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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatcttaaactcataaacatttccctcttctataccgcttgttcttcactcctcagtttccaaaatcttcagattcttttgtttactccggaggatactgagttgtgtccttgagtttctaatcttatctttctgttttaagtttaccttttcagtgctttctgatgttttttcccccttcagATTGTTCTCTTGTGGAACGAGTAAAGATGGAGATTCTTTCCTAGTTGAGTGGAATGAAAGTGAAGGATCAATTAAAAGGACGTATAAAGAGTTTCAGAAA

Basic information

species Arabidopsis thaliana
transcript AT5G27030.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G27030.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 14
gtaagatcttaaactcataaacatttccctcttctataccgcttgttcttcactcctcagtttccaaaatcttcagattcttttgtttactccggaggatactgagttgtgtccttgagtttctaatcttatctttctgttttaagtttaccttttcagtgctttctgatgttttttcccccttcagATTGTTCTCTTGTGGAACGAGTAAAGATGGAGATTCTTTCCTAGTTGAGTGGAATGAAAGTGAAGGATCAATTAAAAGGACGTATAAAGAGTTTCAGAAA
                                                                                                | |  | ||| | | | |||  ||  | ||  || |||||           |||   ||   || ||   | |  | |||| |   |  || |||||||| |||||||| ||||||||||||||||| |   |||||||||||||||||||||||||||| || || ||||| |||   | |||||  |||
------------------------------------------------------------------------------------------------gtaagcagaggtat-tactttcgtaccgaaagttgtcttt---------agttattgttgttgtactaatttacttgtttttcatatgaagGTTGTTCTCATGTGGAACAAGTAAAGATGGAGATTCATATTTAGTTGAGTGGAATGAAAGTGAAGGATCTATCAAGAGGACATATTCTGGGTTTCGTAAA

upper sequence: AT5G27030.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 14
gtaagatcttaaactcataaacatttccctcttctataccgcttgttcttcactcctcagtttccaaaatcttcagattcttttgtttactccggaggatactgagttgtgtccttgagtttctaatcttatct--ttct-gttttaagtttaccttttcagtgctttctgatgttttttcccccttcagATTGTTCTCTTGTGGAACGAGTAAAGATGGAGATTCTTTCCTAGTTGAGTGGAATGAAAGTGAAGGATCAATTAAAAGGACGTATAAAGAGTTTCAGAAA
                                                                                               || ||| | || |  |  |||   ||| | | |  |  |  |||| ||||| | |||    |       |  | ||   |||| | |   |  || |||||||| |||||||| || ||||| ||||| || |   | |||||||||||||||||||||||||| || || ||||| |||   |  || |  |||
--------------------------------------------------------------------------------------------gtaagaatagttaggttggctcttatttttatcaccaaagttagttctagttttcaatttttactgaggaaacaatttgcc-ttttcttcatgtgaagGTTGTTCTCATGTGGAACTAGCAAAGAGGGAGACTCCTATTTGGTTGAGTGGAATGAAAGTGAAGGATCTATCAAGAGGACATATTCTGGATTCCGTAAA

upper sequence: AT5G27030.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA10G29090.1 (Glycine max), 3'ss of exon 15
gtaagatcttaaactcataaacatttccctcttctataccgcttgttcttcactcctcagtttccaaaatcttcagattcttttgtttactccggaggatactgagttgtgtccttgagtttctaatcttatctttctgttttaagtttaccttttcagtgctttctgatgttttttcccccttcagATTGTTCTCTTGTGGAACGAGTAAAGATGGAGATTCTTTCCTAGTTGAGTGGAATGAAAGTGAAGGATCAATTAAAAGGACGTATAAAGAGTTTCAGAAA
                                                        | ||||    |    |   | |  || |   |   | | |  || ||  || |  |  | ||  ||  |    |||  |  |     ||||||    ||       ||||  |  | ||||| ||    || || || |||||||| || |||||||||||||| ||||| || ||||| |||||||||||||||||| | ||||| || || || || |  ||    |||
-------------------------------------------------------gtaagttggatatggatgagggtaattattcctttacagtatcatgcttggt-gcttggtggacgtttaagatgtattatatta----aagttt---cttatgacattttccaaaatattttctcc----agGTTATTTTCTTGTGGGACAAGTAAAGATGGAGAGTCTTTTCTTGTTGAATGGAATGAAAGTGAAGGAGCCATTAAGAGAACATACAATGGATTCAGAAAA

upper sequence: AT5G27030.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA20G38230.1 (Glycine max), 3'ss of exon 15
gtaagatcttaaactcataaacatttccctcttctataccgcttgttcttcactcctcagtttccaaaatcttcagattcttttgtttactccggaggatactgagttgtgtccttgagtttctaatcttatctttctgttttaagtttaccttttcagtgctttctgatgttttttcccccttcagATTGTTCTCTTGTGGAACGAGTAAAGATGGAGATTCTTTCCTAGTTGAGTGGAATGAAAGTGAAGGATCAATTAAAAGGACGTATAAAGAGTTTCAGAAA
                                                              |   |    ||  |||     |  ||| ||    || ||| |  |  ||  |   | |   ||||       |  | | ||||  || | | |      |||||  |  | ||||| ||    || || || |||||||| || |||||||||||||| ||||| || ||||| |||||||||||||||||  | || || || || || || |  ||    |||
-------------------------------------------------------------gtaagatggatttggatgagggtaattattc----ggttacagtatcatgctc---aatggataattaagatgtattatattaaagtttcttat--gacactttccaaaatattttctcc----agGTTATTTTCTTGTGGGACAAGTAAAGATGGAGAGTCTTTTCTTGTTGAATGGAATGAAAGTGAAGGCGCCATCAAGAGAACATACAATGGATTCAGAAAA

upper sequence: AT5G27030.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 15
gtaagatcttaaactcataaacatttccctcttctataccgcttgttcttcactcctcagtttccaaaatcttcagattcttttgtttactccggaggatactgagtt--gtgtcc--ttgagtttctaatcttatctttctgttttaagtttaccttttcagtgctttctgatgttttttcccccttcagATTGTTCTCTTGTGGAACGAGTAAAGATGGAGATTCTTTCCTAGTTGAGTGGAATGAAAGTGAAGGATCAATTAAAAGGACGTATAAAGAGTTTCAGAAA-
                                                                        | |||    ||||  | |     || ||  | ||||   ||| |  | ||   |  ||| | |  | | |    |||       ||  ||   ||| ||  |  |  ||    ||  ||| |||| ||||| ||||| |||||||||||||| || || || ||||| |||||||||||||||||| | ||||| || || || || | ||| |||||| 
-----------------------------------------------------------------------gtaagaaggatttgggtgcggataagtat-ttaagtttcatgttcaatggataattgaatttgagatgtattaaataaaaccgtattaacatgtcttcctatttatcattatttctatagACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAGTCATTTCTTGTTGAATGGAATGAAAGTGAAGGAGCCATTAAGAGAACATACAATGGGTT-CAGAAAG

upper sequence: AT5G27030.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA19G41840.2 (Glycine max), 3'ss of exon 14
gtaagatcttaaactcataaacatttccctcttctataccgcttgttcttcactcctcagtttccaaaatcttcagattcttttgtttactccggagg-atactgagttgtgtccttgagtttctaatcttatctttctgttttaagtttaccttttcagtgctttctgatgttttttcccccttcagATTGTTCTCTTGTGGAACGAGTAAAGATGGAGATTCTTTCCTAGTTGAGTGGAATGAAAGTGAAGGATCAATTAAAAGGACGTATAAAGAGTTTCAGAAA-
                                                              |   ||   ||  | | |   |   || |   |    ||  | | | |  |  || || |    ||   ||    | || ||||  |  | |  |   ||  |||   | |||       ||  ||| |||| ||||| ||||| |||||||||||||| || || || ||||| ||||||||||||||| || | ||||| || || || || | ||| |||||| 
-------------------------------------------------------------gtaagaaggatttgggtgcggataagtatttaagtttcatgttcaatgg-ataattaagatgt--attaaataaaaccgtattaacatgtcttcctatttgtcttccattattt-------ctatagACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAATCATTTCTTGTTGAATGGAATGAAAGTGAAAGAGCTATTAAGAGAACATACAATGGGTT-CAGAAAG

upper sequence: AT5G27030.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 14
----------------gtaagatcttaaactcataaacatttccctcttctataccgcttgttcttcactcctcagtttccaaaatcttcagattcttttgtttactccggaggatactgagttgtgtccttgagtttctaatcttatctttctgttttaagttt---accttttcagtg--ctttctgatgttttttcccccttcagATTGTTCTCTTGTGGAACGAGTAAAGATGGAGATTCTTTCCTAGTTGAGTGGAATGAAAGTGAAGGATCAATTAAAAGGACGTATAAAGAGTTTCAGAAA
                  |  ||   | ||  |  || ||||   | || |||    ||| ||  ||| |    | |||| |   |  |   ||  | || |      |     ||||     ||||         || | |||  || | ||||    ||  ||   | ||  |  |||   ||| |  |  | ||   |  ||||||||||||||||||||||| ||||||||||| || |||||  | ||||| |||||||||||||||||| |||| || ||||||||||| | ||||   || 
gtaagattggtgaaattcacaattccagacctaataaaattt---tattttatttttctttttgctcaatttaaaatttcaacttttctgtaatgttgttatagttgtcttttcataccatactgtgct-----acttttgatcaaatatatctgacagaacatttgtaactaatttgtgactttttttttcctcttcttcttttcagATTGTTCTCTTGTGGAACAAGTAAAGATGGGGACTCTTTTTTGGTTGAATGGAATGAAAGTGAAGGAGCAATAAAGAGGACGTATAATGGGTTTAGAAAG

upper sequence: AT5G27030.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: EFJ30926 (Selaginella moellendorffii), 3'ss of exon 14
gtaagatcttaaactcataaacatttccctcttctataccgcttgttcttcactcctcagtttccaaaatcttcagattcttttgtttactccggaggatactgagttgtgtccttgagtttctaatcttatctttctgttttaagtttaccttttcagtgctttc-tgatgttttttcccccttcagATTGTTCTCTTGTGGAACGAGTAAAGATGGAGATTCTTTCCTAGTTGAGTGGAATGAAAGTGAAGGATCAATTAAAAGGACGTATAAAGAGTTTCAGAAA
                                                                                                                                            |||   |  ||||||   ||  || | | |  |  |||     | ||||||||| ||||||||||| || || ||||| || ||||| || || ||||||||||||||||||||  |||||||||  || || || |  |||| ||||
-------------------------------------------------------------------------------------------------------------------------------------------gtttgcttcaaccttt--ggtatttccatcacatcctttgtttttccagATTGTTTTCTTGTGGAACAAGCAAGGATGGTGAGTCTTTTCTTGTGGAGTGGAATGAAAGTGAAGGTGCAATTAAAAACACCTACAATGGTTTTCGGAAA

upper sequence: AT5G27030.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: EFJ17248 (Selaginella moellendorffii), 3'ss of exon 14
gtaagatcttaaactcataaacatttccctcttctataccgcttgttcttcactcctcagtttccaaaatcttcagattcttttgtttactccggaggatactgagttgtgtccttgagtttctaatcttatctttctgttttaagtttaccttttcagtgctttctgatgttttttcccccttcagATTGTTCTCTTGTGGAACGAGTAAAGATGGAGATTCTTTCCTAGTTGAGTGGAATGAAAGTGAAGGATCAATTAAAAGGACGTATAAAGAGTTTCAGAAA
                                                                                                                                            |||   |  ||||||   ||  || |      |  ||     | ||||||||| ||||||||||| || || ||||| || ||||| || || ||||||||||||||||||||  |||| ||||  || || || |  |||| ||||
-------------------------------------------------------------------------------------------------------------------------------------------gtttgcttcaaccttt--ggtatttccatcacatcctttgttttccagATTGTTTTCTTGTGGAACAAGCAAGGATGGTGAGTCTTTTCTTGTGGAGTGGAATGAAAGTGAAGGTGCAATAAAAAACACCTACAATGGTTTTCGGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttctgttttaagtttaccttttcagtgctttctgatgttttttcccccttcagATTGTTCTCTTGTGGAACGAGTAAAGATGGAGATTCTTTCCTAGTTGAGTGGAATGAAAGTGAAGGATCAATTAAAAGGACGTATAAAGAGTTTCAGAAA
                               ttctgat  putative branch site (score: 3)
                             ctttctgatgtttttt  CT-rich tract
       ttttaagttta  TA-rich tract