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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatcttatcttttaatccagaaagagtttgaaaagggtagtctcagacaatatctaaataatgttggctggatgcagTTTGTGGCTGGATCTCAACCGGTGAATGCTCTAGCGTTTGTTTTGGATGGGCTCTATTATGGTGTCTCTGACTTCGGATTTGCCGCTTATTCTATG

Basic information

species Arabidopsis thaliana
transcript AT2G38330.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G38330.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os12g01580.1 (Oryza sativa), 3'ss of exon 9
gtaagatcttatcttttaatccagaaagagtttgaaaagggtagtctcagacaatatctaaataat-----gttggctggatgcagTTTGTGGCTGGATCTCAACCGGTGAATGCTCTAGCGTTTGTTTTGGATGGGCTCTATTATGGTGTCTCTGACTTCGGATTTGCCGCTTATTCTATG
||||   ||  |||   ||  ||  |   | || |  | | |  | |   |   | |   | ||||     | ||| |   ||||||||||  |||  ||||||||  | |||||| | ||||||||  ||||||||||||| |||||||| |||||||| |  || |  || || ||||  
gtaatgactattctgagaagtcaatacttgatttaccaag-tgatatgcaatggttttatagtaattggctgatggatttttgcagTTTGTCACTGTTTCTCAACCAATAAATGCTGTTGCGTTTGTGATGGATGGGCTCTACTATGGTGTTTCTGACTTTGCTTTCGTGGCATACTCTACA

upper sequence: AT2G38330.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA07G19210.1 (Glycine max), 3'ss of exon 13
------------------gtaagatcttatcttttaatccagaaagagtttgaaaagggtagtctcagac--aatatctaaataatgttggctggatgcagTTTGTGGCTGGATCTCAACCGGTGAATGCTCTAGCGTTTGTTTTGGATGGGCTCTATTATGGTGTCTCTGACTTCGGATTTGCCGCTTATTCTATG
                  ||    |  |   |  |      | |||  | || |||  |||  |||      ||||||| ||   | ||  |  | |||||||||| |||||||||||||| ||||||||| | || |||||| | |||||| | |||||||| || || ||||| |||| ||| ||||| || |||
aatgttcattatatgcaagtgcagttctccatactttctgtggaagcatgtgtaaatagtaacctctattggaatatctgaaatttatttacatg-tgcagTTTGTTGCTGGATCTCAACCAGTGAATGCTTTGGCATTTGTTATTGATGGGATTTATTATGGGGTATCAGACTTTGGATATGCTGCTTACTCGATG

upper sequence: AT2G38330.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA18G43740.1 (Glycine max), 3'ss of exon 13
------------------gtaagatcttatcttttaatccagaaagagtttgaaaagggtagtctcag--acaatatctaaataatgttggctggatgcagTTTGTGGCTGGATCTCAACCGGTGAATGCTCTAGCGTTTGTTTTGGATGGGCTCTATTATGGTGTCTCTGACTTCGGATTTGCCGCTTATTCTATG----
                  ||   ||  |   || |      | |||  | |  | |  |||   |||     ||| ||| ||   | ||  |  | |||||||||| |||||||||||||| ||||||||| | || |||||| | |||||| | ||||| || || || ||||| || | ||| ||||| || |||    
aagggttcattatatgcagtgcaattctccattctttctgtggaagcatgtatacacagtaacgtcaattggaatgtctgaaatttatttacatg-tgcagTTTGTTGCTGGATCTCAACCAGTGAATGCTTTGGCATTTGTTATTGATGGGATTTATTACGGGGTATCAGACTTTGGTTATGCTGCTTACTCGATGGTAA

upper sequence: AT2G38330.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv08s0058g00510.t01 (Vitis vinifera), 3'ss of exon 10
--------gtaagatcttatcttttaatccagaaag-agtttgaaaagggtagt-ctcagacaatatc---taaataatgttggctgga------tgcagTTTGTGGCTGGATCTCAACCGGTGAATGCTCTAGCGTTTGTTTTGGATGGGCTCTATTATGGTGTCTCTGACTTCGGATTTGCCGCTTATTCTATG
        ||   ||  |||   | | | || |||   | ||        | || |   | | || ||   |||  ||| |  | |  |      |||||||||| ||||||||||||||  |||||||| | || |||||| | ||||| ||||| ||||| || || ||||| |||| ||| || || || |||
gtttccatgtggcattctattggtgagtgcataaactggcttacctcatttggtgcatgggctatgtcatttaagaaatttatgttataaaattttgcagTTTGTTGCTGGATCTCAACCAATGAATGCTATTGCATTTGTTATTGATGGACTCTACTATGGGGTTTCAGACTTTGGATATGCTGCCTACTCCATG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|19742531|gb|AU227884.1|AU227884
EST:     ATTCACAACGGATTCAGAAGTTTTAAAGATTGCTTTGTCA-GGACCCTTA                         TTTGTGCCTGGATCTCAACCGTTGAATGCTCTAGCCTTTGTTTT-GAT-G
genomic: ATTCACAACGGATTCAGAAGTTTTAAAGATTGCTTTGTCAGGGA-CCTTAgtaagatctt ... ctggatgcagTTTGTGGCTGGATCTCAACCGGTGAATGCTCTAGCGTTTGTTTTGGATGG
EST: gi|124870010|gb|EH954447.1|EH954447
EST:     ATTCAGAAGTTTTAAAGATTGCTTTGTCAGGGACCTTA                         TTTGTGGCTGGATCTCAACCGGTGAATGCTCTAG
genomic: ATTCAGAAGTTTTAAAGATTGCTTTGTCAGGGACCTTAgtaagatctt ... ctggatgcagTTTGTGGCTGGATCTCAACCGGTGAATGCTCTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagtttgaaaagggtagtctcagacaatatctaaataatgttggctggatgcagTTTGTGGCTGGATCTCAACCGGTGAATGCTCTAGCGTTTGTTTTGGATGGGCTCTATTATGGTGTCTCTGACTTCGGATTTGCCGCTTATTCTATG
                             atctaaa  putative branch site (score: 3)
                          aatatctaaataatgt  TA-rich tract