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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgctttattatgtgattaaactatctgtgaagaactgtgcacattggagtttggtgtggggagctaccccccttttgacatgattaaatcattttccctggcagGTTCATAATGATGATGAGGTTAGAGCGCTGTTTAAGCAAGTACAAGGTGAAGTCCCTGGCTCCCCAATATTTGTCATGAGGCTTGCATCCCAG

Basic information

species Zea mays
transcript GRMZM5G858094_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G858094_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g22940.1 (Oryza sativa), 3'ss of exon 7
gtgtgctttattatgtgattaaactatctgtgaagaactgtgcacattggagtttggtgtggggagctacccc----ccttttgacatgattaaatcattttccctggcagGTTCATAATGATGATGAGGTTAGAGCGCTGTTTAAGCAAGTACAAGGTGAAGTCCCTGGCTCCCCAATATTTGTCATGAGGCTTGCATCCCAG
      ||| || | |  |  |  ||||     |    |  |       | |||| |||     || || | |    | || | |||||| ||| |||  || | || ||||||||||||||||||||||||||  |  | ||||||||||| ||||| ||||| ||||| |||||||||||| |||||||||| ||  | |||
-----gtttgttct-tcttgtagttatcaagagattgtttggattgcaagtgtttagtgcccatagttaactctggtctttctaacatgagtaactcaactttcttg-cagGTTCATAATGATGATGAGGTTAGGACATTATTTAAGCAAGTTCAAGGCGAAGTACCTGGTTCCCCAATATTTATCATGAGGCTAGCTGCTCAG

upper sequence: GRMZM5G858094_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 3
gtgtgctttattatgtgattaaactatctgtgaagaactgtgcacattggagtttggtgtggggagct-accccccttttgacatgattaaatcattttccctggcagGTTCATAATGATGATGAGGTTAGAGCGCTGTTTAAGCAAGTACAAGGTGAAGTCCCTGGCTCCCCAATATTTGTCATGAGGCTTGCATCCCAG
   ||| | | ||  |     ||| |     |||    |||||  ||   | |||||| ||    | |   |    ||| || |  |  |      |    ||   |||||||||||||||||||||| || ||  |||| |||||||| ||||||||||| || || || || |||||| | |||| | |||||||||||
---tgcataaatacctataagaacaa-----gaaactttgtgccaatcttattttggtatgatttgtttggcaaagtttagaaactaacaggcatatggatcttttagGTTCATAATGATGATGAGGTAAGGGCATTGTTCAAGCAAGTTCAAGGTGAAGTTCCAGGTTCTCCCATATTTATAATGAAGGTTGCATCCCAG

upper sequence: GRMZM5G858094_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 3
gtgtgctttattatgtgattaaactatctgtgaagaactgtgcacattggagtttggtgtggggagct-accccccttttgacatgattaaatcattttccctggcagGTTCATAATGATGATGAGGTTAGAGCGCTGTTTAAGCAAGTACAAGGTGAAGTCCCTGGCTCCCCAATATTTGTCATGAGGCTTGCATCCCAG
   ||| | | ||  |     ||| |     |||    |||||  ||   | |||||| ||    | |   |    ||| || |  | ||      |     |   |||||||||||||||||||||| || ||  |||| |||||||| ||||||||||| || || || || |||||| | |||| | |||||||||||
---tgcataaatacctataagaacaa-----gaaactttgtgccaatcttattttggtatgatttgtttggcaaagtttagaaactaataggcatatggattttttagGTTCATAATGATGATGAGGTAAGGGCATTGTTCAAGCAAGTTCAAGGTGAAGTTCCGGGTTCACCCATATTTATAATGAAGGTTGCATCCCAG

upper sequence: GRMZM5G858094_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT1G36180.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgtgctttattatgtgattaaactatctgtgaagaactgtgcacattggagtttggtgtggggagctaccccccttttgacatgattaaatcattttccctggcagGTTCATAATGATGATGAGGTTAGAGCGCTGTTTAAGCAAGTACAAGGTGAAGTCCCTGGCTCCCCAATATTTGTCATGAGGCTTGCATCCCAG
                       ||   | || |||  ||     | ||    ||  |      ||| |        ||    |  ||   |||||||    |  ||||||||||||||||||||||||| || || || |||||||| |||||||| ||||| ||||| || |||||| | |||| | |||| || |||
---------------------gtctgcttctgtagatatg-----actgtcactttttccactaagccaaagtgtacttattgtagtttt-tcattttg---gtaagGTTCATAATGATGATGAGGTTAGGGCTCTATTCAAGCAAGTTCAAGGTGAGGTCCCGGGCTCGCCGATATTTATAATGAAGGTTGCTTCACAG

upper sequence: GRMZM5G858094_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT1G36160.2 (Arabidopsis thaliana), 3'ss of exon 4
gtgtgctttattatgtgattaaactatctgtgaagaactgtgcacattggagtttggtgtggggagctaccccccttttgacatgattaaatcattttccctggcagGTTCATAATGATGATGAGGTTAGAGCGCTGTTTAAGCAAGTACAAGGTGAAGTCCCTGGCTCCCCAATATTTGTCATGAGGCTTGCATCCCAG
                       |    | || |||  | ||| | || || | |||  |  |  | |  |    |    || |  |    |  |||    |   ||||||||||||||||||||||||| || || || |||||||| || ||||| ||||| ||||| ||||||||  | |||| | |||| || |||
---------------------gtcagcttctgtaga--tatgc-cttttgattgtggactaagccgattactatataagtacttattctggt--tttaaatttatagGTTCATAATGATGATGAGGTTAGGGCTCTATTCAAGCAAGTTCAGGGTGAGGTCCCAGGCTCACCAATATTCATAATGAAGGTTGCGTCACAG

upper sequence: GRMZM5G858094_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 4
gtgtgctttattatgtgattaaactatctgtgaagaactgtgcacattggagtttggtgtggggagctaccccccttttgacatga-------ttaaatcattttcc--ctggcagGTTCATAATGATGATGAGGTTAGAGCGCTGTTTAAGCAAGTACAAGGTGAAGTCCCTGGCTCCCCAATATTTGTCATGAGGCTTGCATCCCAG
                ||    ||    | ||  ||  ||   |  ||||| | |  ||         |   | |   ||| ||||        | | |||||||    ||   ||||||||||||||||||| || |  ||  |||| |||||||| ||||||||||| ||||||||||| |||||    |||| | |||| ||||||
----------------gaagtcacgggttatgttgagatgattagtttggactgtcatgattttcctaatttctcaactgaaatgaagttaaccttattcatttttgaacttttagGTTCATAATGATGATGAAGTCAAGGCTTTGTTCAAGCAAGTTCAAGGTGAAGTTCCTGGCTCCCCCATATTCACGATGAAGGTTGCTTCCCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggtgtggggagctaccccccttttgacatgattaaatcattttccctggcagGTTCATAATGATGATGAGGTTAGAGCGCTGTTTAAGCAAGTACAAGGTGAAGTCCCTGGCTCCCCAATATTTGTCATGAGGCTTGCATCCCAG
                       ttttgac  putative branch site (score: 3)
                                       tcattttccct  putative PPT
                              atgattaaatcatttt  TA-rich tract