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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgcttatataccagaagtagatccattagtttctacaagaaaatagtttataggttacgttttcagtaatatttttattggagaaatacaaaagagttccttatctgaaatttaaacgcaaaagcagattggtactgctcgcttattcacttttaacgtttttgtttattcaatgtttcagAATCTTTATTGGGCGGACAGTGGTGATCTAGTTGCAATTGCCAGTGATACATCATTCTACATCCTTAAGTTCAAT

Basic information

species Arabidopsis thaliana
transcript AT1G79990.5
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 13
gtaagtgcttatataccagaagtagatccattagtttctacaagaaaatagtttataggttacgttttcagtaatatttttattggagaaatacaaaagagttccttatctgaaatttaaacgcaaaagcagattggtactgctcgcttatt-cacttttaacgtttttgtttattcaatgt---ttcagAATCTTTATTGGGCGGACAGTGGTGATCTAGTTGCAATTGCCAGTGATACATCATTCTACATCCTTAAGTTCAAT
                                                                                                    ||   | |  |   || ||     |     |||||| ||||  |  |  ||| ||   | ||     | ||||  ||| |||   || |||| ||||||||||| || || ||||| ||||||||||| || |||||||||||||||||||| || |||| ||| 
----------------------------------------------------------------------------------------------------gtgagtcaaatattatctattgatatttatagattgatacttttaacgaatttcatactgaaataactagttttgtcactgtatttttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 13
gtaagtgcttatataccagaagtagatccattagtttctacaagaaaatagtttataggttacgttttcagtaatatttttattggagaaatacaaaagagttccttatctgaaatttaaacgcaaaagcagattggtactgctcgcttattcacttttaacgtttttgtttattcaatgtttcagAATCTTTATTGGGCGGACAGTGGTGATCTAGTTGCAATTGCCAGTGATACATCATTCTACATCCTTAAGTTCAAT
                                                                                              ||    ||||||    | ||||||          |    |||| |        ||||     |  |  |  | || ||  | | |  |  ||||||| |||||||| || ||||||||| ||||  ||||||| ||||| || |||||||||||  | |||| ||||
----------------------------------------------------------------------------------------gtgagtaattttgttcctggatttaaatttttttttgcgtgtcatttggaata------ttatgatgctaaataggatctgctttcttatt--tgtagAATCTCTATTGGGCCGATAGTGGTGATTTAGTGACAATTGCAAGTGACACCTCATTCTACATTTTGAAGTACAAT

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 4
gtaagtgcttatataccagaagtagatccattagtttctacaagaaaatagtttataggttacgttttcagtaatatttttattggagaaatacaaaagagttccttatctgaaatttaaacgcaaaagcagattggtactgctcgcttattcacttttaacgtttttgtttattcaatgtttcagAATCTTTATTGGGCGGACAGTGGTGATCTAGTTGCAATTGCCAGTGATACATCATTCTACATCCTTAAGTTCAAT
                                                                                                 ||   |  |  ||    ||| |||   |      |  ||  | |       |  | |   | ||     |    | |   || ||  ||||||| |||||||| || ||||||||| ||||  ||||||| ||||| || |||||||||||  | |||| ||||
----------------------------------------------------------------------------------------------gtgagtaattttgttcatggattcaaatttatt--ttgcgtgtcatttggaatattatgatgctaaataggatccgctttcttat-ttgtagAATCTCTATTGGGCCGATAGTGGTGATTTAGTGACAATTGCAAGTGACACCTCATTCTACATTTTGAAGTACAAT

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 13
gtaagtgcttatataccagaagtagatccattagtttctacaagaaaatagtttataggttacgttttcagtaatatttttattggagaaatacaaaagagttccttatctgaaatttaaacgcaaaagcagattggtactgctcgcttattcacttttaacgtttttgtttattcaatgttt-cagAATCTTTATTGGGCGGACAGTGGTGATCTAGTTGCAATTGCCAGTGATACATCATTCTACATCCTTAAGTTCAAT
                                                                                       |  |  ||||||  ||  || ||      ||    | |||      || ||| ||   |    || | | |||||  ||||||||||    |||||  ||||| |||| ||||| || |||||||| ||||||||||| || ||||||||||||||||||||||| |||| ||||
---------------------------------------------------------------------------------------gtgagtcaaaagtattatttttcc-----ttgggtggaaat-----tttgta-tgtatga--gtttaatattaac-cttttgtttatcatgtgtttatagAATGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 12
gtaagtgcttatataccagaagtagatccattagtttctacaagaaaatagtttataggttacgttttcagtaatatttttattggagaaatacaaaagagttccttatctgaaatttaaacgcaaaagcagattggtactgctcgcttattcacttttaacgtttttgtttattcaatgttt-cagAATCTTTATTGGGCGGACAGTGGTGATCTAGTTGCAATTGCCAGTGATACATCATTCTACATCCTTAAGTTCAAT
                                                                                           |  |  |    |  || | |     ||    | |||    |  || ||           || ||| ||||| ||||  |||||      |||  ||||  |||| ||||| || |||||||| ||||||||||| || ||||||||||||||||||||||| |||| ||||
------------------------------------------------------------------------------------------gtgaatcaagtattatttttt----cttgggtggaaattttgtatg-taaaatgtatgagtttactattaaccttttc-tttatcatgcatttatagAACGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 13
gtaagtgcttatataccagaagtagatccattagtttctacaagaaaatagtttataggttacgttttcagtaatatttttattggagaaatacaaaagagttccttatctga--aatttaaacgcaaaagcagattggtactgctcgc----ttat-tcacttttaacgtttttgtttattcaatgtttcagAATCTTTATTGGGCGGACAGTGGTGATCTAGTTGCAATTGCCAGTGATACATCATTCTACATCCTTAAGTTCAAT
                                                                                              ||  || ||  ||| || |  | || ||||        | |||  | |   | |     || |  ||||   ||| | ||| ||| |  |        ||||||||| ||||| |||||||||||| ||||  ||||||| |||||||| |||||||||||  | || |  |||
--------------------------------------------------------------------------------------------gtaatggaatttgttaccttattatttcaaacctttttttacattcatgccatttgaaatgttgtgccactcaaaacatgtttctttgtgta--------gAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 13
gtaagtgcttatataccagaagtagatccattagtttctacaagaaaatagtttataggttacgttttcagtaatatttttattggagaaatacaaaag-agttccttatctgaaatttaaacgcaaaagcagattggtact--gctcgcttattcacttttaacgtttttgtttattcaatgtttcagAATCTTTATTGGGCGGACAGTGGTGATCTAGTTGCAATTGCCAGTGATACATCATTCTACATCCTTAAGTTCAAT
                                                          || | |   |  |  || || ||     | || | ||||    |||    || |  ||| | || | ||  |||  |||  | |      | |    ||||    || | ||| ||| |  |        ||||||||| ||||| |||||||||||| ||||  ||||||| |||||||| |||||||||||  | || |  |||
----------------------------------------------------------gtaatgacatttgacat-ttgttgccttataatttcaaacctggttttgcatttccaatgtgaaggtaatggcat-ttgacatttgaaatgttgtgccactgaagacatgtttctttgtgta--------gAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 13
gtaagtgcttatataccagaagtagatccattagtttctacaagaaaatagtttataggttacgttttcagtaatatttttattggagaaatacaaaagagttccttatctgaaatttaaacgcaaaagcagattggtactgctcgcttattcacttttaacgtttttgtttattcaatgtttcagAATCTTTATTGGGCGGACAGTGGTGATCTAGTTGCAATTGCCAGTGATACATCATTCTACATCCTTAAGTTCAAT
                                                                                              ||     ||  |||  ||| || ||          |   |   |  |  ||| |  || |  |||||  || || |||||    ||| |||||| || || ||||| |||||||||||||||||  ||||||| |||||||||||||||||||| || |||| ||||
--------------------------------------------------------------------------------------------gtaagtactttgattaggtgacatctagttatctgctcttttccttcttattcgttgtttaa--tttaattttgttatttatct--tgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGTGATACATCATTCTACATTCTGAAGTACAAT

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
gtaagtgcttatataccagaagtagatccattagtttctacaagaaaatagtttataggttacgttttcagtaatatttttattggagaaatacaaaagagttccttatctgaaatttaaacgcaaaagcagattggtactgctcgcttattcacttttaacgtttttgtttattcaatgtttcagAATCTTTATTGGGCGGACAGTGGTGATCTAGTTGCAATTGCCAGTGATACATCATTCTACATCCTTAAGTTCAAT
                                                                                              ||     ||  |||  ||| |||||          |   |   |  |  ||  |  || |  | |||  || || || ||    ||| |||||| || || ||||| |||||||||||||||||  ||||||| || ||||||||||||||||| || |||| ||||
--------------------------------------------------------------------------------------------gtaagtactttgattaggtgacatttagttatctgctcttttccttcttattcattgtttaa--tataattttgttattaatct--tgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 2
gtaagtgcttatataccagaagtagatccattagtttctacaagaaaatagtttataggttacgttttcagtaatatttttattggagaaatacaaaagagttccttatctgaaatttaaacgcaaaagcagattggtactgctcgcttattcacttttaacgtttttgttta---ttcaatgtttcagAATCTTTATTGGGCGGACAGTGGTGATCTAGTTGCAATTGCCAGTGATACATCATTCTACATCCTTAAGTTCAAT
                                                                                                   |  | |||   |||  |   |   ||         |  || | ||  |||| |   | ||     ||||||| |   ||   ||| |||||| || || ||||| || ||||||||||||||  | ||||| ||||||||||||||||| ||||| |||| ||||
-------------------------------------------------------------------------------------------------gtaagtgcttgcatgaggt--gacatcagctttctgcttttatttctt-cttactgtttcttgttaattttgttaaaattttcttgtgtcagAACCTCTACTGGGCTGATAGTGGTGATCTAGTGACGATTGCTAGTGATACATCATTCTATATCCTGAAGTACAAT

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 13
gtaagtgcttatataccagaagtagatccattagtttctacaagaaaatagtttataggttacgttttcagtaatatttttattggagaaatacaaaagagttccttatctgaaatttaaacgcaaaagcagattggtactgctc--gcttattcacttttaacgtttttgtttattcaatgtttcagAATCTTTATTGGGCGGACAGTGGTGATCTAGTTGCAATTGCCAGTGATACATCATTCTACATCCTTAAGTTCAAT
                                                                                                   |  | |||   |||  |      |||  |||    || |  |  |    |||| |   | |||   || ||   | ||   ||| |||||| || || ||||| || || |||||| ||||  | ||||| ||||||||||||||||| |||||||||| ||||
-------------------------------------------------------------------------------------------------gtaagtgcttgcatgaggtg-----gcatcagctttctgcttttatttcttcttactgtttcttatttttgttaaatttttcttgtgtcagAACCTGTACTGGGCTGATAGCGGTGATTTAGTGACGATTGCTAGTGATACATCATTCTATATCCTTAAGTACAAT

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 13
gtaagtgcttatataccagaagtagatccattagtttctacaagaaaatagtttataggttacgttttcagtaatatttttattggagaaatacaaaagagttccttatctgaaatttaaacgcaaaagcagattggtactgctcgcttattcacttttaacgtttttgtttattcaatgtttcagAATCTTTATTGGGCGGACAGTGGTGATCTAGTTGCAATTGCCAGTGATACATCATTCTACATCCTTAAGTTCAAT
                                                               ||   || ||| ||  |     |     |||    |  ||  ||   ||  |    |  |||  |   ||||             | |||  ||||    || || ||| |||| | |||||||| || |||||||| || ||||| ||| | || || |||||||||||||||||||| |||||||| |||| ||||
---------------------------------------------------------------gtaagcactaacatgatggcctgttggctaccgtggtattgttttcatgccac---actgcaggaattgattaaa----------tgttccttttttcttttctttttttttcactatttcagAACCTCTATTGGGCTGATAGTGGGGATTTGGTGGCCATTGCCAGTGATACATCATTTTACATCCTGAAGTACAAT

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 13
gtaagtgcttatataccagaagtagatccattagtttctacaagaaaatagtttataggttacgttttcagtaatatttttattggagaaatacaaaagagttccttatctgaaatttaaacgcaaaagcagattggtactgctcgcttattcacttttaacgtttttgtttattcaatgtttcagAATCTTTATTGGGCGGACAGTGGTGATCTAGTTGCAATTGCCAGTGATACATCATTCTACATCCTTAAGTTCAAT
                                                                                    | |      |||||   || |||  |    |              ||||  |  |||  | | | |||  ||||    | |||        |||| |||||||||||||||||||| || ||||||||| |||| |||||||| |||||| ||||||| |||||| | |||| ||||
------------------------------------------------------------------------------------gcatgttctcaaaaagcttacttcacaattaccaggttttggccacaga--gaaactaatagttcattt-ctttgggtggttt--------caatatttcagAATCTTTATTGGGCTGATAGTGGTGATTTAGTGGCAATTGCAAGTGATTCATCATTTTACATCTTAAAGTACAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattggtactgctcgcttattcacttttaacgtttttgtttattcaatgtttcagAATCTTTATTGGGCGGACAGTGGTGATCTAGTTGCAATTGCCAGTGATACATCATTCTACATCCTTAAGTTCAAT
                        ttttaac  putative branch site (score: 2)
                                tttttgtttattcaat  TA-rich tract