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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaagaactctggtttgactctgaatgcactcatgtgacttaatttttctttacgatgttctgcttatttccataccaatccttgacttttcatgtgcagTTTATCCTGATGGACGGGTTTGCATTTCAATTCTACATGCTCCTGGTGATGATCCAAATGGTTATGAATTGGCGAGTGAGCGTTGGTCTCCCGTGCATAC

Basic information

species Physcomitrella patens
transcript PP1S75_236V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S75_236V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os01g62244.3 (Oryza sativa), 3'ss of exon 1
gaaagaactctggtttgactctgaatgcactcatgtgacttaatttttcttta-cgatgttctgcttatttccataccaatccttgacttttcatgtgc-agTTTATCCTGATGGACGGGTTTGCATTTCAATTCTACATGCTCCTGGTGATGATCCAAATGGTTATGAATTGGCGAGTGAGCGTTGGTCTCCCGTGCATAC
                   || |  | |     ||| |||| || ||||| || |    |  | | || ||  |   ||       | |  |||  ||| ||||||||| |||||||| || |||||||| ||||| ||| | |||||||||||||| |||||||||||  | ||||||||||||||| | || ||||||||
------------------gtcagctttcctcattgtaacttcatgtttctgtaactccatgatccataattttaacacagcataatattggtcaattgccagTTTATCCGGATGGACGTGTATGCATTTCTATTCTTCATCCGCCTGGTGATGATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATAC

upper sequence: PP1S75_236V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G012052_T01 (Zea mays), 3'ss of exon 3
gaaagaactctggtttgactctgaatgcactcatgtgacttaatttttctttacgatgttctgcttatttccataccaatccttg-acttttcatgtgcagTTTATCCTGATGGACGGGTTTGCATTTCAATTCTACATGCTCCTGGTGATGATCCAAATGGTTATGAATTGGCGAGTGAGCGTTGGTCTCCCGTGCATAC
                      | | |||    | | |  |  || |    ||     |  |||  |  | |  || | || ||    |||  ||   ||||||||||||||||||| ||||||||||| ||||| ||| | |||||||| ||||| |||||||||||  | || || || || ||| | || ||||| ||
----------------------gtaagcatcgctatcatgtc-ttgtctactatttgatcatgccaaagttctgacaattctttttgttttgaattctcagTTTATCCTGATGGACGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAGATCCCAATGGTTATGAGCTTGCAAGCGAACGATGGACACCAGTGCACAC

upper sequence: PP1S75_236V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G007276_T03 (Zea mays), 3'ss of exon 3
gaaagaactctggtttgactct--gaatgcactcatgtgacttaatttttctttacgatgttctgcttatttccataccaatccttgacttttcatgtgcagTTTATCCTGATGGACGGGTTTGCATTTCAATTCTACATGCTCCTGGTGATGATCCAAATGGTTATGAATTGGCGAGTGAGCGTTGGTCTCCCGTGCATAC
            | || ||| |  || || ||||||||    ||  |  || |  | | ||||||   |||   ||           | |||  ||   |||||||||| ||||| || ||||||||||| ||||| ||| | |||||||| ||||| | |||||||||  | || || || || ||| | || ||||| ||
--------gtaagcttcactatcggactgtactcatgtctactatctgatcatgtcaaagttctgacaattcttatt----------attttgaattctcagTTTATCCGGATGGGCGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAGATCCCAGTGGTTATGAGCTTGCAAGCGAACGGTGGACACCAGTGCACAC

upper sequence: PP1S75_236V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G085600_T03 (Zea mays), 3'ss of exon 3
gaaagaactctggtttgactctgaatgcactcatgtgacttaatttttctttacgatgttctgcttatttccataccaatccttgacttttcatgtgcagTTTATCCTGATGGACGGGTTTGCATTTCAATTCTACATGCTCCTGGTGATGATCCAAATGGTTATGAATTGGCGAGTGAGCGTTGGTCTCCCGTGCATAC
     | || |   ||       | || | | || | |||| || |    ||  | | |||||      | ||||   ||  ||||     |     |||| ||||||||||| |||||||| || || ||||| ||| | |||||||| |||||||| ||||||||  | || |||||||| ||| | || ||||| ||
--gtcagctttttattagtgaaaattgtatttattt-acttcatctgcagttctgtt-ttctgacatcatgcata---atatttgaggaaacgc---cagTCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAGATCCAAACGGTTATGAGCTCGCAAGTGAGCGATGGACACCTGTGCACAC

upper sequence: PP1S75_236V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA11G14980.1 (Glycine max), 3'ss of exon 3
gaaagaactctggtttgactctgaatgcactcatgtgacttaatttttctttacgatgttctgcttatttccataccaatccttgacttttcatgtgcagTTTATCCTGATGGACGGGTTTGCATTTCAATTCTACATGCTCCTGGTGATGATCCAAATGGTTATGAATTGGCGAGTGAGCGTTGGTCTCCCGTGCATAC
          | ||||   | |   |  | |  ||||| ||   |||  |     |     ||    |   ||      |       |     | |||||| ||||||||||| ||||||||||| |||||||| ||| |||||||||| |||||||||||||||||  | || |||||||| ||| | || || |||||
--------gttagttttttttttttta-att--tgtgattttgctttgatagg-aacaacatgaaagtgatcagtgatgtttcctgttcaatttttgcagTATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGGATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATAC

upper sequence: PP1S75_236V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA12G06960.1 (Glycine max), 3'ss of exon 3
gaaagaactctggtttgactctgaatgcactcatgtgactta--atttttctttacgatgttctgc-ttatttccataccaatccttgacttttcatgtgcagTTTATCCTGATGGACGGGTTTGCATTTCAATTCTACATGCTCCTGGTGATGATCCAAATGGTTATGAATTGGCGAGTGAGCGTTGGTCTCCCGTGCATAC
                     | | ||   |  |   | ||   ||||| ||||    ||  || | | |     ||        || | ||||    |||||| ||||| ||||| ||||||||||| |||||||| ||| |||||||||| |||||||||||||| ||  | ||||||||||| ||| | || || |||||
--------------------gttagtgttttttttgaatttgtgattttgctttgatttgaactacatgaaagtgatgttttctgttcaatttt----tgcagTATATCCCGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGGATCCAAATGGTTACGAGCTTGCGAGTGAGCGCTGGACACCTGTTCATAC

upper sequence: PP1S75_236V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA13G40990.1 (Glycine max), 3'ss of exon 3
gaaagaactctggtttgactctgaatgcactcatgtgacttaatttttctttacgatgttctgcttatttc--cataccaatccttgacttttcatgtgcagTTTATCCTGATGGACGGGTTTGCATTTCAATTCTACATGCTCCTGGTGATGATCCAAATGGTTATGAATTGGCGAGTGAGCGTTGGTCTCCCGTGCATAC
                              |  | ||||  |  |||| ||||   || |  | ||| | |   | |   |    ||   ||  || |||||| ||||||||||| || |||||||| |||||||| ||| |||||||||| || ||||||||||||||  | || |||||||| ||| | || || |||||
----------------------------gttggtctgacaca--ttttttttatcctgcttcgattaatacatgaaattcaatgatgttgttcaatttgcagTGTATCCTGATGGGCGAGTTTGCATATCAATTCTTCATCCTCCTGGTGACGACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATAC

upper sequence: PP1S75_236V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA15G04470.2 (Glycine max), 3'ss of exon 3
gaaagaactctggtttgactctgaatgcactcatgtgacttaatttt-tctttacgatgttctgcttatttcc--ataccaatccttgacttttcatgtgcagTTTATCCTGATGGACGGGTTTGCATTTCAATTCTACATGCTCCTGGTGATGATCCAAATGGTTATGAATTGGCGAGTGAGCGTTGGTCTCCCGTGCATAC
                              |  | || || | |||| | ||||   || | || ||  | |   |||   |    ||   || ||| |||||| || || ||||| || |||||||| |||||||| ||| | || |||||||| ||||||||||||||  | || |||||||| ||| | || || |||||
----------------------------gttggtttggctcatttttatttttatcttgctttgattgatacatgataatgaatgatgctgttccatttgcagTGTACCCCGATGGGCGAGTTTGCATATCAATTCTTCATCCACCCGGTGATGACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATAC

upper sequence: PP1S75_236V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT3G46460.1 (Arabidopsis thaliana), 3'ss of exon 3
gaaagaactctggtttgactctgaatgcactcatgtgacttaatttttctttacgatgttctgcttatttccataccaatccttgacttttcatgtgcagTTTATCCTGATGGACGGGTTTGCATTTCAATTCTACATGCTCCTGGTGATGATCCAAATGGTTATGAATTGGCGAGTGAGCGTTGGTCTCCCGTGCATAC
|  ||  || |   | |  |    |||| ||||| |  || | |  |  | |  ||    ||      ||   |   |||  | | ||| |  | |||||||||||| ||||| || ||||| || || ||||||||| |||||||||||||||||| ||| |||||  | || |||||||||||| | || || || ||
gttagttctttctctcggtt----atgcgctcat-tagctcattgatcttgtttgagtagctaa--ggttttgtgaaaatgttcgtcttgtggtctgcagTTTATCCCGATGGCCGCGTTTGTATATCTATTCTACATCCTCCTGGTGATGATCCAAGTGGATATGAGCTTGCAAGTGAGCGTTGGACGCCTGTTCACAC

upper sequence: PP1S75_236V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT3G55380.2 (Arabidopsis thaliana), 3'ss of exon 3
gaaagaactctggtttgactctgaatgcactcatgtgacttaatttttctttacgatgttctg-cttatttccataccaatccttgacttttcatgtgcagTTTATCCTGATGGACGGGTTTGCATTTCAATTCTACATGCTCCTGGTGATGATCCAAATGGTTATGAATTGGCGAGTGAGCGTTGGTCTCCCGTGCATAC
               |||||    ||           |  ||  | ||  |   | | ||  |  ||| |    |    ||   |    |||    |||||||||| ||||||||   ||||||||||| ||||| ||| ||||||||||||||||  |||| || ||  | ||   ||| |||||| | || || |||||
--------------gtgact---gatttttctggaaaatatatctctttctcgagcttttaggatttagtcttctgatgatttatactcttttgactgcagTTTATTCTGATGGAAAAGTTTGCATTTCTATTCTTCATCCTCCTGGTGATGATCCTCATGGATACGAGCTTGCCTCTGAACGTTGGACCCCTGTCCATAC

upper sequence: PP1S75_236V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT5G59300.1 (Arabidopsis thaliana), 3'ss of exon 3
gaaagaactctggtttgactctgaatgcactcatgtgacttaatttttctttacgatgttctgcttatttccataccaatccttgact----tttcatgtgcagTTTATCCTGATGGACGGGTTTGCATTTCAATTCTACATGCTCCTGGTGATGATCCAAATGGTTATGAATTGGCGAGTGAGCGTTGGTCTCCCGTGCATAC
        |  | |||  ||||    |   | ||  |       ||      |  |||    |   |    | |   |||  || |||    |||    |||||||||| ||||||| || |||||||| || ||||| ||| |||| ||||||||||| |  ||||||||  | || || ||||||||| |||| || |||||
-------gttagttttctctctatcggttttgatcggggaaggattcaaaggaatatgaatagaagacagacgtttgaatggtttacttatatttgtcctgcagTTTATTCTGATGGTCGTGTTTGCATATCTATTCTTCATCCTCCCGGTGATGATCCTAGCGGTTATGAGCTTGCAAGCGAGCGTTGGACTCCTGTTCATAC

upper sequence: PP1S75_236V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv08s0007g00120.t01 (Vitis vinifera), 3'ss of exon 3
gaaagaactctggtttgactctga-atgcactcatgtgacttaatttttctttacgatgttctgcttatttccataccaatccttgacttttcatgtgcagTTTATCCTGATGGACGGGTTTGCATTTCAATTCTACATGCTCCTGGTGATGATCCAAATGGTTATGAATTGGCGAGTGAGCGTTGGTCTCCCGTGCATAC
     ||||    | || |||| | || ||   || |   | ||||| || ||       ||| || ||    ||   |   | |   | || |  ||||||||||||||||||||| |||||||| |||||| ||||| |||||||||| || |||||||| |||||  | || |||||||||||| | || || || ||
--gttaacttct-tatgcctctcatatacatatatatatatgaatttctcattggagcactct-ctgatgctaattgta---cctacttcttaaactgcagTTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGGACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctttacgatgttctgcttatttccataccaatccttgacttttcatgtgcagTTTATCCTGATGGACGGGTTTGCATTTCAATTCTACATGCTCCTGGTGATGATCCAAATGGTTATGAATTGGCGAGTGAGCGTTGGTCTCCCGTGCATAC
                                   ccttgac  putative branch site (score: 4)
                                         cttttcat  CT-rich tract
                   ttattt  TA-rich tract