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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgatttgcttattatcctccacaactactcatattgctcatactttgtgtacaatgtaagccaaactatcaatctttttttttaatttattactttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGTGCCGAAGATGAAGTCAATGTTGCATGCTTTCATCCTTTACCAGGAGGTGGCCTTG

Basic information

species Zea mays
transcript GRMZM2G353548_T04
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G353548_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os02g18820.2 (Oryza sativa), 3'ss of exon 13
aatgatttgcttattatcctccacaactactcatattgctcata--ctttgtgtacaat-gtaagccaaactatcaatctttttttttaatttattactttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGTGCCGAAGATGAAGTCAATGTTGCATGCTTTCATCCTTTACCAGGAGGTGGCCTTG
  | || || | |||     |  |   | ||  |    || | |  ||  ||    | |  | |   || |  | |     || ||   ||| || || |||||| |||||||| || || |||||||| || ||||| ||||||||||| ||||||||||| || |||||||||||||||||||  || |||||||| ||||
--tcatgtgttaattgcttgctccggtttct-gtgccacttacaagctcagttcttacttatgaatgaagccttaatctcattattcctattcatcacgttagGTCTATAGAGTATCGGACATGGAGCTGGTAAGAGTTCTTCCTAGTGCTGAAGATGAAGTAAACGTTGCATGCTTTCATCCTTCCCCTGGAGGTGGTCTTG

upper sequence: GRMZM2G353548_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA19G35370.3 (Glycine max), 3'ss of exon 11
aatgatttgc-ttattatcctccacaactactcatattgctcatactttgtgtacaatgtaagccaaactatca-atctttttttttaatttattactttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGTGCCGAAGATGAAGTCAATGTTGCATGCTTTCATCCTTTACCAGGAGGTGGCCTTG
   |       || || || | || |   |   ||     |  |    |    |   | | || |  | | | |  |||||   |||  ||| |   |||||||||| ||||| ||||||||||| ||||| || |||||||||||||| |||||||| |||||||| |||||||||||||||||  | ||||| || || |
gccggcacaaattgttgtcattcata-tcatctatgccctttttgtagttctaatggttttagtctgaatttaatgtctttgaatttgctttgtc-ttttagGTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAAGATGAGGTCAATGTGGCATGCTTTCATCCTTTTGCCGGAGGAGGACTAG

upper sequence: GRMZM2G353548_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA03G32620.4 (Glycine max), 3'ss of exon 11
aatgatttgc-ttattatcctccacaactact-catattgctcatactttgtgtacaatgtaagccaaactatcaatctttttttttaatttattactttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGTGCCGAAGATGAAGTCAATGTTGCATGCTTTCATCCTTTACCAGGAGGTGGCCTTG
  ||       || ||  | | || | |  ||      |  |  || ||    |    | ||| |  || |     ||| |   |||  ||| |   |||||||||| | ||| ||||||||||| ||||| || |||||||||||||| ||||| || |||||||| |||||||||||||||||  | || || || || |
gctggcacaaattgttgccattcatatcatctatgccctttttgtagttcaaatg-gttttaatctgaatttaatgtctatgaatttgctttgtc-ttttagGTATACAAAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAAGACGAGGTCAATGTGGCATGCTTTCATCCTTTTGCTGGGGGAGGACTAG

upper sequence: GRMZM2G353548_T01 (Zea mays), 3'ss of exon 12
lower sequence: AT1G04140.1 (Arabidopsis thaliana), 3'ss of exon 11
----------------------------------------------aatgatttgcttat--tatcctccacaactactcatattgctcatactttgtgtacaatgtaagccaaactatcaatctttttttttaatttattactttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGTGCCGAAGATGAAGTCAATGTTGCATGCTTTCATCCTTTACCAGGAGGTGGCCTTG
                                              |||| || ||  ||   ||  |  |  | ||   ||||     | |||| |  ||  ||  |||  |   ||       |||||     | |||| ||| || | || ||||||||||||||||| || |||||||| ||||| ||  | || |||||||| |||||||| |||||||||||||  || || || || ||||
gtaacgtctatgctccagtagttatgaatttctagaccagcagaacaatgtttagcagatgccattttatatcattaactatat-----acacttggaatatcatacaag--agtttagactgtgtttttccctttctattccttcagATTTACAGAGTTTCAGATATGGAACTGGTGAGAGTACTTCCAAGCTCAGAGGATGAAGTTAATGTTGCTTGCTTTCATCCTTCTCCTGGGGGAGGTCTTG

upper sequence: GRMZM2G353548_T01 (Zea mays), 3'ss of exon 12
lower sequence: AT5G43930.1 (Arabidopsis thaliana), 3'ss of exon 11
aatgatttgcttattatcctccacaactactcatattgctcatac-tttgtgtacaatgtaagccaaactatcaatctttttttttaatttattactttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGTGCCGAAGATGAAGTCAATGTTGCATGCTTTCATCCTTTACCAGGAGGTGGCCTTG
                        ||   || ||  | ||  ||| |   ||| ||      |   |  || ||      || |||   |       | || |||| ||||||||||||||||||||||||||||| || || ||| | || |||||||| || ||||| || ||||||||||  || ||||| || ||||
----------------------gtaaagccttatgctactagtacatccatgttcagaacttggagatataacacagaacttgtttgtgtgggccggtcagATATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTGCCAAGTTCAGAGGATGAAGTGAACGTTGCGTGTTTTCATCCTTCTCCTGGAGGAGGTCTTG

upper sequence: GRMZM2G353548_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv05s0077g00140.t01 (Vitis vinifera), 3'ss of exon 11
----aatgatttgcttattatcctccacaactactcatattgctcatactttgtgtacaatgtaagccaaactatcaatctttttttttaatttattactttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGTGCCGAAGATGAAGTCAATGTTGCATGCTTTCATCCTTTACCAGGAGGTGGCCTTG
    | | || |  | |||||       ||   ||   |||  | ||   || | |    | ||    |   | ||||  ||     |   ||||| | |  |||| || |||||||| |||||||| ||||||||||| ||||||||||| || ||||| || ||||| || |||||||||||||     |||||||||||||
tgctacttatgttgtgattataggaataaaactcttggattttttatttatttttttatttctatttta---tttcaactttcaaaatatttttatca-tgcagGTCTACAGAGTTTCTGATATGGAACTTGTGAGAGTTCTTCCTAGTGCAGAGGATGAGGTTAATGTAGCTTGCTTTCATCCTTCTGTTGGAGGTGGCCTTG

upper sequence: GRMZM2G353548_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 11
-------------------------------aatgatt-tgcttattatcctccacaactactcatattgctca--tactttgtgtacaatgtaagccaaactatc--aatcttt----ttttttaatttattact-----ttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGTGCCGAAGATGAAGTCAATGTTGCATGCTTTCATCCTTTACCAGGAGGTGGCCTTG
                               | | | | || |  | |   ||  ||| |     |  || |||  |||||| |   |  |  ||  |  ||| |    ||||||    | |   |   | ||  |     | |||| ||  |||| ||||||||||| ||||| ||||||||||| ||||| |||||||| |||||||| || ||||||||||||||||| ||||| || ||||
gtaacacttcaaaattttaatagcattaggcagtaaatatggtactgaagatctccaattgaa-gtgctggtcaagtactttattatctgttcaaatcttactgttctgatctttcaggtctcacaggctctttttgtcactcagGTTTACCGAGTCTCAGATATGGAACTTGTTAGAGTGCTTCCCAGTGCTGAAGATGAGGTCAATGTAGCTTGCTTTCATCCTTTACCTGGAGGAGGTCTTG

upper sequence: GRMZM2G353548_T01 (Zea mays), 3'ss of exon 12
lower sequence: PP1S150_95V6.1 (Physcomitrella patens), 3'ss of exon 11
----------------------------------------------------------------aatgatttgcttattatcctccacaactactcatattgctcatactttgtgtacaatgtaagccaaactatcaatctttttttttaatttattactttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGTGCCGAAGATGAAGTCAATGTTGCATGCTTTCATCCTTTACCAGGAGGTGGCCTTG
                                                                ||  |||||    | | | ||     ||| |  |  ||||         |    ||| | |      | | | | || | | | |  | | ||     |||| || |||||||||||||||||||||||||| ||  | |||||||| |||||||| || ||||| || |||||||||||   |   || ||||| ||||
gtttgggattcttttcattcaacccaatagtcttagtggcaagtaactacttgtgtaacttttaaaaaatttgacagtgaacgtcagtt-cta-tattcctgcttgattcagttaagtaattttacttgggccaacca-ctgtctctctcttgtgttttaacagGTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAAGATGAGGTGAATGTGGCGTGCTTTCATCCCCAAGTTGGTGGTGGTCTTG

upper sequence: GRMZM2G353548_T01 (Zea mays), 3'ss of exon 12
lower sequence: PP1S58_234V6.1 (Physcomitrella patens), 3'ss of exon 12
----------------------------------------------------------------aatgatttgcttattatcctccacaactactcatattgc--tcatactt-tgtgtacaatgtaagcc----aaactatcaatc--tttttttttaatttattactttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGTGCCGAAGATGAAGTCAATGTTGCATGCTTTCATCCTTTACCAGGAGGTGGCCTTG
                                                                  || ||| | |     || |    | |    ||  | |  || |||||  ||  | ||   || |       ||||   |    |||| | ||  | | ||   | ||||||| ||||||||||||||||||||||||||||| ||||| ||||| || |||||||| ||||| || || ||||||||   |   || || || ||||
gtttgaatatcttctctcagtcacgctcttgcaagtcgctatctgtgtccccttggttccttgacgtgtttttcctgagtcccacagtgaatggcaattctacattcctacttgcgttgataactcaatcttcctggactaagcacaggttttctctttttctgttcaatcagGTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAGGATGAAGTGAATGTGGCGTGTTTTCATCCCCAAGTTGGTGGCGGTCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtgtacaatgtaagccaaactatcaatctttttttttaatttattactttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGTGCCGAAGATGAAGTCAATGTTGCATGCTTTCATCCTTTACCAGGAGGTGGCCTTG
                                    ttttaat  putative branch site (score: 3)
                                              ttacttt  putative PPT
                   aaactatcaatctttt  TA-rich tract