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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttttctgaattctaagtttatatatgctactgtatggccaagcgcagaacagcgggggacatcttgtgattcctcgttgtgcttcttatcgttcatgctctttacctacatgtgtttcctactaagtgtctgttttcgctttgatttctgctcaagtattaactatgcgtttcttttcttcagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG

Basic information

species Arabidopsis thaliana
transcript AT3G50500.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G50500.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g41460.1 (Oryza sativa), 3'ss of exon 3
gtttgttttctgaattctaagtttatatatgctactgtatggccaagcgcagaacagcgggggacatcttgtgattcctcgttgtgcttcttatcgttcatgctctttacctacatgtgtttcctactaagtgtctgttttcgctttgatttctgctcaagtattaactatgcgtttctt-ttcttcagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG
                                                                                  ||||| | |  || |   |   ||||     |  |   ||  | |   |  ||| ||||  ||||   ||||| ||| ||  | ||| |   ||  |  ||  |||||| |||||||||||||| |||||||| || |||||||| ||||| |||||||| || || ||| |||| ||     ||||||||||||| |||
---------------------------------------------------------------------------------ctgtgcatgt-gtcttgtttagccttt-----cggggaatttgtgcctggaatcttttttaacttta--ttctgatcatgtcatgacttttttttcttcatttgtcagTCGTCTGTTCTTCATTCGCAACCAAAATCTACTGTTGGAACTCCGGCATACATCGCTCCTGAGGTTCTGCTGAAGAAGGAATATGATGGAAAG

upper sequence: AT3G50500.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os12g39630.1 (Oryza sativa), 3'ss of exon 5
gtttgttttctgaattctaagtttatatatgctactgtatggccaagcgcagaacagcgggggacatcttgtgattcctcgttgtgcttcttatcgttcatgctctttacctacatgtgtttcctactaagtgtctgttttcgctttgatttctgctcaagtatta----actatgcgtttcttttctt-cagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG
                                                                                      |||  | | ||   ||      |   | |      |    |||  | |   || ||| | ||||| ||||     || ||    ||| |   |||||  | || ||||| || ||||||||||| |||||||| ||||| ||||| ||||| || || ||||| |||||  || | ||     | ||||| ||||| |||
-------------------------------------------------------------------------------------actttctgtagta-gtgaa----aagaagagagaactttcgctagattt---ttctcgatgtgattgctgcctggataatattgtactgttgctttctgattttgcagTCATCGGTTCTTCATTCACAACCAAAATCAACAGTTGGAACTCCAGCTTATATTGCTCCAGAAGTTTTGCTCAAGAAAGAATACGATGGAAAG

upper sequence: AT3G50500.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G171435_T02 (Zea mays), 3'ss of exon 5
gtttgttttctgaattctaagtttatatatgctactgtatggccaagcgcagaacagcgggggacatcttgtgattcctcgttgtgcttcttatcgttcatgctctt-tacctacatgtgtttcctactaagtgtctgttttcgctttgatttctgctca-agtattaactatgcgtttcttttcttcagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG
                                                                                         ||||  ||| |  |  |  ||     |||       |  | |  |   ||| ||  |||  |||   || | | ||  |   || | ||  || ||| ||||| |||||||||||||||||||| |||||||||||||| || ||||| || |||||||| ||  ||||  |   | | |||||||||||||||
---------------------------------------------------------------------------------------ggcttaatgtttacacgatagtagtagaatgatgaatatgttcatagg--gttgtcagtttccttttaactaacaataccatgcattc-ttcattctctgcagTCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTCTGTTGAAAAAAGAATATGATGGCAAG

upper sequence: AT3G50500.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G138861_T01 (Zea mays), 3'ss of exon 6
gtttgttttctgaattctaagtttatatatgctactgtatggccaagcgcagaacagcgggggacatcttgtgattcctcgttgtgcttcttatcgttcatgctctttacctacatgtgtttcctactaagtgtctgttttcgctttgatttctgctca-agtattaactatgcgtttcttttcttcagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG
                                                                                         ||||  ||| |  |  |     || |  |  |   ||  |       ||| ||  |||  |||   || | | ||  |   ||   ||  || ||| ||||| ||||||||||||||||| || ||||| |||||||| || ||||| || |||||||| ||  || |  |   | | |||||||||||||||
---------------------------------------------------------------------------------------ggcttaatgtttacacgatggtagtaga-ataatgaatatgatcatagcgttgtcagttttcttttaactaacaataccatgcattt-ttcattctctgcagTCATCTGTTCTTCATTCCCAGCCGAAGTCCACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTTTGTTGAAAAAAGAATATGATGGCAAG

upper sequence: AT3G50500.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G09460.1 (Glycine max), 3'ss of exon 5
gtttgttttctgaattctaagtttatatatgctactgtatggccaagcgcagaacagcgggggacatcttgtgattcctcgttgtgcttcttatcgttcatgctctttacctacatgtgtttcctactaagtgtctgttttcgctttgatttctgctcaagtattaactatgcgtttcttttcttcagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG
                                                                                 | |||  | |||      |   |   ||  |  || |||||     |  || | |||||  | |||  |||   | ||| | |     ||| || |  ||    |||||||| || |||||||| ||||||||||||||||| || ||||||||||| ||||| |||||  |  |  |   ||| || ||||||||||||
--------------------------------------------------------------------------------atagtggattttaca----acaatagatagatgaat-tgtttgtagtt--gtatttgtttgagttttttttttctcacaaatctgtttgatg-gtgtgattcgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGTTGAAACAAGAGTATGATGGCAAG

upper sequence: AT3G50500.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G20610.4 (Glycine max), 3'ss of exon 5
gtttgttttctgaattctaagtttatatatgctactgtatggccaagcgcagaacagcgggggacatcttgtgattcctcgttgtgcttcttatcgttcatgctctttacctacatgtgtttcctactaagtgtctgttttcgctttga-----tttctgctcaagtattaactatgcgtttcttttcttcagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG
                                                                                           ||   |    | | |  | ||| |  || |   |  |   ||| |||||| | |||||     ||| | | ||| | | |   ||| || |  |||   |||||||| || |||||||| ||||||||||||||||| || ||||||||||| ||||| |||||  |  | ||   ||| || ||||||||||||
-------------------------------------------------------------------------------------------tacaatagtggatttacaactatagatgatcattgtttcctgt-tgtttttgttttgagtttttttttccccaaatctgattgatg-gtgtgatttgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAG

upper sequence: AT3G50500.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G39020.2 (Glycine max), 3'ss of exon 5
gtttgttttctgaattctaagtttatatatgctactgtatggccaagcgcagaacagcgggggacatcttgtgattcctcgttgtgcttcttatcgttcatgctctttacctacatgtgtttcctactaagtgtctgttttcgctttgatttctgc-tcaagtattaactatgcgtttcttttctt-cagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG
                                                                                          || || ||| | || | ||      | | |||   |  |  ||  |  ||| | |   |||||||  ||  | |      ||   |||  ||  |  |||||||| || |||||||| ||||| ||||||||||| || ||||| ||||| ||||| |||||  |  | ||    || || ||||||||||||
-----------------------------------------------------------------------------------------tttttctttcgtcctttgtattctattttattttaaagaatttgaattgttttgatc-aatttctgtatcctgcaaatgtaatagattttgttattggcagTCTTCCGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG

upper sequence: AT3G50500.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 5
gtttgttttctgaattctaagtttatatatgctactgtatggccaagcgcagaacagcgggggacatcttgtgattcctcgttgtgcttcttatcgttcatgctctttacctacatgtgtttcctactaagtgtctgttttcgctttgatttctgctcaagtattaactatgcgtttcttttcttcagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG
                                                                                 | | | |  |    || || | |  | ||  |     ||    || ||  ||     || |    |   | || |  |  || ||  |     ||| || |   |||||||| || |||||||| ||||| ||||||||||| || ||||| ||||| ||||| |||||  |  | ||    || || ||||||||||||
------------------------------------------------------------------------------aaatagaggtcatccatgtacaag-taatgacacatcaaggtccattaatagttgatcaattac----tatatcctacaaatctaatagat-----tttgttattggcagTCTTCGGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG

upper sequence: AT3G50500.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 5
gtttgttttctgaattctaagtttatatatgctactgtatggccaagcgcagaacagcgggggacatcttgtgattcctcgttgtgcttcttatcgttcatgctctttacctacatgtgtttcctactaagtgtctgttttcgct--ttgatttctgctcaagtattaactatgcgtttcttttcttcagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG
                                                                                     || |||   | |      ||  |   ||         | |  |    ||     |  | |  ||  | | ||||||| | | |     ||  ||||      |||||||| || |||||||| |||||||| ||||||||||| ||||||||||||||||| |||||  |  |  |  | || ||||| |||||||||
------------------------------------------------------------------------------------agcatctgtacatcagcattcaatgggtattcaatcccctttgttcacgttatcctaggatcattattatttgctcaaatctgacagtggcacttct------cagTCTTCGGTGCTTCATTCACAACCAAAATCAACTGTTGGAACTCCTGCATACATTGCTCCAGAAGTATTAATGAGGCAAGAATACGATGGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgttttcgctttgatttctgctcaagtattaactatgcgtttcttttcttcagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG
                            tattaac  putative branch site (score: 1)
                                     tgcgtttcttttcttc  putative PPT
                            tattaactat  TA-rich tract