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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttattttattctattttattttattttaagcacctactagttacgtgctgtttcttttcttgaagctggtcactgacaagtgttggcatgacactgcagGTGACATCCATGGGCAGTATTCCGACCTCTTGAAACTTTTTGAATATGGTGGTTTTCCACCTGAGGCCAACTACTTGTTTTTAGGGGATTATGTTGACAG

Basic information

species Physcomitrella patens
transcript PP1S283_48V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S283_48V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os06g06880.1 (Oryza sativa), 3'ss of exon 1
tttattttattctattttatttta-ttttaagcacctacta--gttacgtgctgtttcttttcttgaagctggtcactgacaagtgttggcatgacactgcagGTGACATCCATGGGCAGTATTCCGACCTCTTGAAACTTTTTGAATATGGTGGTTTTCCACCTGAGGCCAACTACTTGTTTTTAGGGGATTATGTTGACAG
   |   ||     | || || ||  | ||| ||  |  ||   |   ||    | |  || | | | |||   ||       |  |    |        |||| || |||||||| |||||||| || ||  |     | ||||| ||||| || || ||||| ||||| |||||||||||| |||| |||||||||||| |
---acgctaaaacttcttgttctaactataaacaatttgtaacatgttgtagaatgtgattgcatcatgcttaccatcattctgcctacttactcattgacagGAGATATCCATGGCCAGTATTCTGATCTTCTTCGGTTATTTGAGTATGGGGGCTTCCCACCAGAGGCAAACTACTTGTTTCTAGGTGATTATGTTGACCG

upper sequence: PP1S283_48V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA03G41200.1 (Glycine max), 3'ss of exon 1
-tttattttattctattttattttatttta--agcacctactagttacgtgctgtttcttttcttgaagctggtcactgacaagtgttggcatgacactgcagGTGACATCCATGGGCAGTATTCCGACCTCTTGAAACTTTTTGAATATGGTGGTTTTCCACCTGAGGCCAACTACTTGTTTTTAGGGGATTATGTTGACAG
  |||     || ||   |||  || | ||         || ||  |  |  ||| | ||||   | || |  |   | | |    ||    |||   | |||||||  | |||||||| ||||| || || || |  |||||||| || ||||| || || ||||| |||||||| |||||||| ||||||||||||||  |
tattacacatttgtaccatataatactctattgttgtacacaagaaaaatattgtgtgtttta--ggagtttctgtttcatatcc-ttatattgatgtttcagGTGATGTACATGGGCAATATTCTGATCTTTTAAGGCTTTTTGAGTACGGTGGATTACCTCCTGAAGCCAACTATTTGTTTTTGGGGGATTATGTTGATCG

upper sequence: PP1S283_48V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA03G39440.1 (Glycine max), 3'ss of exon 1
------tttattttattctattttattttattttaagcacctactagttacgtgctgtttcttttcttgaagctggtcactgacaagtgttggcatgacactgcagGTGACATCCATGGGCAGTATTCCGACCTCTTGAAACTTTTTGAATATGGTGGTTTTCCACCTGAGGCCAACTACTTGTTTTTAGGGGATTATGTTGACAG
         |||||     |    | |  |||||| | |  ||  |   |  |  |||  | | |       || ||  || |    |||||   |     ||||||||| || ||||| |||||    ||| |  |||  ||||||||||||||||| |  || |||| ||| |||||||||||| | ||||||||||| || ||
agataagggattttggctgaggggagtgcattttagg-atataaaatcca-ataatgtcccatcttcaatcccttgttcctaa----tgttgcagttctcttgcagGTGATATACATGGTCAGTACCAGGACTTGCTGAGGCTTTTTGAATATGGTGGCTACCCTCCTGCGGCAAACTACTTGTTTCTGGGGGATTATGTGGATAG

upper sequence: PP1S283_48V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA20G36510.1 (Glycine max), 3'ss of exon 1
tttattttattctattttattttattttaagcacctactagttacgtgctgtttcttttcttgaa--------gctggtcactgacaagtgttggcat-gacactgcagGTGACATCCATGGGCAGTATTCCGACCTCTTGAAACTTTTTGAATATGGTGGTTTTCCACCTGAGGCCAACTACTTGTTTTTAGGGGATTATGTTGACAG
         || || |   |  ||||  ||   |    ||||   ||  | |   ||     |||        | || |  || | ||||  |    | ||     |||||||  | ||||| || ||||| || || || |  |||||||| ||||| ||  | || ||||||||||||||||| ||||| ||||||||||| ||  |
---------ttgtagtccttagtattgcaattgctacatagtactgtattttggtttacagagaaaaaattgtgatgatttcttaaaagtccttttgttgatctctcagGTGATGTACATGGTCAATATTCTGATCTTTTAAGGCTTTTTGAGTATGGCGGACTACCTCCTGAGGCCAACTACTTATTTTTGGGGGATTATGTGGATCG

upper sequence: PP1S283_48V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA10G30970.1 (Glycine max), 3'ss of exon 1
tttattttattctattttattttattttaagcacctac-tagttacgtgctgtttcttttcttgaagc-----tggtcactgacaagtgttggcat---gacactgcagGTGACATCCATGGGCAGTATTCCGACCTCTTGAAACTTTTTGAATATGGTGGTTTTCCACCTGAGGCCAACTACTTGTTTTTAGGGGATTATGTTGACAG
           | || | |     |||  |    |||| ||||   ||  | |   ||     |||       || | | |    | |||     |   ||     |||||||  | ||||| || ||||| || || || |  |||||||| ||||||||  | || || |||||||||||||| ||||| ||||||||||| ||  |
---------aacaatatcaacagttttgcaattgctacatagtactgtattatggtttacagagaaaaatgtgtgattatttcttaatgtccttttgttgatctctcagGTGATGTACATGGTCAATATTCTGATCTTTTAAGGCTTTTTGAGTATGGTGGACTACCTCCCGAGGCCAACTACTTATTTTTGGGGGATTATGTAGATCG

upper sequence: PP1S283_48V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA19G42050.1 (Glycine max), 3'ss of exon 1
---tttattttattctattttattttattttaagc-acctactagttacgtgctgtttcttttcttgaagctggtcactgacaagtgttggcatgacactgcagGTGACATCCATGGGCAGTATTCCGACCTCTTGAAACTTTTTGAATATGGTGGTTTTCCACCTGAGGCCAACTACTTGTTTTTAGGGGATTATGTTGACAG
    ||      |     | ||    | |  || |  | ||  |||       ||   | | |       || ||  ||||    |||||   |     ||||||||| || ||||| |||||    ||| |  |||  ||||||||||||||||| |  || |||| ||| |||||||||||| | ||||||||||| || ||
gcactttcaccttctcgctctagaggagtcaaatccgcatatcagtatgcaattgccccatcttcaatcccttgttcctga----tgttgcagttctcttgcagGTGATATACATGGTCAGTACCAGGACTTGCTGAGGCTTTTTGAATATGGTGGCTACCCTCCTGCGGCAAACTACTTGTTTCTGGGGGATTATGTGGATAG

upper sequence: PP1S283_48V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA19G43800.1 (Glycine max), 3'ss of exon 1
tttattttattctattttattttattttaagcacctactagttacgtgctgt---ttcttttcttgaagctggtcactgacaagtgttggcatgacactgcagGTGACATCCATGGGCAGTATTCCGACCTCTTGAAACTTTTTGAATATGGTGGTTTTCCACCTGAGGCCAACTACTTGTTTTTAGGGGATTATGTTGACAG
   || |||  |  || ||   |||  ||  |   |  |    ||  |       || | || | |  | | ||   | | |    |||   |||   | |||||||  | |||||||| ||||| || || || |  |||||||| || ||||| || || || || ||||||||||||||||| ||||||||||| ||  |
--catattacacatttgtaccatataatactctattgttgtacacaagaaaaatattgtgttttaggggtttgtttttcatatcc-ttgtattgatgtttcagGTGATGTACATGGGCAATATTCTGATCTTTTAAGGCTTTTTGAGTACGGTGGATTACCTCCAGAAGCCAACTACTTGTTTTTGGGGGATTATGTGGATCG

upper sequence: PP1S283_48V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT4G11240.1 (Arabidopsis thaliana), 3'ss of exon 1
tttattttattctattttattttattttaagcacctactagttacgtgctgtttcttttcttgaagctggtcactgacaagtgttggcatgacact--gcagGTGACATCCATGGGCAGTATTCCGACCTCTTGAAACTTTTTGAATATGGTGGTTTTCCACCTGAGGCCAACTACTTGTTTTTAGGGGATTATGTTGACAG
 | | |||  | |||  ||  | |||  |  |  ||  |  |  | |     |    ||  | |   || | |  |      |||   |||    |  ||||| ||  | ||||| |||| | | |||||||||    | ||||| |||||||||| |||||| |  || |||||||||||| | ||||||||||||||  |
-tgaatttggtgtatgatagat-attaaacccttctgttgctatcataactgtatgatttgtaattttgttgatggttttaagtttatatgttgatgagcagGAGATGTTCATGGTCAGTTTCCAGACCTCTTGCGGTTGTTTGAGTATGGTGGTTATCCACCAGCTGCGAACTACTTGTTTCTTGGGGATTATGTTGATCG

upper sequence: PP1S283_48V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ32796 (Selaginella moellendorffii), 3'ss of exon 1
-------tttattttattctattttattttattttaagcacctactagttacgtgctgtttcttttcttgaagctggtcactgacaagtgttggcatgacactgcagGTGACATCCATGGGCAGTATTCCGACCTCTTGAAACTTTTTGAATATGGTGGTTTTCCACCTGAGGCCAACTACTTGTTTTTAGGGGATTATGTTGACAG
         | |||  |    || |  | |    ||  ||| | ||  ||   ||   ||||||||      | |  |||| || |||  ||  | |        |||||||||||| || ||||| || || ||||||| ||| ||||| |||||||| ||||| || |||||||||||||||||  | || || ||||||||  |
ttttgcccgtgtttagtgtctttgttctatggcatagccacttgctctttgtctgaaatttctttt------gtttctcac-gagaagatttttcttcgtgtgctagGTGACATCCACGGCCAGTACTCGGATCTCTTGAGACTGTTTGAGTATGGTGGCTTTCCTCCCGAGGCCAACTACTTGTTCCTGGGTGACTATGTTGATCG

upper sequence: PP1S283_48V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ20637 (Selaginella moellendorffii), 3'ss of exon 1
tttattttattctattttattttattttaagcacctactagttacgtgctgtttcttt-----tcttgaagctggtcactgacaagtgttggcatgacactgcagGTGACATCCATGGGCAGTATTCCGACCTCTTGAAACTTTTTGAATATGGTGGTTTTCCACCTGAGGCCAACTACTTGTTTTTAGGGGATTATGTTGACAG
    ||||   |   |||||| | |||     |     |||  || |||| ||| | |     |  |   | |  |||| || |||  ||  | |        |||||||||||| || ||||| || || ||||||| ||| ||||| |||||||| ||||| || |||||||||||||||||  | || || ||||||||  |
----ttttgcccgtgtttattgtctttgttctatggcatagccacttgctctttgtctgaaatttctttggtttctcac-gagaagatttttcttcgtgtgctagGTGACATCCACGGCCAGTACTCGGATCTCTTGAGACTGTTTGAGTATGGTGGCTTTCCTCCCGAGGCCAACTACTTGTTCCTGGGTGACTATGTTGATCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgctgtttcttttcttgaagctggtcactgacaagtgttggcatgacactgcagGTGACATCCATGGGCAGTATTCCGACCTCTTGAAACTTTTTGAATATGGTGGTTTTCCACCTGAGGCCAACTACTTGTTTTTAGGGGATTATGTTGACAG
                          cactgac  putative branch site (score: 2)
      tttctttt  TA-rich tract