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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactctttttcttctacacattttgatttgatttggacatgatttggccagaggttccttccttagcatgtgatttgggtgaccggttgattctgtatcgaatttggtctaagactttctgctttatgtgattctaattttgaagGGACGTAATGTTGTGATTGAGCAAAGTTGGGGTGCTCCTAAAGTGACAAAAGATGGTGTTACTGTTGCCAAAAGTATTGAGTTCAAAGACAAAATTAAGA

Basic information

species Arabidopsis thaliana
transcript AT3G23990.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os03g04970.1 (Oryza sativa), 3'ss of exon 3
gtactctttttcttctacacattttgatttgatttggacatgatttggccagaggttccttccttagcatgtgatttgggtg-accggttgattctgtatcgaatttggtctaagactttctgctttatgtgattctaattttgaagGGACGTAATGTTGTGATTGAGCAAAGTTGGGGTGCTCCTAAAGTGACAAAAGATGGTGTTACTGTTGCCAAAAGTATTGAGTTCAAAGACAAAATTAAGA
                                             |     ||| || |||  ||||  | | ||     |  | | ||  ||| ||      ||   |   |  |  ||  |||  || | | |   || ||| ||||||| | |||||| ||||||||||| |  |||||||||||||| ||||| ||||| |||||||||||||| || ||||| ||||   |||   ||||||
--------------------------------------------gttatgtgagattgcttttttagttttttatggatctttaacagtacattttgggagttatcatgcaaacaatgttgagctcaatataact---atgttgcagGGACGCACTGTTGTTATTGAGCAAAGCTTTGGTGCTCCTAAAGTTACAAAGGATGGAGTTACTGTTGCCAAGAGCATTGAATTCAGTAACAGGGTTAAGA

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 3
gtactctttttcttctacacattttgatttgatttggacatgatttggccagaggttccttccttagcatgtgatttgggtgaccggttgattctgtatcgaatttggtctaagactttctgctttatgtgattctaattttgaagGGACGTAATGTTGTGATTGAGCAAAGTTGGGGTGCTCCTAAAGTGACAAAAGATGGTGTTACTGTTGCCAAAAGTATTGAGTTCAAAGACAAAATTAAGA
                                                    | |  |  |  | |   ||   |||  |||    |   ||| || |  |  | | ||||  |  | |     ||  ||  || | || ||  |||| |||||||||||||||||||||||||  ||||| |||||||| || |||||||| || |||||||| || || ||||| ||||| || ||| ||||||
-------------------------------------------aacaaaagaatgaacgatgttaatgctggactttttgtgtattgcc-attgtgcaatgggtgttgtctgtgtttgttgatgttgagt--ttattatcttttagGGCCGTAATGTTGTGATTGAGCAAAGTTTTGGTGCCCCTAAAGTAACCAAAGATGGAGTAACTGTTGCAAAGAGCATTGAATTCAAGGATAAAGTTAAGA

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 3
gtactctttttcttctacacattttgatttgatttggacatgatttggccagaggttccttccttagcatgtgatttgggtgaccggttgattctgtatcgaatttggtctaagactttctgctttatgtgattctaattttgaagGGACGTAATGTTGTGATTGAGCAAAGTTGGGGTGCTCCTAAAGTGACAAAAGATGGTGTTACTGTTGCCAAAAGTATTGAGTTCAAAGACAAAATTAAGA
                                               | || || |        | |  |||    |  |||    |   ||| || |     | | ||||  |    |     ||  ||  || |  | ||  |||| |||||||||||||||||||||||||  ||||| |||||||| || |||||||| || |||||||| || || ||||| ||||| || ||| ||||||
-------------------------------------------aacagtcaaagatgttaatgctggactgttgagtttgtgtattgcc-attgtgcaataggtgttgtctgtgttggttgatgttgagt--ttattctcttttagGGGCGTAATGTTGTGATTGAGCAAAGTTTTGGTGCCCCTAAAGTAACCAAAGATGGAGTAACTGTTGCAAAGAGCATTGAATTCAAGGATAAAGTTAAGA

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 3
---------------------------------------gtactctttttcttctacacattttgatttgatttggacatgatttggccagaggttccttccttagcatgtgatt--tgggtgaccggttgattctgtatcgaatttggt-ctaagactttctgctttatgtga-ttctaattttgaagGGACGTAATGTTGTGATTGAGCAAAGTTGGGGTGCTCCTAAAGTGACAAAAGATGGTGTTACTGTTGCCAAAAGTATTGAGTTCAAAGACAAAATTAAGA
                                       ||||   | || || | ||    || ||||   || |   |  |  ||  ||||  |   |  |     |  ||||  |   | |    | |   | | ||   | |||||  | |       || ||| |   | || |  ||||  |||| |||||||| || |||||||||||||  || || ||||||||||| |||||||| || || ||||| || || ||||| ||||| |||||| | ||||
gtaaccaagcttatgcctgatagtttcttggcaaaagttgtacctgtgtttttattcaatcatttattta--ttcggttttctaagggtagagcatgtcttttggatctaggattgatatttcaatcctagtcccggcattttagttggtgttgatcacgattgttttgttaaacttgtgtttttttagGGGCGTAATGTGGTTATTGAGCAAAGTTTTGGAGCACCTAAAGTGACGAAAGATGGAGTAACCGTTGCTAAGAGCATTGAATTCAAGGACAAAGTCAAGA

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 3
gtactctttttcttctacacattttgatttgatttggacatgatttggccagaggttccttccttagcatgtgatttgggtgaccggttgattctgtatcgaatttggtctaagactttctgctttatgtgattctaattttgaagGGACGTAATGTTGTGATTGAGCAAAGTTGGGGTGCTCCTAAAGTGACAAAAGATGGTGTTACTGTTGCCAAAAGTATTGAGTTCAAAGACAAAATTAAGA
                                   | |  |  |||||    ||| |        | ||| | | |   ||   |  || ||| || || |   ||| || | || | |     |||  |   | |  ||||  |||| |||||||| || |||||||||||||  || || || ||||||||||||||||| || || ||||| || || ||||| ||||| || ||| | ||||
-----------------------------------gaatgtcttttggatccaggcttga-----aacatatcaat--agtagtcccttcattttg-attggtgttgatc-acgattgttattgttaaattggtgt--ttttatagGGGCGTAATGTGGTTATTGAGCAAAGTTTTGGAGCACCCAAAGTGACAAAAGATGGAGTAACCGTTGCTAAGAGCATTGAATTCAAGGATAAAGTCAAGA

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 3
gtactctttttcttctacacattttgatttgatttggacatgatttggccagaggttccttccttagcatgtgatttgggtgaccggttgattctgtatcgaatttggtctaagactttctgctttatgtgattctaattttgaagGGACGTAATGTTGTGATTGAGCAAAGTTGGGGTGCTCCTAAAGTGACAAAAGATGGTGTTACTGTTGCCAAAAGTATTGAGTTCAAAGACAAAATTAAGA
                                        |||||   |  |  |   |||  ||    | |   ||| | |   |||| |||  |    |  ||     ||| |     |  |    ||  |  |  ||    |||| ||||| || ||  | ||||||||||  ||||| || |||||||||||||||||||| |||||||| ||||| ||||||||||| ||   ||| ||||
---------------------------------------ttgatt---cttggtgcatcttatttcaattctctattgagggttgggttaatt--gatgtggtttatacttaaaaaaggttaatcagcgttttgttgtttcc--agGGGCGTAACGTGGTACTAGAGCAAAGTTTTGGTGCCCCAAAAGTGACAAAAGATGGTGTAACTGTTGCAAAAAGCATTGAGTTCAAGGATCGAATCAAGA

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S52_245V6.1 (Physcomitrella patens), 3'ss of exon 3
------------gtactctttttcttct--------acacattttga----tttgatt-tggacat----gatttggccagaggttccttccttagcatgtgatttgggtgaccggttgattctgtatcgaattt---ggtctaagactttctgctttatgtgattctaatttt---gaagGGACGTAATGTTGTGATTGAGCAAAGTTGGGGTGCTCCTAAAGTGACAAAAGATGGTGTTACTGTTGCCAAAAGTATTGAGTTCAAAGACAAAATTAAGA
             | || |||| ||| |        |   ||   ||    | | ||| | |  ||    | ||| |      | |  | | ||  | |    |    ||    ||  ||||   || |  | ||   |   |||   |     | | | ||  | ||   |||     |||| || | |||| | || ||||||  ||  ||  ||||||||||||| || ||||||||||||||||| ||||| ||||| ||||| ||||   ||||||
gtaacctgctgcctgctattttgcttttcagtagggatcaatcccgaactgtctaattcttggtattctagctttagatccgagattttactttgacttagagtcgtagttttagggggatttgataacatagtttacgaattaactgtaatgtcgtgacgttgtgctctctttccaacagGGCCGGACTGTTATCATCGAGCAATCTTTTGGATCTCCTAAAGTGACCAAGGATGGTGTTACTGTTGCGAAAAGCATTGAATTCAAGGACAGGCTTAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgtatcgaatttggtctaagactttctgctttatgtgattctaattttgaagGGACGTAATGTTGTGATTGAGCAAAGTTGGGGTGCTCCTAAAGTGACAAAAGATGGTGTTACTGTTGCCAAAAGTATTGAGTTCAAAGACAAAATTAAGA
                                         ttctaat  putative branch site (score: 2)
                                        attctaattttgaa  TA-rich tract