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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgagaaaaaaatgtctcgtttttttctttgcattgagtgtgtgtttatggatcgtgtttttgacatgctagtcttgctggtggtatagATTATCTCGGGTGTTGAGTACTGTCATAGAAACATGGTCGTTCATCGTGACCTCAAGCCAGAGAATTTGCTTCTCGGCTCCAAATGCAGTGTCAAGATAG

Basic information

species Selaginella moellendorffii
transcript EFJ16445
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ16445 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os05g45420.3 (Oryza sativa), 3'ss of exon 3
--gtacgagaaaaaaatgtctcgtttttttctttgcattgagtgtgtgt-ttatggatcgtgtttttg-acatgctagtcttgctgg-----tggtatagATTATCTCGGGTGTTGAGTACTGTCATAGAAACATGGTCGTTCATCGTGACCTCAAGCCAGAGAATTTGCTTCTCGGCTCCAAATGCAGTGTCAAGATAG
   | ||    | | || |     |||||| | |||||||      | |  |   | | |  |    | | |   |  | ||| | |     ||   ||||| || || |||||||| || || |||||||||||||| ||||||||||| || |||||||||||  | ||| | | ||||||||||| ||| ||||| |
gcttccgcattacagatttggtaattttttatatgcattgtactgatatgcttcagttagcatccgaggataattttcttttgtttgatctttgaattagATCATATCTGGTGTTGAATATTGCCATAGAAACATGGTGGTTCATCGTGATCTTAAGCCAGAGAACCTTCTTTTGGACTCCAAATGCAATGTTAAGATTG

upper sequence: EFJ16445 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os03g17980.2 (Oryza sativa), 3'ss of exon 3
------gtacgagaaaa---aaatgtctcgtttttttctttgcattgagtgtgtgt---ttatggatcgtgtttttgacatgctagtcttgctggtggtatagATTATCTCGGGTGTTGAGTACTGTCATAGAAACATGGTCGTTCATCGTGACCTCAAGCCAGAGAATTTGCTTCTCGGCTCCAAATGCAGTGTCAAGATAG
       || | || ||    | | | || || || |  ||   |||| | ||| |   ||||   || |  | || | | | ||   ||  |  ||| | ||||||| || || ||||| ||||| || ||||||||||| ||||||||||| || |||||||| || ||||| || |  || || |  | ||| ||| | |
attattttatgggagaacttgagtttttcattgttctgatt-tgttgaatatgtatacattatctctcttaatatttataaggtaaaatt--ttatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGATCTGAAGCCAGAAAACTTGCTACTGGATTCAAAGTATAATGTAAAGCTTG

upper sequence: EFJ16445 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os08g37800.1 (Oryza sativa), 3'ss of exon 3
------gtacgagaaa--aaaatgtctcgtttttttctttgcattgagtgtgtgt---ttatggatcgtgtttttgacatgctagtcttgctggtggtatagATTATCTCGGGTGTTGAGTACTGTCATAGAAACATGGTCGTTCATCGTGACCTCAAGCCAGAGAATTTGCTTCTCGGCTCCAAATGCAGTGTCAAGATAG
       || | |||   | | | | || ||  | |  ||   |||| |   | |   ||||   || |  | || | | | ||   ||  |  ||| | ||||||| || || ||||| ||||| || ||||||||||| ||||||||||| || |||||||| || ||||| || |  || || |  |  || ||| | |
attattttatgggaacttagagtttttcattgctctgattttgttgaatacatatacattatttctcttaatatttagaaggtaaaatt--ttatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGATCTGAAGCCAGAAAACTTGCTACTGGATTCAAAGTATAACGTAAAGCTTG

upper sequence: EFJ16445 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G180704_T01 (Zea mays), 3'ss of exon 3
----------------------------------------------------gtacgagaaaaaaatgtctcgt----ttttttctttgcattgagtgtgtgtttatggatcgtgtttttgacatgctagtcttgctggtggtatagATTATCTCGGGTGTTGAGTACTGTCATAGAAACATGGTCGTTCATCGTGACCTCAAGCCAGAGAATTTGCTTCTCGGCTCCAAATGCAGTGTCAAGATAG
                                                     ||| |||| | |     ||      | | |  | | | |     ||||| || |   |  |  | ||  | | || | |   ||  || || ||||||| || |||||||| || || |||||||||||||| || |||||||| || |||||||| ||  | ||  | |  || ||||||| ||| ||||| |
gtgataccatttctttctgtttgtttgtgctacaattatgataaacttaggtttacaagaagacagcaaatcaaaacatctgtgatattcttctcaagtgtgcttgtatgtgatagtattctctttcttgcccc-ctcttgatacagATTATATCCGGTGTTGAATATTGCCATAGAAACATGGTGGTGCATCGTGATCTAAAGCCAGAAAACCTCCTATTGGATTCAAAATGCAATGTTAAGATTG

upper sequence: EFJ16445 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S7_365V6.1 (Physcomitrella patens), 3'ss of exon 2
--gtacgagaaaaaaatgtctcgttt--ttttctttgcattgagtgtgtgtttatggatcgt---gtttttgacatgctagtcttgctggtg--gtatagATTATCTCGGGTGTTGAGTACTGTCATAGAAACATGGTCGTTCATCGTGACCTCAAGCCAGAGAATTTGCTTCTCGGCTCCAAATGCAGTGTCAAGATAG
  |||           ||| |   |    ||| |  | |||  |||||    | | | || |   | ||||  |  |      |||||  ||  |   ||||| | || || || || || || ||| | || ||||| |||||||||||| | ||||||||||| || ||||||| ||||||||| |  ||||||||||
aggtaaattccttggttgtttgaatggaatttttgaggattctgtgtggtcctcttgctcttcaggcttttatctggtataaattgctcatgctgcgcagATTGTGTCTGGCGTGGAATATTGCCATCGGAATATGGTTGTTCATCGTGACTTGAAGCCAGAGAACTTACTTCTCGACTCCAAATGGAACGTCAAGATAG

upper sequence: EFJ16445 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S28_12V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------gtacgagaaaaaaatgtctcgtttttttctttgcattgagtgtgtgtttatggatcgtgtttttgacatgctagtcttgctggtggtatagATTATCTCGGGTGTTGAGTACTGTCATAGAAACATGGTCGTTCATCGTGACCTCAAGCCAGAGAATTTGCTTCTCGGCTCCAAATGCAGTGTCAAGATAG
               ||  |||  | |||||| || |      ||||| |||  |||||   |  |  ||| ||    |||        ||||  |    ||| ||||| | || || || ||||| |||||| | |||||||| |||||||||||| | ||||||||||| || ||||| |  ||||| |  |  |||||||| |
gagagtgtgtcttttgtctgagggataaatgtttcatgaaa--ctttgtatttcgtgtgcactctt--atcttgaagctgattgaactttcttatt--ctgtacagATTGTGTCCGGAGTGGAGTATTGTCATCGGAACATGGTAGTTCATCGTGACTTGAAGCCAGAGAACTTACTTCTTGATTCCAAGTCTAACGTCAAGATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagtgtgtgtttatggatcgtgtttttgacatgctagtcttgctggtggtatagATTATCTCGGGTGTTGAGTACTGTCATAGAAACATGGTCGTTCATCGTGACCTCAAGCCAGAGAATTTGCTTCTCGGCTCCAAATGCAGTGTCAAGATAG
                        ttttgac  putative branch site (score: 3)
        tgtttat  TA-rich tract