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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagattgtgtatgcttggttcttatttcttttccttctttttgttttctaattatgaccttctgctacatgatgcctgttgactatcaacttccatactcattttttttcagGCCATTCTGTTGTTTCAGAAGATTGAAGGTGTTGAAGTATGCTTATTTGGCATGTATGTCCAGGAATTTGGAACAGATTCTGCGTCTCCCAATCAGCGCC

Basic information

species Arabidopsis thaliana
transcript AT3G12980.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G12980.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os06g49130.2 (Oryza sativa), 3'ss of exon 8
-----------------gtacagattgtgtatgcttggttcttatttcttttccttctt-----tttgttttctaattatgaccttct--gctacatgatgcctgttgactatcaacttccatactcattt-------tttttcagGCCATTCTGTTGTTTCAGAAGATTGAAGGTGTTGAAGTATGCTTATTTGGCATGTATGTCCAGGAATTTGGAACAGATTCTGCGTCTCCCAATCAGCGCC
                   |       | | || | |  ||||  |  |  |  ||||      ||  ||   |||| |     || |    || || | |    |  | |   || |  | |   |||||       |||| ||||| ||||| || |||||||| || |||||||| ||||||||||||||||||||||||||||| |||| |||  |||| |     |  || || || || |
gtgagaaagtggtctgatcatttgaaatatgtgatcgcctcttgatgttagtagttctaagaaattctttccgtaatgaaagttttattaaataaatcaagaaaataaaatcctaattctctttaacatttccaaatattttgcagGCTATTCTTTTATTTCAGAAAATAGAAGGTGTGGAAGTATGCTTATTTGGCATGTATGTCCAAGAATATGGTGCAGAATGCAAATTCCCAAACCAACGTC

upper sequence: AT3G12980.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G470556_T01 (Zea mays), 3'ss of exon 8
gtacagattgtgtatgcttggttcttatttcttttccttctttttgttttctaattatgaccttctgctaca-tgatgcctgttgactatcaacttccatactcattttttttcagGCCATTCTGTTGTTTCAGAAGATTGAAGGTGTTGAAGTATGCTTATTTGGCATGTATGTCCAGGAATTTGGAACAGATTCTGCGTCTCCCAATCAGCGCC
                           |     ||| ||||| |  |||   ||  ||||      | |||| | |    | |   | |     ||   ||   | | ||   |||||  |||| ||||| ||||  || |||||||| ||||||||  |||||||||||||||| || ||||||||  |||| |   | || || || |||||||
--------------------------gtaagaattcattcttgtcatttg--aagcatgaatcgtagttacactcactaatttctgcaacactattttttatgaaatgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGCATGTATGTTCAAGAATTTGGTGCAGAATGCTCTTCCCCGAACCAGCGCC

upper sequence: AT3G12980.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 9
gtacagattgtgtatgcttggttcttatttcttttccttctttttgttttctaattatgaccttctgctacatgatgcctgttgactatcaacttccatactcattttttttcagGCCATTCTGTTGTTTCAGAAGATTGAAGGTGTTGAAGTATGCTTATTTGGCATGTATGTCCAGGAATTTGGAACAGATTCTGCGTCTCCCAATCAGCGCC
         ||  | |   ||||  | ||     |  |  | || ||  || | |  | |   | |  |   ||     || ||||| |    ||||||           ||||||  ||  ||||||||||||||||||||||||| ||||||||| | |||||||||||||| || || |||||| | || | |   | ||| ||||| || |
---------gtaaagggaaggttgct-ttagagctagtcatgttggtaatcaagtcgttattatttattc--tggattttgatgacttttggtttccat-----------ttcagGTAATCTTGTTGTTTCAGAAGATTGAAGGTGTGGAAGTATGCCTCTTTGGCATGTATGTTCAAGAGTTTGGATCTGAATGTCAATTTCCGAATCAACGGC

upper sequence: AT3G12980.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 11
gtacagattgtgtatgcttggttcttatttcttttccttctttttgttttctaattatgaccttctgcta--catgatgcctgttgactatcaacttccatactcattttttttcagGCCATTCTGTTGTTTCAGAAGATTGAAGGTGTTGAAGTATGCTTATTTGGCATGTATGTCCAGGAATTTGGAACAGATTCTGCGTCTCCCAATCAGCGCC
                                |          ||| ||| | | | ||| | |   | |  ||| |  | ||   | |||    | || |   | || | || ||||   || |||||||||| ||||| |||||||| ||||| ||| |||||||||||||||| || ||||||||| | || | |   | ||| ||||||||||
-------------------------------gtgatgagaaagttgatttatcaatctgatcgtaatcgaatcattaatcatgaatattatttgatgcccttagctttctattccagGTAGTTTTGTTGTTTCAAAAGATAGAAGGTGTGGAAGTTTGCCTATTTGGCATGTATGTTCAAGAATTTGGATCTGAATGTCAATTTCCTAATCAGCGCC

upper sequence: AT3G12980.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 9
gtacagattgtgtatgcttggttcttatttcttttccttctttttgttttctaattatgaccttctgctacatgatgcctgttgactatcaacttccatactcattttttttcagGCCATTCTGTTGTTTCAGAAGATTGAAGGTGTTGAAGTATGCTTATTTGGCATGTATGTCCAGGAATTTGGAACAGATTCTGCGTCTCCCAATCAGCGCC
              || | ||    |   | || ||| ||   ||||  || ||| || |          |||||   || ||||        |||| |   | || | || ||||   || |||||||||| | ||| |||||||| ||||| ||| |||||||||||||||| || ||||||||| | || | |   | ||| ||||||||||
-------------gtgatgggaaagttgattttatccatccgattgtaatcaaatcattaat--------catgaatacttttga--------ttcccttagctttctattccagGTAGTTTTGTTGTTTCAAAGGATAGAAGGTGTGGAAGTTTGCCTATTTGGCATGTATGTTCAAGAATTTGGATCTGAATGTCAATTTCCTAATCAGCGCC

upper sequence: AT3G12980.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 8
gtacagattgtgtatgcttggttcttatttcttttccttctttttgttttctaattatgaccttctgctacatgatgcctgttgactatcaacttccatactcattttttttcagGCCATTCTGTTGTTTCAGAAGATTGAAGGTGTTGAAGTATGCTTATTTGGCATGTATGTCCAGGAATTTGGAACAGATTCTGCGTCTCCCAATCAGCGCC
           ||||||  | |   ||||   ||    | ||||  | |  |    |    |||    ||        |||  || | ||           |  ||  ||| ||||  ||| |||||||||||||||||||||| || ||||||||||||||||| |||||||| || ||||||||| |||| | |   |  || ||||| || |
-----------gtatgcaggatgtatattaagttgatgttttttcatatagttgacaaagacttaaattatgaa----ctgaagattgtc-----------tttttcgtttccagGTAATTTTGTTGTTTCAGAAGATTGAAGGAGTAGAAGTATGCTTATTTGGGATGTATGTTCAAGAATTTGGATCAGAATGTCTATTCCCAAATCAACGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttctgctacatgatgcctgttgactatcaacttccatactcattttttttcagGCCATTCTGTTGTTTCAGAAGATTGAAGGTGTTGAAGTATGCTTATTTGGCATGTATGTCCAGGAATTTGGAACAGATTCTGCGTCTCCCAATCAGCGCC
                   tgttgac  putative branch site (score: 3)
                                cttccatactcatttt  putative PPT
                                     atactcatttttttt  TA-rich tract