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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaaaaaagggagctcctcctcctgctcctctctcaacggttttcatcccaatcgttcctcgatttttgttccagcaattttgtattgtcactcactgaggctcagagagaaaaaaggccctcaaacttcctaattactattgccagGGAGATCATGCACGCCATGTACAAACCCAGCAAGTTCAAGTACGTTTTCCTGTTGGCGACGCTGTACGTGTTCACGCTGACAATCCCCTCCGCAGTGGCA

Basic information

species Physcomitrella patens
transcript PP1S213_89V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S213_89V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os01g63770.2 (Oryza sativa), 3'ss of exon 2
gtaagtaaaaaagggagctcctcctcctgctcctctctcaacggttttcatcccaatcgttcctcgatttttgttccagcaattttgtattgtcactcactgaggctcagagagaaaaaaggcc--ctcaaacttcctaattactattg--ccagGGAGATCATGCACGCCATGTACAAACCCAGCAAGTTCAAGTACGTTTTCCTGTTGGCGACGCTGTACGTGTTCACGCTGACAATCCCCTCCGCAGTGGCA
                                                          || ||  |    || |  | |    ||||| |  | | | ||        | ||| || || | |    |     |  ||  ||   ||||   |||||||||||||||||| ||||  |||||   ||||||||||||| | | |||| ||||||||||||||||||||||||||||  | || || ||   ||| 
------------------------------------------------------gcatgtgccgaggccgttttgtccgttgatttgt-tgattaataacctgcaagaaaagaaaataatgactgattgggggtggctgttttggattggtgcagGGAGATCATGCACGCGATGTGGAAACCGGCCAAGTTCAAGTACATCTACCTGCTGGCGACGCTGTACGTGTTCACGCTGACGCTGCCGTCGGCGTCGGCC

upper sequence: PP1S213_89V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os05g37470.1 (Oryza sativa), 3'ss of exon 5
gtaagtaaaaaagggagctcctcctcctgctcctctctcaacggttttcatcccaatcgttcctcgatttttgttccagcaattttgtattgtcactcactgaggctcagagagaaaaaaggccctcaaacttcctaattactattgccagGGAGATCATGCACGCCATGTACAAACCCAGCAAGTTCAAGTACGTTTTCCTGTTGGCGACGCTGTACGTGTTCACGCTGACAATCCCCTCCGCAGTGGCA
                                               |  |    |||| | | ||||    |   | |  |   || |   ||   | |||| | || ||       | |    | ||  |  ||  ||||   ||| || |||||||||||||| ||||  || ||    |||||||||||| | | |||| ||||||||||||||||||||||||||||  | || || ||   ||| 
----------------------------------------------gtgctgttgatcggttcacgatgaacgaagctg--acagtgaacaatcgtgc-ctgaagttctgaacagttgacgaagtttaa-ttaactttttacgcgtgc-agAGAGATCATGCACGCGATGTGGAAGCCGCAGAAGTTCAAGTACATCTACCTGGTGGCGACGCTGTACGTGTTCACGCTGACGCTGCCGTCGGCGTCGGCC

upper sequence: PP1S213_89V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G067022_T02 (Zea mays), 3'ss of exon 5
gtaagtaaaaaagggagctcctcctcctgctcctctctcaacggttttcatcccaatcgttcctcgatttttgttccagcaattttgtattgtcactcactgaggctcagagagaaaaaaggccctcaaacttcctaattactattgccagGGAGATCATGCACGCCATGTACAAACCCAGCAAGTTCAAGTACGTTTTCCTGTTGGCGACGCTGTACGTGTTCACGCTGACAATCCCCTCCGCAGTGGCA
                                                   |   |  |   |||  ||||| |  |||||  |      |||| ||  || |   ||      |||     | || |    |  |            |||||||||||||||||| ||||  || ||  |||||||||||||| | | |||| ||||||||||||||||||||||||||||  | || || || | ||| 
---------------------------------------------------cgtgaaggactctccttttttttatcagcatatactctatgtctctatctcattttctattttaaatttctcactgatttctgatgccccgcgcgcgcagGGAGATCATGCACGCGATGTGGAAGCCTCGCAAGTTCAAGTACATCTACCTGCTGGCGACGCTGTACGTGTTCACGCTGACGCTTCCGTCGGCGGCGGCC

upper sequence: PP1S213_89V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G127949_T03 (Zea mays), 3'ss of exon 3
gtaagtaaaaaagggagctcctcctcctgctcctctctcaacggttttcatcccaatcgttcctcgatttttgttccagcaattttgtattgtcactcactgaggctcagagagaaaaaaggccctcaaac---ttcctaattactattgccagGGAGATCATGCACGCCATGTACAAACCCAGCAAGTTCAAGTACGTTTTCCTGTTGGCGACGCTGTACGTGTTCACGCTGACAATCCCCTCCGCAGTGGCA
                                                      |  |  |  |        | |  |   | |     | | |     ||   |  ||     | || |   || |       ||| |  ||  | ||| ||| |||||||||||||| ||||  || |||  ||||||||| ||| | | |||| ||||||||||||||||||||||||||||  | || ||  | | ||| 
-----------------------------------------------------tatacactgatgatgaacagctttactgaatgcaggtagccgaaagctagagaacaagctaacaataataccacgtttgtgttcttggtttgt-ttggcagCGAGATCATGCACGCGATGTGGAAGCCCGCCAAGTTCAAATACATCTACCTGCTGGCGACGCTGTACGTGTTCACGCTGACGCTGCCGTCGTCGGCGGCC

upper sequence: PP1S213_89V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G045057_T02 (Zea mays), 3'ss of exon 5
gtaagtaaaaaagggagctcctcctcctgctcctctctcaacggttttcatcccaatcgttcctcgatttttgttccagcaattttgtattgtcactcactgaggc--tcagagagaaaaaaggccctcaaacttcctaattactattgccagGGAGATCATGCACGCCATGTACAAACCCAGCAAGTTCAAGTACGTTTTCCTGTTGGCGACGCTGTACGTGTTCACGCTGACAATCCCCTCCGCAGTGGCA
            |  |||  |  || |      ||| | | |  |   ||  |  | |     |  | ||| | ||     |   |  |  |  ||  ||  | |   | || |  | |    |    ||||    |   ||  |     |||||||||||||||||| ||||  |||||   ||||||||||  | | | |||| ||||||||||||||||| | ||||||||  | || |||||    || 
------------gtaagcctcagctgccagcagtctat-atctatacccacacacagcagaagtgaagtttaggtcacttcagagttcagagctacgtacgtacgtgatgagtgtcacagtgtgtgtacaaatgggccggttggtg----cagGGAGATCATGCACGCGATGTGGAAACCGCACAAGTTCAAGCTCATCTACCTGGTGGCGACGCTGTACGTGCTGACGCTGACGCTGCCGTCCGCCTCCGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcactgaggctcagagagaaaaaaggccctcaaacttcctaattactattgccagGGAGATCATGCACGCCATGTACAAACCCAGCAAGTTCAAGTACGTTTTCCTGTTGGCGACGCTGTACGTGTTCACGCTGACAATCCCCTCCGCAGTGGCA
                                    tcctaat  putative branch site (score: 2)
                                       taattactatt  TA-rich tract