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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatgcaactgctttctgagtttatgtgtcctcctgctttctctttgctcaaattctaatgaaagatttttcttgtggttaagGTTTTGTGTTCTGCTTGGAAAGATGATGGAACCACAGTCTTTACCGGAGGATGTGATAAGCAGGCAAAAATGTGGCCATTGTTGTCTGGTGCTCAACCAT

Basic information

species Arabidopsis thaliana
transcript AT1G15850.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G15850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os08g07960.2 (Oryza sativa), 3'ss of exon 4
--------gtaatatgcaactgctttctgagtttatgtgtcctcctgctttctctttgctcaaattc----taatgaaagatttttcttgtggttaagGTTTTGTGTTCTGCTTGGAAAGATGATGGAACCACAGTCTTTACCGGAGGATGTGATAAGCAGGCAAAAATGTGGCCATTGTTGTCTGGTGCTCAACCAT
          |||||    ||     |    || |  |    | | |  ||   ||| ||   |||     |  | |  ||||| | || |   | ||||  | ||||| |||||||| ||||||||||| || || ||  | ||||| |||||||| || | ||||||||||||  ||||||||||||  ||  |  
gtatgatctcaatatttctctcaagaccacattcacataatgtacagtattgattttcctagtatttagtgtgctcattgatttgttttcta--tcagGTCCTCTGTTCAGCTTGGAAGGATGATGGAACTACTGTGTTCTCTGGAGGCTGTGATAAACAAGTAAAAATGTGGCCTCTGTTGTCTGGTGGGCAGGCTC

upper sequence: AT1G15850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G058498_T01 (Zea mays), 3'ss of exon 4
--------------------gtaatatgcaactgctttc--tgagtttatgtgtcctcctgctttctctttgctcaaattctaatgaaagatttttcttgtggttaagGTTTTGTGTTCTGCTTGGAAAGATGATGGAACCACAGTCTTTACCGGAGGATGTGATAAGCAGGCAAAAATGTGGCCATTGTTGTCTGGTGCTCAACCAT
                    |  |||||  | |   ||   |  |    |   |  || | | |    ||||       | |  | |  ||||| | |  |  || ||||| | || || |||||||| ||||||||||| || |||||  | ||||| ||||| |||||||  |||||||||||  |  |||| ||||  || ||  
gtatgatcttagtgttttctgggatatgttaatatatttgattgggcggtagattgtcttccatgtagtttgtatctggtatcctcattgatttgtttcct--tttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGCTGTGACAAGCAGGTCAAAATGTGGCCTCTTCTGTCAGGTGGGCAGCCTC

upper sequence: AT1G15850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA01G09290.1 (Glycine max), 3'ss of exon 3
--------gtaatatgcaactgctttctgagtttatgtgtcctcctgctt------tctctttgctcaaattctaatgaaagatttttcttgtggtt--aagGTTTTGTGTTCTGCTTGGAAAGATGATGGAACCACAGTCTTTACCGGAGGATGTGATAAGCAGGCAAAAATGTGGCCATTGTTGTCTGGTGCTCAACCAT
        |||   ||  | |      | |   | | ||   ||    ||      |  | || |  |  || |  |    | ||| | |||| |||  ||||||||||| || |||||||| ||||||||||| ||||| ||| | || || ||||| |||||||  || ||||||||| |    |||||||  || ||| 
taggatttgtagattgggaatctacatttaccatgtttggtatcaattttaaaaaatgacattcccgatgttttgtttt--gttttgttttgttgtttgaagGTTTTGTGCTCCGCTTGGAAGGATGATGGAACAACAGTTTTTTCTGGGGGCTGTGACAAGCAGGTCAAGATGTGGCCACTAACATCTGGTGGGCAGCCAA

upper sequence: AT1G15850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv12s0055g00900.t01 (Vitis vinifera), 3'ss of exon 4
gtaatatgcaactgctttct----gagtttatgtgtcctcctgctttctctttgctc-aaattctaatgaaagatttt---------------tcttgtggttaagGTTTTGTGTTCTGCTTGGAAAGATGATGGAACCACAGTCTTTACCGGAGGATGTGATAAGCAGGCAAAAATGTGGCCATTGTTGTCTGGTGCTCAACCAT
|||| |    | |   || |     | | ||  | |     |  |||   |||  |  ||||| |  |    ||||||               | || | ||  ||||| | || ||||||||||| ||||||||||| || |||||  | ||||| ||||| ||||| |  ||||||||||| ||||||||||| |  |||||  
gtaacaaattattctatttttacaaaatctacatttttatttatttttctttttttggaaatttttgttttggattttaaatttggtacatgttatttttgtgtagGTTCTATGCTCTGCTTGGAAGGATGATGGAACAACTGTCTTCTCTGGAGGCTGTGACAAGCAAGTGAAAATGTGGCCTTTGTTGTCTGGCGGGCAACCTA

upper sequence: AT1G15850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv09s0002g09150.t01 (Vitis vinifera), 3'ss of exon 3
gtaatatgcaactgctttctgagtttatgtgtcctcctgct---ttctctttgctcaaattctaatgaaagatttttcttgtggttaagGTTTTGTGTTCTGCTTGGAAAGATGATGGAACCACAGTCTTTACCGGAGGATGTGATAAGCAGGCAAAAATGTGGCCATTGTTGTCTGGTGCTCAACCAT
    ||   |||     |   |||  || | |   |   ||   || ||| |  |  |||   ||      |  | || | |  |  |||||||||| || |||||||| ||||||||||| |  |||||| | ||||| ||||| ||||| |  || |||||||| ||| ||||||||| ||||||| 
---gtaaaaaaccaaagttgaagtccatatttttacacactcagttttctgttgttgaatctaaaactgtaaaatctcattttttacagGTTTTGTGCTCGGCTTGGAAGGATGATGGAACAATTGTCTTTTCTGGAGGCTGTGACAAGCAAGTGAAGATGTGGCCTTTGCTGTCTGGTGGTCAACCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctcctgctttctctttgctcaaattctaatgaaagatttttcttgtggttaagGTTTTGTGTTCTGCTTGGAAAGATGATGGAACCACAGTCTTTACCGGAGGATGTGATAAGCAGGCAAAAATGTGGCCATTGTTGTCTGGTGCTCAACCAT
                         ttctaat  putative branch site (score: 2)
                                      tttttcttgt  putative PPT
                      aaattctaatgaaaga  TA-rich tract