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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattctcacaaacattgttaagtggtattatttgtcttctgaattacttgaaatttgataaagtgatgttgttatggaatcagTTTGATTATCTTAAGAGCTTGGAAATTGAAGAGAAGATTAACCAAATAAAATGGTGTCAAGCAGCAAATGGTGCATTGTATCTTCTATCCACAAATGACA

Basic information

species Zea mays
transcript GRMZM2G164185_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 3
gtatattctcacaaac--attgttaagtggtattatttgtcttctgaattacttgaaatttgataaagtgatgttgttatggaatcagTTTGATTATCTTAAGAGCTTGGAAATTGAAGAGAAGATTAACCAAATAAAATGGTGTCAAGCAGCAAATGGTGCATTGTATCTTCTATCCACAAATGACA
||||||| |   | ||  | || | ||||  | ||  |||      |||| || |   ||| |  || |  | |||| |||  || ||||||||||||| |||||||||||||||||||||||||||||| | ||||| ||||| ||| |||||||||| ||||||| |||||| ||||||||||| |
gtatattgtacaagactaactgcttagtga-agtacctgt------aatttct-gttgtttaactaatttgtcttgtcatgcgattagTTTGATTATCTGAAGAGCTTGGAAATTGAAGAGAAGATTAACAAGATAAAGTGGTGCCAAACAGCAAATGGAGCATTGTTTCTTCTGTCCACAAATGATA

upper sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 3
gtatattctcacaaacattgttaagtggtat------tatttgtcttctgaattacttgaaatttgataaagtgatgttgttatggaatcagTTTGATTATCTTAAGAGCTTGGAAATTGAAGAGAAGATTAACCAAATAAAATGGTGTCAAGCAGCAAATGGTGCATTGTATCTTCTATCCACAAATGACA
   || | |  ||  || || | | || |        |  ||||       |   ||| | |||| || |  ||   ||||| |    ||||||||| |||||||||||  ||||||| |||||||| |||||| |||| |||||||| ||| |||| |||||||| ||||  ||||||||||||||||| |
--gtaatttt-cagtcactggttaatgctgcccgaaatgcttgtggagcagaaatcttaacattt-atgacttgtgattgttgt---ttcagTTTGACTATCTTAAGAGTCTGGAAATAGAAGAGAAAATTAACAAAATCAAATGGTGCCAAACAGCTAATGGTGCTTTGTTCCTTCTATCCACAAATGATA

upper sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 3
gtatattctcacaaacattgttaagtggtattatttgtcttctgaattacttgaa--atttgataaagtgatgttgttatggaatcagTTTGATTATCTTAAGAGCTTGGAAATTGAAGAGAAGATTAACCAAATAAAATGGTGTCAAGCAGCAAATGGTGCATTGTATCTTCTATCCACAAATGACA
||| ||  |||        || | || | |  |    || | ||  | |   ||   | |   || | || | |  | || |  ||||||||| ||||||||||| ||||||||||||||||| || ||| |||| | |||||| |||  ||| ||||||||  | |  ||||| || |||||||| |
gta-atcatcatttggtcagtaatgttgcaccaac-atcctatgggtcagaagagtcaatatttataatg-tatgatcattgtttcagTTTGACTATCTTAAGAGTTTGGAAATTGAAGAGAAAATCAACAAAATCAGATGGTGCCAAATAGCTAATGGTGCCCTCTTCCTTCTTTCTACAAATGATA

upper sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 3
gtatattctcacaaacattgttaagtggtattatttgtcttctgaattacttgaa--atttgataaagtgatgttgttatggaatcagTTTGATTATCTTAAGAGCTTGGAAATTGAAGAGAAGATTAACCAAATAAAATGGTGTCAAGCAGCAAATGGTGCATTGTATCTTCTATCCACAAATGACA
||| ||  |||        || | || | |  |    || | ||  | |   ||   | |   || |    | |  | || |  ||||||||| ||||||||||| ||||| ||||||||||| || ||| |||| | |||||| ||| |||| ||||||||  |||  ||||| || |||||||| |
gta-atcatcatttggtcagtaatgttgcaccaac-atcctatgggtcagaagagtcaatatttataaatgtatgatcattgtttcagTTTGACTATCTTAAGAGTTTGGAGATTGAAGAGAAAATCAACAAAATCAGATGGTGCCAAACAGCTAATGGTGCCCTGTTCCTTCTTTCTACAAATGATA

upper sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 3
gtatattctcacaaacattgttaagtggtattatttgt-cttctgaattacttgaaat-ttgata---aagtgatgttgttatggaatcagTTTGATTATCTTAAGAGCTTGGAAATTGAAGAGAAGATTAACCAAATAAAATGGTGTCAAGCAGCAAATGGTGCATTGTATCTTCTATCCACAAATGACA
   || | |  ||  || || | | || |        | ||| || |  |   ||||| || | |   | |  ||||  || | |  ||||||||| ||||||||||| |||||||| |||||||| |||||| |||| |||||||| ||| |||| |||||||| ||||  ||||||||||||||||| |
--gtaatttt-cagtcactggttaatgctgcctgaaatgcttgtggagca---gaaatgttaacatttatgacatgtgattgttgtttcagTTTGACTATCTTAAGAGTTTGGAAATAGAAGAGAAAATTAACAAAATCAAATGGTGCCAAACAGCCAATGGTGCTTTGTTCCTTCTATCCACAAATGATA

upper sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 3
gtatattctcacaaacattgttaagtggtattatttgtcttctgaattacttgaa--atttgataaagtgatgttgttatg-gaatcagTTTGATTATCTTAAGAGCTTGGAAATTGAAGAGAAGATTAACCAAATAAAATGGTGTCAAGCAGCAAATGGTGCATTGTATCTTCTATCCACAAATGACA
   ||   | | |   ||    |  |   | |          ||  || |||||   | |  ||||  |    ||   ||  |  ||||||||| ||||| ||||| ||||| || || ||||| || ||| |||| | |||||||||  |||| ||||||||||||| ||| || || ||||| || |
--gtacattaaaacttatcaccagatttcacttacgagtaattgtgttccttgagctactcaataagcttgcttttcaatctgtttcagTTTGACTATCTCAAGAGTTTGGAGATAGAGGAGAAAATCAACAAAATCAGATGGTGTCAGCCAGCTAATGGTGCATTGTTTCTGCTTTCTACAAACGATA

upper sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 5
gtat---attctcacaaacattgttaagtggtattatttgtct-tctgaattacttgaaatttgataaagtgatgttgttatggaatcagTTTGATTATCTTAAGAGCTTGGAAATTGAAGAGAAGATTAACCAAATAAAATGGTGTCAAGCAGCAAATGGTGCATTGTATCTTCTATCCACAAATGACA
||||   |||  | |     |  |          |||||| || |     |||  ||   ||| ||    |    |||||     | ||||||||||| || ||||| ||||| || || ||||| |||||| |||| | |||||||||| |||||||||| ||  | | ||| || || || ||||| |
gtatttgatttactctgttttcttcttactcagctatttggctataccttttatctgtcttttcatgctctatccttgttt----accagTTTGATTACCTCAAGAGTTTGGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATA

upper sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 3
gtatattctcacaaacattgttaag----tggtattatttgtcttc-tgaatt---acttgaaatttgataaagtgatgttgttatggaat---cagTTTGATTATCTTAAGAGCTTGGAAATTGAAGAGAAGATTAACCAAATAAAATGGTGTCAAGCAGCAAATGGTGCATTGTATCTTCTATCCACAAATGACA
|||| | ||        ||| |||     |  |  |  | || |||  | |||   | ||     ||  ||||   |   | ||     ||   |||||||||||||| ||||| |||||||| || ||||| || ||  | || | |||||||||| |||| ||   |||||||| |||||| ||||| |||||||
gtatttacttttctgtgttgctaacactctaatcattgtagttttcacggatttgtatttttttcttactaaatctagactattcgttcatttccagTTTGATTATCTCAAGAGTTTGGAAATAGAGGAGAAAATCAATAAGATTAGATGGTGTCAAACAGCTAACAATGCATTGTTTCTTCTCTCCACCAATGACA

upper sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------gtatattctcacaaacattgttaagtggtattatttgtcttctgaattacttgaaatttg--ataaagtgatgttgtta-------tggaatcagTTTGATTATCTTAAGAGCTTGGAAATTGAAGAGAAGATTAACCAAATAAAATGGTGTCAAGCAGCAAATGGTGCATTGTATCTTCTATCCACAAATGACA
                         |  |  |       ||  | |    |  | || | |||||||     |   || | | ||  ||  | |  ||   |||       || | ||||||||| ||||| ||||||||||||||||| ||||| || ||| | || | |||||||||  |||| ||  | ||| ||| |||||| ||||| ||||| |
gtgtcctttaagaatttcgtttctgggttgctgatgattaccatatccttttatcttgtctgtcttccatccttactggactctggaatttaattctgcatttaatatgtttgaattcagTTTGACTATCTCAAGAGCTTGGAAATTGAGGAGAAAATCAACAAGATTAGATGGTGTCAGACAGCTAACAGCGCACTGTTTCTTCTCTCCACTAATGATA

upper sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 3
---------------gtatattctcacaaacattgttaagtggtattatttgtct-------tctgaattacttgaaatt-tgataaagtgatgttgttatggaatcagTTTGATTATCTTAAGAGCTTGGAAATTGAAGAGAAGATTAACCAAATAAAATGGTGTCAAGCAGCAAATGGTGCATTGTATCTTCTATCCACAAATGACA
               ||   | ||  |  |  ||  |  |    |   ||||          |||||| |  || || |  ||  | | || |  |  | ||   ||||||||| ||||| |||||||||||||| || ||||| || ||  | || | |||||| ||  |||||||||||||  ||| ||||||||| || ||||| |
gtatttctttcatcagttactcctgcctgaagtttgtttgcaccaccctttgctcactaggctctgaaatgttttaattgatgccacattgcttattctctgtgctcagTTTGACTATCTGAAGAGCTTGGAAATAGAGGAGAAAATCAATAAGATCAGATGGTGCCAGACAGCAAATGGTGCCCTGTTTCTTCTATCTACGAATGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttgtcttctgaattacttgaaatttgataaagtgatgttgttatggaatcagTTTGATTATCTTAAGAGCTTGGAAATTGAAGAGAAGATTAACCAAATAAAATGGTGTCAAGCAGCAAATGGTGCATTGTATCTTCTATCCACAAATGACA
                        atttgat  putative branch site (score: 5)
             aattacttgaaatttg  TA-rich tract