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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatctttgccatacttccctgtttttccgatttggtattgcgttattagtttttaaccaattaacatcaacatcatttggggtttcttacatagGGATTTGAGAAGATGATATCAGGAATGTATCTGGGTGACATTGTTCGTAGAGTAATTCTCCGCATGTCAGAAGATTCTGATATCTTTGGACCCATCTCGC

Basic information

species Arabidopsis thaliana
transcript AT1G50460.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G50460.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os01g71320.1 (Oryza sativa), 3'ss of exon 6
---gtaatctttgccatacttccctgtttttccgatttggtattgcgttattagtttttaaccaattaacatcaacatcatttggggtttcttacatagGGATTTGAGAAGATGATATCAGGAATGTATCTGGGTGACATTGTTCGTAGAGTAATTCTCCGCATGTCAGAAGATTCTGATATCTTTGGACCCATCTCGC--
   | || ||  |  | | |    | || |    || | || ||| | | ||||  |   | || ||   |  | ||| |||  ||| ||              |||||| |||||||||||||||||||| || || ||||   |    ||| |||   | ||| |  | || || ||| | |||||    ||   ||  
gtagcaacctgggtaaaattcaattattctggt-atcttgtgttgtggt-ttagact--gaacactttgtactaccatgattcagGGCTT--------------TGAGAAAATGATATCAGGAATGTATCTTGGGGAAATTGCAAGATTGGTATTTCATAGAATGGCCCAGGAATCAGATGTTTTTGG--TGATGCTGCTG

upper sequence: AT1G50460.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA01G43650.1 (Glycine max), 3'ss of exon 6
gtaatctttgccatacttccctgtttttccgatttggtattgcgttattagtttttaaccaattaacatcaacatcattt-ggggtttcttacatagGGATTTGAGAAGATGATATCAGGAATGTATCTGGGTGACATTGTTCGTAGAGTAATTCTCCGCATGTCAGAAGATTCTGATATCTTTGGACCCATCTCGC
                           |  | || || |||   | | |  | ||     | ||  ||| |  |  |||| || | ||       |||| |||||||| |||||||||||||||||||| |||||||||||  | ||||| |||||    ||||||  ||| || ||||| |||||||| || || |
--------------------------gtgaggttcggcatttgatgactcctgttgcttgatttgtcatgactaaaattttggagatttgggtgcagGGTTTTGAGAAAATGATATCAGGAATGTATCTTGGTGACATTGTGAGAAGAGTCATTCTTAAGATGTCATTAGAGTCGGATATGTTTGGACCAATTTCTC

upper sequence: AT1G50460.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA11G10130.1 (Glycine max), 3'ss of exon 6
gtaatctttgccatacttccctgtttttccgatttggtattgcgttattagtttttaaccaattaacatcaacatcatttggggtttcttacatagGGATTTGAGAAGATGATATCAGGAATGTATCTGGGTGACATTGTTCGTAGAGTAATTCTCCGCATGTCAGAAGATTCTGATATCTTTGGACCCATCTCGC
                      ||| |   | |   | ||   |||  | | ||       | | | ||||  ||  |||||   || | |  ||||| |||||||| |||||||||||||||||||| |||||||| ||  | ||||| |||||  | ||||    ||| || ||||| |||||||| || ||  
-----------------gttaggttctgttgctcacgaatccagttgcttgattcaggatgactcaaatcag-at--tttggaaattttgatgtagGGTTTTGAGAAAATGATATCAGGAATGTATCTTGGTGACATCGTGAGGAGAGTCATTCTAAGGATGTTGCTAGAGTCAGATATGTTTGGACCTATTTCTT

upper sequence: AT1G50460.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA11G01820.1 (Glycine max), 3'ss of exon 6
gtaatctttgccatacttccctgtttttccg-atttggtattgcgttattagtttttaaccaattaacatcaacatcatttggggtttcttacatagGGATTTGAGAAGATGATATCAGGAATGTATCTGGGTGACATTGTTCGTAGAGTAATTCTCCGCATGTCAGAAGATTCTGATATCTTTGGACCCATCTCGC
                     ||  |||| | || || |       |  |  |  || |    | |  |  || ||  ||||| | ||       |||| |||||||| |||||||||||||||||||| |||||||| ||  | ||||| ||||||   ||||||  ||| || ||||| |||||||| || || |
--------------------gtgagtttctgcatctgatg----actcctgttgcttgatttgtcatgactaaaat--tttggagatttgggtgcagGGTTTTGAGAAAATGATATCAGGAATGTATCTTGGTGACATCGTGAGAAGAGTCATTCTCAAGATGTCATTAGAGTCGGATATGTTTGGACCAATTTCTC

upper sequence: AT1G50460.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA12G02450.1 (Glycine max), 3'ss of exon 6
gtaatctttgccatacttccctgtttttccgatttggtattgcgttattagtttttaaccaattaacatcaacatcatttggggtttcttacatagGGATTTGAGAAGATGATATCAGGAATGTATCTGGGTGACATTGTTCGTAGAGTAATTCTCCGCATGTCAGAAGATTCTGATATCTTTGGACCCATCTCGC
                      ||| | | | |   | ||   |||  | | ||  |    | | | ||||  ||  ||||    || | |  ||||| |||||||| |||||||| ||||||||||| |||||||| ||  | ||||| |||||  | |||||   ||| || |||||  ||||||| || ||  
-----------------gttaggttctgctgctcatgaatcctgttgcttgattcaagatgactcaaatcag-at--tttgctaattttgatgtagGGTTTTGAGAAAATGATATCTGGAATGTATCTTGGTGACATCGTGAGGAGAGTCATTCTAAGGATGTCGCTAGAGTCAGATATGCTTGGACCTATTTCTT

upper sequence: AT1G50460.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv06s0061g00040.t01 (Vitis vinifera), 3'ss of exon 6
gtaatctttgccatacttccctgtttttccgatttggtattgcgttattagtttttaaccaattaacatcaacatcatttggggtttcttacatagGGATTTGAGAAGATGATATCAGGAATGTATCTGGGTGACATTGTTCGTAGAGTAATTCTCCGCATGTCAGAAGATTCTGATATCTTTGGACCCATCTCGC
                        ||     | |||   |||  |  |   | ||  |   |  || ||||| ||  |||| || || |     |||| |||||||| ||||||||||| |||||  |||||||||||||  | ||||| |||||| | |||||| | || || || || ||||||||  | ||  
------------------gtacagttcaattacttgcccttgtctcttcgatgttccagtgaacaa-atcaagat--tttgaggcttttgtttcagGGTTTTGAGAAAATGATATCAGGGATGTACTTGGGTGACATTGTGAGGAGAGTTATTCTCAGAATGTCACAGGAGTCAGACATTTTTGGACCTGTTTCTT

upper sequence: AT1G50460.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ14634 (Selaginella moellendorffii), 3'ss of exon 6
gtaatctttgccatacttccctgtttttccgatttggtattgcgttattagtttttaaccaattaacatcaacatcatttggggtttcttacatagGGATTTGAGAAGATGATATCAGGAATGTATCTGGGTGACATTGTTCGTAGAGTAATTCTCCGCATGTCAGAAGATTCTGATATCTTTGGACCCATCTCGC
                                               | || |  |  | ||||      |           | | |      ||||  ||||||||| || | || |||||||||||||||||||||||  | || || ||||||    |  |  | ||| |     | |||||   || |   |
----------------------------------------------gtgagatacttgc-aattgcttgtacagctgacgcagctgtgcctggtagGCGTTTGAGAAGCTGTTTTCGGGAATGTATCTGGGTGACATTGTGAGGAGGGTCATTCTCAAGCTTGCGCAGGATGCCTGCCTATTTGGCGGCAGCATAC

upper sequence: AT1G50460.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ25912 (Selaginella moellendorffii), 3'ss of exon 6
gtaatctttgccatacttccctgtttttccgatttggtattgcgttattagtttttaaccaattaacatcaacatcatttggggtttcttaca---tagGGATTTGAGAAGATGATATCAGGAATGTATCTGGGTGACATTGTTCGTAGAGTAATTCTCCGCATGTCAGAAGATTCTGATATCTTTGGACCCATCTCGC
                                       |    ||   | |    |   ||  ||   | ||   |       | | ||  |   |||  ||| |||||||||||||| |||||||| ||||||||||||||  | |||||  |        || | |  ||  | |   ||||||||   |     |
--------------------------------------gtaagcttgaaaatgaccacaaaaacaattcctaccctaccctacctgtgttggactgtagATATTCGAGAAGATGATATCTGGAATGTACCTGGGTGACATTGTGAGGAGAGTGTTGTGGAAACTGGCTGCCGAAGCGGCATTCTTTGGAGGAAAGGTAC

upper sequence: AT1G50460.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ10895 (Selaginella moellendorffii), 3'ss of exon 6
gtaatctttgccatacttccctgtttttccgatttggtattgcgttattagtttttaaccaattaacatca-acatcatttggggtttcttacatagGGATTTGAGAAGATGATATCAGGAATGTATCTGGGTGACATTGTTCGTAGAGTAATTCTCCGCATGTCAGAAGATTCTGATATCTTTGGACCCATCTCGC
                                  |    |||    || |      || |||||   | |  ||   |  || | ||   |   |||  ||| ||||| |||||||| |||||||| ||||||||||||||  | |||||  |        || | |  ||  | |   ||||||||   |     |
---------------------------------gtaagcttgaaa-atgaccacaaaaacaattcctaccctaccctacctgtgtttgactg--tagATATTCGAGAAAATGATATCTGGAATGTACCTGGGTGACATTGTGAGGAGAGTGTTGTGGAAACTGGCTGCCGAAGCGGCATTCTTTGGAGGAAAGGTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgttattagtttttaaccaattaacatcaacatcatttggggtttcttacatagGGATTTGAGAAGATGATATCAGGAATGTATCTGGGTGACATTGTTCGTAGAGTAATTCTCCGCATGTCAGAAGATTCTGATATCTTTGGACCCATCTCGC
                                            ttcttac  putative branch site (score: 2)
                                           tttcttac  CT-rich tract
          tttttaaccaattaa  TA-rich tract