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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaattaatcactcttttaccattttcttgaaaactttgatttaagcttattggctgattagttattacttctattgtctggccattgtagAGATACGCATAGCGAGGATATTCAACACATATGGTCCTCGTATGAACATTGATGATGGTCGCGTTGTGAGCAACTTCATTGCTCAGGCTCTCAG

Basic information

species Arabidopsis thaliana
transcript AT2G28760.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g16980.3 (Oryza sativa), 3'ss of exon 7
gtaaaattaatcactcttttaccattttcttg-aaaactttgatttaagcttattggctgattagttattacttctattgtctggccattgtagAGATACGCATAGCGAGGATATTCAACACATATGGTCCTCGTATGAACATTGATGATGGTCGCGTTGTGAGCAACTTCATTGCTCAGGCTCTCAG
|||| |||  |   || |      || |||||  |     ||  ||    || |   || | ||  ||||  ||| | | | |   |  ||||||||| || || || ||||| |||||||| ||||| ||| | ||||||||||||||||| || ||||| || |||||||||||||||||  |  |
gtaatatttttagttcatacctttttgtcttgtgatgtactggattgtagttctc--cttaataagtatt--ttccaatctat---ctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACG

upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g16980.5 (Oryza sativa), 3'ss of exon 8
gtaaaattaatcactcttttaccattttcttgaaaact-ttgatttaagcttattggctgattagttattacttctattgtctggccattgtagAGATACGCATAGCGAGGATATTCAACACATATGGTCCTCGTATGAACATTGATGATGGTCGCGTTGTGAGCAACTTCATTGCTCAGGCTCTCAG
|||| |||  |   || |      || |||||  |  |  ||  ||    || |   || | ||  ||||  ||| | | | |   |  ||||||||| || || || ||||| |||||||| ||||| ||| | ||||||||||||||||| || |||                             
gtaatatttttagttcatacctttttgtcttgtgatgtactggattgtagttctc--cttaataagtatt--ttccaatctat---ctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTGATGATGGGCGTGTT-----------------------------

upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G157772_T02 (Zea mays), 3'ss of exon 4
---------gtaaaattaatcactcttttaccattttcttgaaaactttgatttaagcttattggctgattagttattacttctattgtctggccattgtagAGATACGCATAGCGAGGATATTCAACACATATGGTCCTCGTATGAACATTGATGATGGTCGCGTTGTGAGCAACTTCATTGCTCAGGCTCTCAG
           || |||| |  ||| |   ||  ||| ||   |  |    | |  ||||||    |  ||  | |     | |||  |||      |||||| || || || || ||||| |||||||| ||||| ||| | |||||||||||||||||||| ||||| ||||||||||||||||||||| |  |
acttaaacttcaatattagtagctcatagccctctttgttatgagata-actctgggcttatgatttttttcttaacagtatttatcatctatgt-ctgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGTCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG

upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G157772_T01 (Zea mays), 3'ss of exon 5
--------------------------gtaaaattaatcactcttttaccattttcttgaaaactttgatttaagcttattggctgattagttattacttctattgtctggccattgtagAGATACGCATAGCGAGGATATTCAACACATATGGTCCTCGTATGAACATTGATGATGGTCGCGTTGTGAGCAACTTCATTGCTCAGGCTCTCAG
                            || |||| |  ||| |   ||  ||| ||   |  |    | |  ||||||    |  ||  | |     | |||  |||      |||||| || || || || ||||| |||||||| ||||| ||| | |||||||||||||||||||| ||||| ||||||||||||||||||||| |  |
gtaacacttcatctttcacttaaacttcaatattagtagctcatagccctctttgttatgagata-actctgggcttatgatttttttcttaacagtatttatcatctatgt-ctgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGTCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG

upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 14
--------------------------gtaaaattaatcactcttttaccattttcttgaaaactttgatttaagcttattggctgattagttattact-tctattgtctggccattgtagAGATACGCATAGCGAGGATATTCAACACATATGGTCCTCGTATGAACATTGATGATGGTCGCGTTGTGAGCAACTTCATTGCTCAGGCTCTCAG
                            || |||| |  ||| |   ||  ||| ||      |    | |  ||||||    |  ||  |||  | | | |||  |||      |||||| || || || || ||||| |||||||| ||||| ||| | ||||||||||||||||| || ||||| ||||||||||||||||||||| |  |
gtaacacttcatctttcacttaaacttcaatattagtagctcatagtcctctttgttatgtgata-actctgggcttatgattttttttcttaacagtgtttatcatctatgt-ctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG

upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 7
--------------------------gtaaaattaatcactcttttaccattttcttgaaaactttgatttaagcttattggctgattagttattacttctattgtctggccattgtagAGATACGCATAGCGAGGATATTCAACACATATGGTCCTCGTATGAACATTGATGATGGTCGCGTTGTGAGCAACTTCATTGCTCAGGCTCTCAG
                            || |||| |  ||| |   ||  ||| ||      |    | |  |||||| |  |  ||| | |     | |||  |||      |||||| || || || || ||||| |||||||| ||||| ||| | ||||||||||||||||| || ||||| ||||||||||||||||||||| |  |
gtaacacttcatctttcacttaaacttcaatattagtagctcatagccctctttgttatgtgata-actctgggcttat-gattttttattaacagtatttatcatctatgt-ctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG

upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G177373_T02 (Zea mays), 3'ss of exon 8
--------------------------gtaaaattaatcactcttttaccattttcttgaaaactttgatttaagcttattggctgattagttattacttctattgtctggccattgtagAGATACGCATAGCGAGGATATTCAACACATATGGTCCTCGTATGAACATTGATGATGGTCGCGTTGTGAGCAACTTCATTGCTCAGGCTCTCAG
                            || |||| |  ||| |   ||  ||| ||      |    | |  ||||||    |  ||  | |     | |||  |||      |||||| || || || || ||||| || ||||| ||||| ||| | ||||||||||||||||| || ||||| ||||||||||||||||||||| |  |
gtaacacttcatctttcacttaaacttcaatattagtagctcatagccctctttgttatgtgata-actctgggcttatgatttttttcttaacggtatttatcatctatgt-ctgtagAAATCCGGATTGCCAGGATTTTTAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG

upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G382038_T01 (Zea mays), 3'ss of exon 9
--------------------------gtaaaattaatcactcttttaccattttcttgaaaactttgatttaagcttattggctgattagttattacttctattgtctggccattgtagAGATACGCATAGCGAGGATATTCAACACATATGGTCCTC-GTATGAACATTGATGATGGTCGCGTTGTGAGCAACTTCATTGCTCAGGCTCTCAG
                            || |||| |  ||| |   ||  ||| ||      |    | |  ||||||    |  ||  | |     | |||  |||      |||||| || || || || ||||| || ||||| ||||| |||  | ||||||||||||||||| || ||||| ||||||||||||||||||||| |  |
gtaacacttcatctttcacttaaacttcaatattagtagctcatagccctctttgttatgtgata-actctgggcttatgatttttttcttgacagtatttatcatctatgt-ctgtagAAATCCGGATTGCCAGGATTTTTAACACCTATGGGCCTAAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG

upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 8
-------------------gtaaaattaatcactcttttaccattttcttgaaaactt--tgatttaagcttattggctgattagttattacttctattgtctggccattgtagAGATACGCATAGCGAGGATATTCAACACATATGGTCCTCGTATGAACATTGATGATGGTCGCGTTGTGAGCAACTTCATTGCTCAGGCTCTCAG
                    |||| |  |  | |   | |      |||| |     |  | | |  ||  |  ||  |  |        |  | |||  |||      |||||| || || || || ||||| |||||||| ||||| ||  | ||||||||||| ||||| || ||||| ||||||||||||||||||||| |  |
gtaatacttcatcttgcacttaaactgtaatattagctcatagccctctttattgtgtgataactctaggcttatgatttgtcctcagcaatatttataatctatgt-ctgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG

upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 8
-----------------------------------------gtaaaattaatc-actcttttaccattttcttgaaaactttgatttaagcttattggc--tgattagttattacttctattgtctggccattgt---agAGATACGCATAGCGAGGATATTCAACACATATGGTCCTCGTATGAACATTGATGATGGTCGCGTTGTGAGCAACTTCATTGCTCAGGCTCTCAG
                                          |   ||| ||  |       | || |          |  || | | | || ||  ||  | | |   | | |    |||| ||      || |   ||| |||||||| ||||| || |||||||||||||| || || ||||| ||||||||||| || ||||| || |||||||||||||| ||  |  |
gtaattccttatctttattttttccttttctccttggcaacatctcattgattgagggcacaaacagtacacgttttgcactgctgttaactaataagcaataactcaatgtgatgcttattttcatatttttctctcagAAATACGCATTGCGAGAATCTTCAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATTGCTCAAGCAATTCG

upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 9
----------------------gtaaaattaatcactcttttaccattttcttgaaaactttgatttaagcttattggctgattagttattacttctat-tgtctggccattgtagAGATACGCATAGCGAGGATATTCAACACATATGGTCCTCGTATGAACATTGATGATGGTCGCGTTGTGAGCAACTTCATTGCTCAGGCTCTCAG
                       |  ||||  |     ||||         |    |     ||||||   || ||   | | |  || |    | ||| | ||    ||   |||| |||||||| || || || || ||||||||||| || || ||||| ||||||||||| || ||||| ||||||||||||||||| || ||  |
gtaatttcttgtcttcttttccttgtaatttcttctcattttgtttacacatatccagtagagatttatctttgtttcttaactccttgtggtgtttatgtctcctttcaacatagAAATACGCATTGCAAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTTAGCAACTTCATTGCTCAAGCACTTCG

upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA15G04500.2 (Glycine max), 3'ss of exon 9
---------------gtaaaattaatcactcttttaccattttcttgaaaacttt--------gatttaagcttattggctgattagttattacttctat-tgtctggccattgtagAGATACGCATAGCGAGGATATTCAACACATATGGTCCTCGTATGAACATTGATGATGGTCGCGTTGTGAGCAACTTCATTGCTCAGGCTCTCAG
                |     | || | |  ||  |  |||  || |    | |        |||||    || ||   | | |  ||      | ||| | ||    ||   |||| |||||||| || || || || ||||||||||| || || ||||| ||||||||||| || ||||| ||||||||||||||||| || ||  |
gtaatttattgtctttttttccttataatttcttctcgttttgtttaaggcatatccaatagagatttttctttgttttttaactccttgaggtgtttatatatcctttcaacatagAAATACGCATTGCAAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGCAACTTCATTGCTCAAGCACTGCG

upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 8
----------------------------------------------gtaaaattaatcactcttttaccattttcttgaaaactttgatttaagcttattg-gctgattagttattacttctattgtctggccattgtagAGATACGCATAGCGAGGATATTCAACACATATGGTCCTCGTATGAACATTGATGATGGTCGCGTTGTGAGCAACTTCATTGCTCAGGCTCTCAG
                                              ||    || ||   | | ||    |  |  | | | ||   |   ||  || ||  |    |||  |     || |||  |     ||   |||| |||||  | || || || || ||||||||||| || || ||||| ||||||||||| || ||||| ||||||||||||||||| ||  |  |
gtaatttctgctcttcttttcttcatagttgttgttgattgttgttgttttcttcatagttgtcttttgttccttgttatagctggtagaaaattttcttttgtaagttaactgagttttttatatttctttcaacatagAAATACGTGTTGCAAGAATCTTTAACACATATGGGCCACGCATGAATATTGATGATGGACGTGTTGTCAGCAACTTCATTGCTCAAGCGATTCG

upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 8
-----------------gtaaaattaatcactcttttaccattttcttgaaaactttgatttaagcttattggctgattagttattacttctattgtctggccattgtagAGATACGCATAGCGAGGATATTCAACACATATGGTCCTCGTATGAACATTGATGATGGTCGCGTTGTGAGCAACTTCATTGCTCAGGCTCTCAG
                  |    || ||   | | |     |  |  | | ||||   |   |   || |  |    |||  |     ||||||  |     ||   |||| |||||  | || || || || ||||||||||| || || ||||| ||||||||||| || ||||| ||||||||||||||||| ||  |  |
gtaatttcttctcttcttttttcttcatagttgtctgttgctccttgttataactggtagaaatttttctctgtaatttaactgagttttctatatttctttcaacatagAAATACGTGTTGCAAGAATCTTTAACACATATGGGCCGCGCATGAATATTGATGATGGACGTGTTGTCAGCAACTTCATTGCTCAAGCAATTCG

upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA12G06980.3 (Glycine max), 3'ss of exon 8
--------------------------------------------gtaaaattaatcactcttttaccattttcttgaaaactttgatttaagcttattggctgattagttattacttctattgtctggccattgtagAGATACGCATAGCGAGGATATTCAACACATATGGTCCTCGTATGAACATTGATGATGGTCGCGTTGTGAGCAACTTCATTGCTCAGGCTCTCAG
                                            | | ||  | |     |||| |  |    || |  | |  |   |||    ||  | || ||| || | | || | || |||         ||| |||||||| ||||| || || ||||||||||| || || ||||| ||||||||||| || ||||| || |||||||| ||||| ||  |  |
gtaattccttatcttttctccttggcaacatctcattgttgagggcacaaacagtagaagttttgcactgccgttaactaataagcaataactcaatgtgatgcttattt-tcattttttttctct--------cagAAATACGCATTGCGAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATCGCTCAAGCAATTCG

upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 8
gtaaaattaatcactcttttaccattttcttgaaaactttgatttaagcttattggctgattagttattacttctattgtctggccattgtagAGATACGCATAGCGAGGATATTCAACACATATGGTCCTCGTATGAACATTGATGATGGTCGCGTTGTGAGCAACTTCATTGCTCAGGCTCTCAG
||||  ||  |   | ||||   | |       ||||||  ||   |   |   |  | | ||  |||   |  |  | | |         ||| |||||||| || || || |||||||||||||| || || ||||| ||||||||||| || ||||| ||||| ||||| ||||| || ||  |
gtaacttttgtgtttttttttttaatcctgaacaaacttcaat--gaatatgaagttttaatatgtat-gttgtttctttatattttggacagAAATACGCATTGCTAGAATTTTCAACACATATGGGCCCCGCATGAATATTGATGATGGACGTGTTGTCAGCAATTTCATAGCTCAAGCACTTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatttaagcttattggctgattagttattacttctattgtctggccattgtagAGATACGCATAGCGAGGATATTCAACACATATGGTCCTCGTATGAACATTGATGATGGTCGCGTTGTGAGCAACTTCATTGCTCAGGCTCTCAG
                ggctgat  putative branch site (score: 4)
                     attagttattactt  TA-rich tract