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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatttctagcactgtttccattatgtttatgtcagaatatcaagtggtgtttgatgcttgcattgccttttttagggcttgacgatgttgtatcttcctccactcgtgtcacgattgacagGGCCTCGAGTTGATCCCATCAGAGAATTTCACGTCTGTTTCAGTTATGCAGGCAGTAGGTTCCGTCATGACCAATAAGTACAGTGAAGGATATCCTGGT

Basic information

species Physcomitrella patens
transcript PP1S51_296V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S51_296V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 3
gtatgatttctagcactgtttccattatgtttatgtcagaatatcaagtggtgtttgatgcttgcattgccttttttagggcttgacgatgttgtatcttcctccactcgtgtcacgattgacagGGCCTCGAGTTGATCCCATCAGAGAATTTCACGTCTGTTTCAGTTATGCAGGCAGTAGGTTCCGTCATGACCAATAAGTACAGTGAAGGATATCCTGGT-
                                 |  |     | ||            ||| || ||||     | |  ||     ||| |   |       |       | |      || ||||| || ||| | ||||| || ||||| ||||| || || ||||| |||||||| || || |||||||||||||| |||||||| || || || || ||  
--------------------------------gtaaccagcaaccaccaaaaaaaaagtgcgtggattgttcagtgtttggtccaccgacgcattgctgaattgtggcaatctgtttggtg-cagGGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCG

upper sequence: PP1S51_296V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G135283_T01 (Zea mays), 3'ss of exon 3
----------------gtatgatttcta----gcactgtttcca-ttatgtttatgtcagaatatcaagtggtgtttgatgcttgcattgccttttttagggcttgacgatgttgtat-cttcctccactcgtgtcacgattgacagGGCCTCGAGTTGATCCCATCAGAGAATTTCACGTCTGTTTCAGTTATGCAGGCAGTAGGTTCCGTCATGACCAATAAGTACAGTGAAGGATATCCTGGT-
                  ||  ||||      | ||| ||| || | || |  |  ||   |      ||  |||| |||  |   |||   | ||||    |  |||  |  ||  | ||  |        ||   |   || ||||| || ||| | ||||| || |||||||||||||| || ||||| ||||||||||| ||||||||||||||||| |||||||| || || || |||||  
gtccctgtttcttcagtcatcttttcctatacgtactcttttcagtcatttccacttctccagtcattgttttgttggattatattattatttgtttttttccaagaccctactgagttctgtccgtgtcaatgcgtctggtggcagGGTCTGGAGCTCATCCCGTCGGAGAATTTCACGTCGGTGTCAGTGATGCAGGCAGTGGGTTCCGTCATGACCAACAAGTACAGCGAGGGGTACCCTGGCG

upper sequence: PP1S51_296V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA14G36280.2 (Glycine max), 3'ss of exon 3
gtatgatttctagcactgtttccattatgtttatgtcagaatatcaagtggtgtttgatgcttgcattgccttttttagggcttgacgatgttgtatcttcctccactcgtgtcacgattgacagGGCCTCGAGTTGATCCCATCAGAGAATTTCACGTCTGTTTCAGTTATGCAGGCAGTAGGTTCCGTCATGACCAATAAGTACAGTGAAGGATATCCTGGT-
   ||| | | ||     || | |   || || ||      | | ||       || ||   |    |  |   |||   || |||   |  | ||      |    | ||  |   |||   ||||  ||||  | || || || || |||||||||||  | || || ||||| ||||| || || || ||||| ||||| ||||||||||||||||||||| 
--gtgaatccgagtttcatt-ctacagtgctt-tgctttgctttgaa-------ttaataaataagctttccgattttatgcatgattgttgtttacggaagtttgtttgta-cggaatttgtagGGGTTCGAACTTATACCTTCGGAAAATTTCACGTCGCTGTCGGTGATGCAAGCAGTTGGATCGGTGATGACGAATAAATACAGTGAAGGATATCCTGGTG

upper sequence: PP1S51_296V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT5G26780.3 (Arabidopsis thaliana), 3'ss of exon 3
gtatgatttctagcactgtttccattatgtttatgtcagaat-atcaagtggtgtttgatgcttgcattgccttttttagggcttgacgatgttgtatcttcctccactcgtgtcacgattgacagGGCCTCGAGTTGATCCCATCAGAGAATTTCACGTCTGTTTCAGTTATGCAGGCAGTAGGTTCCGTCATGACCAATAAGTACAGTGAAGGATATCCTGGT-
                 || || |  |  |||| || ||||| ||||| |     |  ||    || |||  || ||  |   | |  |||| |||             || ||     ||  |||||  | ||  | || || |||||||||||||| ||| | || || ||||| || || ||||| || ||||| |||||||| ||||||||||| |||||  
-----------------gtatcaacaaaattta-gtgagaatgatcaaattcacatatatagaagctttgatttatt--gatttgggggatgatgt-----------tacgagtt----ttttcagGGATTTGAACTTATACCGTCAGAGAATTTCACTTCTCTATCTGTGATGCAAGCCGTTGGTTCTGTTATGACTAATAAGTATAGTGAAGGATACCCTGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttttagggcttgacgatgttgtatcttcctccactcgtgtcacgattgacagGGCCTCGAGTTGATCCCATCAGAGAATTTCACGTCTGTTTCAGTTATGCAGGCAGTAGGTTCCGTCATGACCAATAAGTACAGTGAAGGATATCCTGGT
          gcttgac  putative branch site (score: 4)