||||||||||||| |||| || ||| | ||    ||| |||| ||||| || ||||| ||||| ||| | ||||||||||| |||||||||||||| ||||| |
-------------gtgatacaattcattccacaaaaagctctcgtca-ttg-tacttgataatccg---catctaaaatcttggttc-----tcttgcagATGATGTGGAGGCTGAACTTCTTTGTAGCGTTTTGCTGTATTGTTCTCAACAACGACTATATGTTATACTACATCTGCCCAATGCACACTCTTTTCACCC

upper sequence: PP1S5_239V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 2
------------ttcgcgatctgctttgagggtgtggaatcaa-----gtatcgtccattcttagttgcttctggataatcggagtcatgcactgactgggt-tcgatgatttg--gcagATGATGTGGCGGCTCAATTTCCTGGTCTTCTTTAGCTGCATTGTACTGAACAATGACTACATGCTCTACTACATCTGTCCAATGCACACTCTCTTCACTC
             |   || ||| ||      |     || |       ||| || | || | | || ||       |||     | ||  |     ||  | |  |   | |   |||||||||||||||||| |||||| | ||    ||| |||||||||| || ||||||||||||||||| ||||| ||||| || |||||||| || |||||||
gtgaccttgttaattctgaactgtttcatcatttctctattagaagtgatattgttccttttcattttctatatttcaattttgataatttaggatgtgaatctttactttctaatgcagATGATGTGGCGGCTAAATTTCTTTGTGGCATTTTGCTGCATTGTTCTTAACAATGACTACATGCTATACTATATCTGCCCCATGCACACGCTTTTCACTC

upper sequence: PP1S5_239V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: Vv05s0077g00620.t01 (Vitis vinifera), 3'ss of exon 7
ttcgcgatctgctttgagggtgtggaatcaagtatcgtccattcttagttgcttctg-gataatcggagtcatgcactgactgggttcgatgatttggcagATGATGTGGCGGCTCAATTTCCTGGTCTTCTTTAGCTGCATTGTACTGAACAATGACTACATGCTCTACTACATCTGTCCAATGCACACTCTCTTCACTC
   |  |    |  | |   | |      |||| |  | |||    |||| | ||   |||| || || ||    | | |    |||   || ||   ||||||||||||||||| |||||| |||| || ||| ||||  |||| || || ||   ||| ||||| |||||||| || || ||||||||||| |||||||
---gtaactgcccctaaatctct-----taagtttgattcatgg--agttccatccatgatattctgattctaatagtaa----gttttttg-ttgaacagATGATGTGGCGGCTTAATTTCTTGGTGTTGTTTTGCTGTGTTGTCCTTAATAACAGCTATATGCTATACTACATTTGCCCCATGCACACTCTTTTCACTC

upper sequence: PP1S5_239V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: EDP02440 (Chlamydomonas reinhardtii), 3'ss of exon 4
---ttcgc-gatctgctttgagggtg----tggaatcaagtatcgtccattcttagttgcttctggataatcggagtcatgcactgactgggttcgat-gatttg-gcagATGATGTGGCGGCTCAATTTCCTGGTCTTCTTTAGCTGCATTGTACTGAACAATGACTACATGCTCTACTACATCTGTCCAATGCACACTCTCTTCACTC
   || || |    ||  ||| |  |    | || |     | | | || || |     |  |  | |   ||    |   |||     || | |    |||| | ||||||||||||||| ||||| ||| |||| ||||| |  ||| | || || |||||   ||||||||||||||||||||| || ||||||||           
gcgtttgctggcacgcgctgaagccgctgctagacttccacaccttgcactcgtctcatccccacgcttcccgcttcccgacaccccgcggttccctcagATTCGCGCAGATGATGTGGCGCCTCAACTTCATGGTGTTCTTCACGTGCGTGGTGCTCAACAACAGCTACATGCTCTACTACATCTGCCCCATGCACACC----------

upper sequence: PP1S5_239V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: EFJ29067 (Selaginella moellendorffii), 3'ss of exon 7
ttcgcgatctgctttgagggtgtggaatcaagtatcgtccattcttagttgcttctggataatcggag--tcatgcactgactgggttcgatgatttggcagATGATGTGGCGGCTCAATTTCCTGGTCTTCTTTAGCTGCATTGTACTGAACAATGACTACATGCTCTACTACATCTGTCCAATGCACACTCTCTTCACTC
                                             ||  |||||||    | ||| |   ||||||  ||       |  | |   | ||||||||||||| ||||||| || || ||   |||| ||||||| || || |||||   |||||||||||||||||||||||| ||||| || ||||||||  
--------------------------------------------gtaactgcttctttgcactcgtaagttcatgctttg-------tgaacgcacttgcagATGATGTGGAGGCTCAACTTTCTTGTGACCTTTTGCTGCATCGTCCTCAACAACAGCTACATGCTCTACTACATCTGTCCTATGCATACCCTCTTCACAT

upper sequence: PP1S5_239V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: EFJ17601 (Selaginella moellendorffii), 3'ss of exon 6
ttcgcgatctgctttgagggtgtggaatcaagtatcgtccattcttagttgcttctggataatcggag--tcatgcactgactgggttcgatgatttggcagATGATGTGGCGGCTCAATTTCCTGGTCTTCTTTAGCTGCATTGTACTGAACAATGACTACATGCTCTACTACATCTGTCCAATGCACACTCTCTTCACTC
                                             ||  |||||||    | ||| |   ||||||  ||       |  | |   | ||||||||||||| ||||||| || || |||  |||| ||||||| || || |||||   ||||||||| |||||||||||||| ||||| || ||||||||  
--------------------------------------------gtaactgcttctttgcactcgtaagttcatgctttg-------tgaacgcacttgcagATGATGTGGAGGCTCAACTTTCTTGTCACCTTTTGCTGCATCGTCCTCAACAACAGCTACATGCTTTACTACATCTGTCCTATGCATACCCTCTTCACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagttgcttctggataatcggagtcatgcactgactgggttcgatgatttggcagATGATGTGGCGGCTCAATTTCCTGGTCTTCTTTAGCTGCATTGTACTGAACAATGACTACATGCTCTACTACATCTGTCCAATGCACACTCTCTTCACTC
                            cactgac  putative branch site (score: 2)
                                           atgattt  TA-rich tract