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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgccagtagatcgaggctcctttgtatcgtgattgcaagaatggggttctttgggatttgcctaaccaacgtggtacggggttggtgtcgtgatggcagGTTTTCCACAAGCGCATGCCTCCAGAAGCAGTAGATCTGGTTTCAAGGCTACTTCAGTACTCTCCGAATCTGCGGTGCAATGCT

Basic information

species Physcomitrella patens
transcript PP1S74_168V6.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os02g14130.1 (Oryza sativa), 3'ss of exon 9
--atgccagtagatcgaggctcctttgtatcgtgattgcaagaatggggttctttgggatttgcctaaccaacgtggtacggggttggtgtcgtgatggcagGTTTTCCACAAGCGCATGCCTCCAGAAGCAGTAGATCTGGTTTCAAGGCTACTTCAGTACTCTCCGAATCTGCGGTGCAATGCT
  ||   | | | |       | || | ||     ||     | ||  ||| |  |  | | |   |    ||    | |        ||  |      ||| ||||||||||||| ||||||||||||||| | || || |  ||| | || || |||||  | || ||||| || |||| ||| 
gtattagaattgttttgtttactttagcattccatttttttaattgatgttat--gatactagtgcatattacaacctgcaaatcctatgctg------cagATTTTCCACAAGCGGATGCCTCCAGAAGCAATTGACCTTGCATCACGTCTTCTCCAGTATGCACCAAATCTACGATGCACTGCC

upper sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G043350_T01 (Zea mays), 3'ss of exon 9
atgccagtagatcgaggctcctttgt-atcgtgattgcaagaatggggttctttgggatttgcctaaccaacgtggta--cggggttggtgtcgtgatg--gcagGTTTTCCACAAGCGCATGCCTCCAGAAGCAGTAGATCTGGTTTCAAGGCTACTTCAGTACTCTCCGAATCTGCGGTGCAATGCT
    ||    ||   |  |   || | ||| ||  | ||| | ||   | | ||    ||    |  |  | |  | |  |    |     | || |||  |||| | ||||||||| | ||||||||||||||| ||||||| |||||  | || |||||||| || ||||||||||| || |  || 
----caaacaataatgtttatgttattatcatgtgtacaata-tgatctcccttattcttgatgttcctgatggtggagtccttatcacaatggttatgctgcagATCTTCCACAAGAGAATGCCTCCAGAAGCAATAGATCTTGTTTCCCGTCTTCTTCAGTATTCGCCGAATCTGCGATGTAGCGCA

upper sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G109624_T01 (Zea mays), 3'ss of exon 10
atgccagtagatcgaggctcctttgtatcgtgattgcaagaatggggttctttgggatttgcctaaccaacgtggtacggggttggtgtcgtgatggcagGTTTTCCACAAGCGCATGCCTCCAGAAGCAGTAGATCTGGTTTCAAGGCTACTTCAGTACTCTCCGAATCTGCGGTGCAATGCT
  |  ||  ||||    ||  | | | | ||| ||     | |   | | |   |  ||  |     || |   ||  |    | ||||         || ||||    ||||||||||| || ||||| || ||||| || |||||||||||||||||||| || || ||||| |||| ||||
--gttag-ggatct---ctaatctctgtggtgtttttttcatttcagctgtaatgagttgacaagctcacctaagtttgattctcgtgt---------agCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCT

upper sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G121790_T01 (Zea mays), 3'ss of exon 9
atgccagtagatcgaggctcctttgtatcgtgattgcaagaatggggttctttgggatttgcctaaccaacgtggtacggggttggtgtcgtgatggcagGTTTTCCACAAGCGCATGCCTCCAGAAGCAGTAGATCTGGTTTCAAGGCTACTTCAGTACTCTCCGAATCTGCGGTGCAATGCT
                        ||||    | |  |   ||   ||| | |          ||   ||| |   ||     |    | |   | |||| ||||||||||||| ||||||||||||||  ||||||| | |||| |  | || ||||| || || |||||  | |||| ||||
------------------------gtatgtgaaatttatttatcatgttatatcattgaatggtagaaaacttaa-actaaaatacctttgctcttgcagATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT

upper sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G151916_T01 (Zea mays), 3'ss of exon 9
atgccagtagatcgaggctcctttgtatcgtgattgcaagaatggggttctttgggatttgcc--taaccaacgtggtacggggttggtgtcgtgatggcagGTTTTCCACAAGCGCATGCCTCCAGAAGCAGTAGATCTGGTTTCAAGGCTACTTCAGTACTCTCCGAATCTGCGGTGCAATGCT
                               |  ||||| | |    |     |  |||      ||   ||| |   |||    |    |     | |||| ||||||||||||| ||||||||||||||  ||||||| | |||| |  | || |||||||| || |||||  | |||| ||||
-------------------------------gtatgcaaaatttatttatcacgttattcaatgatacataacttaaaacgaaaatacctttactgttgcagATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGTTTGCTCCAGTACTCACCAAATCTAAGATGCACTGCT

upper sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA03G38850.2 (Glycine max), 3'ss of exon 10
---------------atgccagtagatcgaggctc---ctttgt--atcgtgattgcaagaatggggttctttgggatttgcct---------aaccaacgtggtacggg-gttggtgtcgtgatggcagGTTTTCCACAAGCGCATGCCTCCAGAAGCAGTAGATCTGGTTTCAAGGCTACTTCAGTACTCTCCGAATCTGCGGTGCAATGCT
                |   ||    ||| |  |    |||| |  | | |  |   || | |    |   | |  | ||| ||          ||||   || ||     |||| | | ||  |   || | || ||||||||||||||||||||||| || |||||||| ||||| ||||| || ||||| || ||  ||||||||| ||||
gtatcacaaataaatttaatagcctttcgtgttttatactttattcaccatagtgaaaatactaatatatctagtaacttgtcttgtttagcgcaccacactgataaatttgttgatttggtccttctagATCTTTCACAAGCGCATGCCTCCAGAAGCTGTTGATCTGGTATCAAGACTACTACAATACTCCCCTAACTTGCGGTGCACTGCT

upper sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA19G41420.3 (Glycine max), 3'ss of exon 10
---------------------atgccagtagatcgaggctcctttgtatcgtgattgcaagaatggggttctttgggatttgcct---------aaccaacgtggtacggg-gttggtgtcgtgatggcagGTTTTCCACAAGCGCATGCCTCCAGAAGCAGTAGATCTGGTTTCAAGGCTACTTCAGTACTCTCCGAATCTGCGGTGCAATGCT
                     |        | |  |  |||  ||  | | |  |   || | |    |   | |  ||||| ||          ||||   || ||     |||| | | ||  |   || | || ||||||||||||||||||||||| || ||| | || ||||| ||||| || ||||| || ||  |||||||||  |||
gtatcacaaataaatttaataacctttcgtgttttatactctatt-caccatagtgaaaatactaatatatctagtaatttgtcttgtttagtgcaccacactgataaatttgttgatttggtccttctagATCTTTCACAAGCGCATGCCTCCAGAAGCTGTTGATTTAGTATCAAGACTACTACAATACTCCCCTAACTTGCGGTGCACAGCT

upper sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA12G15470.2 (Glycine max), 3'ss of exon 9
------atgccagta--gatcgaggctcctttgtatcgtgattgcaagaatggggttctttgggatttgcctaaccaacgtggtacggggttggtgtcgtgatggcagGTTTTCCACAAGCGCATGCCTCCAGAAGCAGTAGATCTGGTTTCAAGGCTACTTCAGTACTCTCCGAATCTGCGGTGCAATGCT----------------
      |||  || |  ||| || |   | |  || | | | |   || ||   |  | ||||    ||  | |   |  |  |  || | |       || |  ||||||||||||||||| |||||||| |||||| | || || |  |||||||| || || || || || | ||| || |||| |||                 
atgagcatgatagcattgattgatgtaacctactacc-tcactaataggataaag--cattggctagtgaattatgcatttattttggtgct----ctatgttt-cagGTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCACCTAGTCTCCGCTGCACTGCGGTGAGTAGGATGAACT

upper sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA12G15470.1 (Glycine max), 3'ss of exon 9
------atgccagta--gatcgaggctcctttgtatcgtgattgcaagaatggggttctttgggatttgcctaaccaacgtggtacggggttggtgtcgtgatggcagGTTTTCCACAAGCGCATGCCTCCAGAAGCAGTAGATCTGGTTTCAAGGCTACTTCAGTACTCTCCGAATCTGCGGTGCAATGCT
      |||  || |  ||| || |   | |  || | | | |   || ||   |  | ||||    ||  | |   |  |  |  || | |       || |  ||||||||||||||||| |||||||| |||||| | || || |  |||||||| || || || || || | ||| || |||| ||| 
atgagcatgatagcattgattgatgtaacctactacc-tcactaataggataaag--cattggctagtgaattatgcatttattttggtgct----ctatgttt-cagGTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCACCTAGTCTCCGCTGCACTGCG

upper sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA06G42840.1 (Glycine max), 3'ss of exon 9
-atgccagtagatcgaggctcctttgtatcgtgattgcaagaatggggttctttgggatttgcctaaccaacgtggtacggggttggtgtcgtgatgg--cagGTTTTCCACAAGCGCATGCCTCCAGAAGCAGTAGATCTGGTTTCAAGGCTACTTCAGTACTCTCCGAATCTGCGGTGCAATGCT
 |||  |     |  |     | | ||   || |  ||     ||  | |  || |   ||| |||   || |  | |     ||     | | |||   ||||||||||||||||| |||||||| |||||| | || || |  |||||||| || || || || || | ||| || |||| ||| 
gatgtaacctact--acctcacctagtgaagtaaa-gctcagttgttgattattagtcattggctagtgaatgatgcatttatttttatgctttatgtttcagGTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCACCTAGTCTACGCTGCACTGCG

upper sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA19G41420.2 (Glycine max), 3'ss of exon 10
---------------------atgccagtagatcgaggctcctttgtatcgtgattgcaagaatggggttctttgggatttgcctaaccaa---cgtggtacggg-------gttggtgtcgtgatggcagGTTTTCCACAAGCGCATGCCTCCAGAAGCAGTAGATCTGGTTTCAAGGCTACTTCAGTACTCTCCGAATCTGCGGTGCAATGCT----------------
                     |        | |  |  |||  ||  | | |  |   || | |    |   | |  ||||| ||     |   |     || |        |||| | | ||  |   || | || ||||||||||||||||||||||| || ||| | || ||||| ||||| || ||||| || ||  |||||||||  |||                
gtatcacaaataaatttaataacctttcgtgttttatactctatt-caccatagtgaaaatactaatatatctagtaatttgtcttgtttagtgcaccacactgataaatttgttgatttggtccttctagATCTTTCACAAGCGCATGCCTCCAGAAGCTGTTGATTTAGTATCAAGACTACTACAATACTCCCCTAACTTGCGGTGCACAGCTGTGAGTATATTTGACT

upper sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 10
atgccagtagatcgaggctcctttgtatcgtgattgcaagaatggggttctttgggatttgcctaaccaa-cgtggtacggggttggtgtcgtgatggcagGTTTTCCACAAGCGCATGCCTCCAGAAGCAGTAGATCTGGTTTCAAGGCTACTTCAGTACTCTCCGAATCTGCGGTGCAATGCT
                     |||||    | || ||| |  ||    | |   |  | ||| |   |||  |   |     || |            ||| ||||||||||||| ||||| || ||||||||||| || || ||||| || ||||||||||| || || || || |||| ||| 
--------------------gtttgttaaataatcgcagg--tgcctctttggtgcgtgtgcttgttcaaatgaaatttaatgtagcatataactcttcagATTTTCCACAAGCGAATGCCACCTGAAGCAGTAGACCTCGTCTCAAGACTCCTTCAGTACTCACCAAACCTTCGTTGCACTGCA

upper sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv14s0060g00600.t01 (Vitis vinifera), 3'ss of exon 10
atgccagtagatcgaggctcctttgtatcgtgattgcaagaatggggttctttgggatttgcctaaccaacgtggtacggggttggtgtcgtgatggcagGTTTTCCACAAGCGCATGCCTCCAGAAGCAGTAGATCTGGTTTCAAGGCTACTTCAGTACTCTCCGAATCTGCGGTGCAATGCT
 | | || | ||| | |    |   |||   | |||           |||| |    ||  | |||      |  ||     |      | || || ||| | ||||| || ||||||||||||||||| || ||| |||||||||| ||||| ||||||||||| ||||| |||||||  |||
gtactag-aaatcaaagtaaatgcatatatagtttgt----------ttctctcatcttatcataaat----ttttatttattcatatccttgttgccagATATTCCATAAACGCATGCCTCCAGAAGCTGTTGATTTGGTTTCAAGACTACTGCAGTACTCTCCTAATCTACGGTGCACAGCT

upper sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv14s0066g01050.t01 (Vitis vinifera), 3'ss of exon 10
atgccagtagatcgaggctcctttgtatcgtgattgcaagaatggggttctttgggatttgcctaaccaacgtggtacggggttggtgtcgtgatggcagGTTTTCCACAAGCGCATGCCTCCAGAAGCAGTAGATCTGGTTTCAAGGCTACTTCAGTACTCTCCGAATCTGCGGTGCAATGCT
        || ||  |  | || |        ||| ||| ||| |     |||||  ||||    | | |  |  |  |    || | || || | |||| |||| |||||||||||||| ||||||||||||||||| || || || || ||||| |||||||| |||||  |||| | ||||
-----gtgagctcttgatttctatac-cgaccatttcaataattgatgcttttggattttgt---atcgaatttatctgaaaatgttctcttgtttgcagATTTTTCACAAGCGCATGCCCCCAGAAGCAGTAGATCTTGTCTCTAGACTTCTTCAATACTCTCCAAATCTAAGGTGTACTGCT

upper sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 10
atgccagtagatcgaggctcctttgtatcgtgattgcaagaatggggttctttgggatttgcctaaccaacgtggtacggggttggtgtcgtgatggcagGTTTTCCACAAGCGCATGCCTCCAGAAGCAGTAGATCTGGTTTCAAGGCTACTTCAGTACTCTCCGAATCTGCGGTGCAATGCT
                                   | ||||      |  |  || || |  ||  |    ||    |  | |  ||| |  | || ||||||||||||||||| |||||||| |||||||| ||  |||| || ||||| |||||||| || || |  || || |||||||| 
-----------------------------------gtaagagca--atcatccggtatatctctctctc-tgtctctcttgat--gtggctcgttgacagGTTTTCCACAAGCGGATGCCTCCTGAAGCAGTGGACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttctttgggatttgcctaaccaacgtggtacggggttggtgtcgtgatggcagGTTTTCCACAAGCGCATGCCTCCAGAAGCAGTAGATCTGGTTTCAAGGCTACTTCAGTACTCTCCGAATCTGCGGTGCAATGCT
               gcctaac  putative branch site (score: 2)