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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaccatgattttgtatatatactttcatcgaatgtttcaaattttcatagggaatctagtcagtagacactatagctctctcattcagattataaaattttatggtaacattttttttctttatctatgcttctgttcagTATACACCGGCAATAGATATATGGAGCATCGGGTGCATTTTTGCAGAACTCTTAACAGGGAAACCTCTTTTCCCCGGGAAAAATGTGGTCCATCAATTGG

Basic information

species Arabidopsis thaliana
transcript AT5G19010.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os11g17080.1 (Oryza sativa), 3'ss of exon 4
gtgaccatgattttgtatatatactttcatcgaatgtttcaaattttcatagggaatctagtcagtagacactatagctctctcattcagattataaaattttatggtaacattttttttctttatctatgcttctgttcagTATACACCGGCAATAGATATATGGAGCATCGGGTGCATTTTTGCAGAACTCTTAACAGGGAAACCTCTTTTCCCCGGGAAAAATGTGGTCCATCAATTGG
                                   |     || |    |   |  || |||   | |   |||||  | |||  ||     |||||    |    ||| |  |     |  |  | |     |   | ||||| ||||| ||||||||||||||||||||||| ||||| ||||||||||| |||||||| ||||||||||||||||||||||||||||| |||||| | |
-----------------------------------gcaatgaaatgctgtctagt-tccagttgctgg---ctatatttttct--ttgtacatataatgcctgg-agtatcggtgaaccttatactgttcaaattcttgcagTACACACCAGCAATAGATATATGGAGCATCGGTTGCATATTTGCAGAACTTTTAACAGGAAAACCTCTTTTCCCCGGGAAAAATGTGGTGCATCAACTTG

upper sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os05g05160.1 (Oryza sativa), 3'ss of exon 4
gtgaccatgattttgtatatatactttcatcgaatgtttcaaattttcatagggaatctagtcagtagacactatagctctctcattcagattataaaattttatggtaacattttttttctttatctatgcttctgttcagTATACACCGGCAATAGATATATGGAGCATCGGGTGCATTTTTGCAGAACTCTTAACAGGGAAACCTCTTTTCCCCGGGAAAAATGTGGTCCATCAATTGG
         | | |  | || || | ||         ||  | ||||   | ||  |              ||||   | ||  ||    ||   ||      |||   | | | | |||| |||| |         | ||||||||||| ||||||||||||||||| || || ||||| ||||| || || ||||| || |||||||||||||| ||||| |||||||| |||||| | |
--------aagtgtacacatgtattctc--------cttttattttttgcatgggctt-------------ctatgtttgtccaat----atccgaagcaccgatgaacataatgtgtttcattattt---------tgcagTATACACCAGCAATAGATATATGGAGTATTGGCTGCATATTTGCCGAGCTTTTAACCGGAAAACCTCTTTTCCCTGGGAAGAATGTGGTTCATCAACTTG

upper sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G089484_T01 (Zea mays), 3'ss of exon 4
gtgaccatgattttgtatatatactttcatcgaatgtttcaaattttcatagggaatctagtcagtagacactatagctctctcattcagattataaaat-tttatggtaacattttttt--tctttatctatgcttctgttcagTATACACCGGCAATAGATATATGGAGCATCGGGTGCATTTTTGCAGAACTCTTAACAGGGAAACCTCTTTTCCCCGGGAAAAATGTGGTCCATCAATTGG
                               || |||| || |||| | |       ||   | ||     | || || ||    |  || || | |||| | |   | | ||||       | | | | | |  || | |  ||||||||||||| |||||||||||||| || || || || ||||||||| | ||||| || |||||||||||||| |||||||||||||| |||||| | |
-------------------------------gattgttgcatatttcctt-------ctcacctgtt----ccatggccct---gtatagtttgtgaaatatctggagcaccattgaacaaatatgtgttttttgttttttgtagTATACACCGGCGATAGATATATGGAGTATTGGCTGTATATTTGCAGAATTGTTAACTGGAAAACCTCTTTTCCCGGGGAAAAATGTGGTACATCAACTTG

upper sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G017351_T01 (Zea mays), 3'ss of exon 3
gtgaccatgattttgtatatatactttcatcgaatgtttcaaattttcatagggaatctagtcagtagacactatagctctctcattcagattataaaattttatggtaacattttttttctttatctatgcttctgttcagTATACACCGGCAATAGATATATGGAGCATCGGGTGCATTTTTGCAGAACTCTTAACAGGGAAACCTCTTTTCCCCGGGAAAAATGTGGTCCATCAATTGG
                                 ||| |     | |||||| | |   |      |      ||||  |  ||  |  || || |   || |    | || | | ||   | || |    | || | | ||||||||||| || |||||||||||||| || || || || ||||| ||||| ||||| || ||||| |||||||| |||||||||||||| |||||| | |
--------------------------------catgctcttt-tgttcataagaagcttcactcttg-----tataattgccttgtatagtttgttcgatatctgaggaatactgttgaacattgt----gtttttttacagTATACACCAGCGATAGATATATGGAGTATTGGTTGTATATTTGCGGAACTATTAACTGGAAAACCGCTTTTCCCGGGGAAAAATGTGGTACATCAACTTG

upper sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G02220.1 (Glycine max), 3'ss of exon 4
gtgaccatgattttgtatatatactttcatcgaatgtttcaaattttcatagggaatctagtcagtagacactatagctctctcattcagattataaaattttatggtaacattttttttctttatctatgcttctgttcagTATACACCGGCAATAGATATATGGAGCATCGGGTGCATTTTTGCAGAACTCTTAACAGGGAAACCTCTTTTCCCCGGGAAAAATGTGGTCCATCAATTGG
                                          ||  | |  |   |  | ||    | | |  | |  |   |  |   | || | ||||      | |  ||   | || ||    | |  ||   |||||||||| || || ||||| ||||||||||| || ||||||||||||||||| ||||| || |||||||||||||| ||||| ||||| |||||||||||||
------------------------------------------atagttactgcttactttgtagtcaaataaaaaaaatggttgctagtgtttgtgaaatgaagatggataatcaatgttgttataatcttttttctttcagTATACCCCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCAGAACTTTTAACTGGAAAACCTCTTTTCCCAGGGAAGAATGTTGTCCATCAATTGG

upper sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G38510.1 (Glycine max), 3'ss of exon 3
gtgaccatgattttgtatatatactttcatcgaatgtttcaaattttcatagggaatctagtcagtagacactatagctctctcattcagattataaaattttatggtaacattttttttctttatctatgcttctgttcagTATACACCGGCAATAGATATATGGAGCATCGGGTGCATTTTTGCAGAACTCTTAACAGGGAAACCTCTTTTCCCCGGGAAAAATGTGGTCCATCAATTGG
                             | | |  | |   ||     ||   |  |   | | | |   |||  | |     | | |   |  | |||       |    || |  |  ||| |||         |||||||||| || || ||||| ||||||||||| || |||||||| |||||||| ||||| || |||||||||||||| ||||| ||||| |||||||||||||
-----------------------------taggagttattttatccctctaaccatgcctattaatggttgctagtgtttgtgaaatgaagatggataatc----aatgttgttataatcttttgtct---------ttcagTATACCCCAGCTATAGACATATGGAGCATTGGCTGCATTTTCGCAGAACTTTTAACTGGAAAACCTCTTTTCCCAGGGAAGAATGTTGTCCATCAATTGG

upper sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G28120.1 (Glycine max), 3'ss of exon 4
gtgaccatgattttgtatatatactttcatcgaatgtttcaaattttcatagggaatctagtcagtagacactatagctctctcattcagattataaaattttatggtaacattttttttctttatctatgcttctgttcagTATACACCGGCAATAGATATATGGAGCATCGGGTGCATTTTTGCAGAACTCTTAACAGGGAAACCTCTTTTCCCCGGGAAAAATGTGGTCCATCAATTGG
                                  ||    |  |||  ||   |  |||    |  | |     |   | ||| || | |    |  | ||    |  ||||| |||  || | | || |  || |  |||||||||||| || ||||| ||||||||||| || ||||||||||||||||| || || || |||||||||||||| ||||| ||||| ||||||||| | |
----------------------------------tggacaatgtttctat---gcttctgtgtaccataatgatttattatcttatcccggacctggacttg---gtaaacatatttggtcataaacttttgtttt--tcagTATACACCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCAGAACTTTTGACGGGAAAACCTCTTTTCCCTGGGAAGAATGTTGTCCATCAACTAG

upper sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G10940.4 (Glycine max), 3'ss of exon 4
gtgaccatgattttgtatatatactttcatcgaatgtttcaaattttcatagggaatctag---tcagtagacactatagctctctcattcagattataaaattttatggtaacattttttttctttatctatgcttctgttcagTATACACCGGCAATAGATATATGGAGCATCGGGTGCATTTTTGCAGAACTCTTAACAGGGAAACCTCTTTTCCCCGGGAAAAATGTGGTCCATCAATTGG
                                         || ||  | |  |  ||||    || ||  ||  ||  | | | | ||    ||  |  | |||   |  || || |||  || | | || |  || |  |||||||||||| || ||||| ||||||||||| || ||||||||||| ||||| || || || |||||||||||||| ||||| ||||| || |||||| | |
---------------------------------------tgaagttggacaatgcttctatgcttctgtgtaccttaatgatttattatctt-atcctggacttt---gtaaatatatttggtcataaacttttgtttt--tcagTATACACCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCTGAACTTTTGACCGGAAAACCTCTTTTCCCTGGGAAGAATGTTGTTCATCAACTAG

upper sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 4
gtgaccatgattttgtatatatactttcatcgaatgtttcaaattttcatagggaatctagtcagtagacactatagctctctcattcagattataaaattttatggtaacattttttttctttatctatgcttc-tgttcagTATACACCGGCAATAGATATATGGAGCATCGGGTGCATTTTTGCAGAACTCTTAACAGGGAAACCTCTTTTCCCCGGGAAAAATGTGGTCCATCAATTGG
                                           |  | ||   |  || |     | |||| ||     |  |  |  || |   | |  | |    | ||  |  ||||| || |   |  ||| | ||||||||||||| |||||||||||||||||||| || ||||| |||||||| || ||||| || |||||||| || || || |||||||| || || |||||||
-------------------------------------------tcatgattcagtgtccatcatattgacaatagttaaccatactctaggtatgatacctgtgatctgactgtcattttcgtttttgctctttcattttcagTATACACCAGCAATAGATATATGGAGCATTGGATGCATCTTTGCAGAGCTTTTAACTGGAAAACCTCTCTTTCCTGGAAAAAATGTTGTTCACCAATTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagattataaaattttatggtaacattttttttctttatctatgcttctgttcagTATACACCGGCAATAGATATATGGAGCATCGGGTGCATTTTTGCAGAACTCTTAACAGGGAAACCTCTTTTCCCCGGGAAAAATGTGGTCCATCAATTGG
                 tggtaac  putative branch site (score: 2)
                         ttttttttctttatct  CT-rich tract
     tataaaattttatggt  TA-rich tract