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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatagtcttacatagcaaaattagttagttagttagtgtattgatgtgtttgaatatttttagGGAGTTTAAGGAGAAGAACAAAGTGGATAAGTTGGTTGTGTTATGGACTGCAAACACAGAGCGTTATAGCAATGTGATTGTAGGACTTAACGATACGACG

Basic information

species Arabidopsis thaliana
transcript AT2G22240.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G22240.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 4
--------------------------------gtat-atagtcttacatagcaaaattagttagttagttagtgtattgatgtgtttgaatattt--ttagGGAGTTTAAGGAGAAGAACAAAGTGGATAAGTTGGTTGTGTTATGGACTGCAAACACAGAGCGTTATAGCAATGTGATTGTAGGACTTAACGATACGACG
                                  || | |  |||         |||    ||   | |     |  | || | ||| | || ||   ||||||||| ||||| |||| ||||||||| ||| |||| ||||| |||||||||||||| ||  | || ||||||||   ||| || || || || || | |
tagttccagtctgcattaagatggttggaacaacatgacaaacttgtgactatgaatgctgtaaacattagacatgat-attttttttattacttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGCAAACACTGAAAGGTACAGCAATGTCTGTGTTGGGCTCAATGACACAATG

upper sequence: AT2G22240.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 4
-----------------------------------gtatatagtcttacatagcaaaattagttagttagttagtgtattgatgtgtttgaatattt--ttagGGAGTTTAAGGAGAAGAACAAAGTGGATAAGTTGGTTGTGTTATGGACTGCAAACACAGAGCGTTATAGCAATGTGATTGTAGGACTTAACGATACGACG
                                     |||| || | || ||| | || || |   |||   |   ||| | | | | |   || |     ||||||||||||||||||||||||||||| ||| | |||||||| |||||||||||||| ||  | ||||||||||||   |  || || ||||| |||| |
acatggtttgaagatctagattaacgtggttgaagaaatatggt-tcac-tagtataagtaatccattacagaagctatggct-tatgtagctaatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGATAGTTGTGTTGTGGACTGCAAACACTGAAAGGTATAGCAATGTGTGCGCTGGTCTCAACGACACGATG

upper sequence: AT2G22240.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 4
--------------------------------gtatatagtcttacatagcaaaattagttagttagttagtgtattgat-gtgtttgaatattt--ttagGGAGTTTAAGGAGAAGAACAAAGTGGATAAGTTGGTTGTGTTATGGACTGCAAACACAGAGCGTTATAGCAATGTGATTGTAGGACTTAACGATACGACG
                                | |    | || || | | | |  || |   |||   |   ||| | |  | | |    | |     ||||||||||||||||||||||||||||| ||| | |||||| | |||||||||||||| ||  | || ||||||||   ||  || || ||||| || | |
atggtttggggatctagattaacatgattgaagcaacatggctcac-tggtatacgtaatccattatagaagctatggcttatatgtagccaatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGGTAGTTGTGCTGTGGACTGCAAACACTGAAAGGTACAGCAATGTATGTGCTGGTCTCAACGACACAATG

upper sequence: AT2G22240.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv07s0031g00920.t01 (Vitis vinifera), 3'ss of exon 4
-----------------gtatatagtcttacatagcaaaattagttagttagttagtgtattgatgtgtttgaatattt--ttagGGAGTTTAAGGAGAAGAACAAAGTGGATAAGTTGGTTGTGTTATGGACTGCAAACACAGAGCGTTATAGCAATGTGATTGTAGGACTTAACGATACGACG
                  |   ||  | |  ||   |||| | |   |    ||  |   ||  ||  |||| || | |  |||||||||||||||||   | ||| ||||||||| |||| ||| | |||||||| ||||||||||| || || ||| ||||||| ||||| || || || |  
gtagtcgtaatcttcaatttcttaaacatgaatcttaaaaatggaatgggcttttcttcttttctgattttgtatgtatgattagGGAGTTTAAGGAGGCAACCAAGGTGGATAAGGTGGTGGTGCTGTGGACTGCCAACACAGAGCGATACAGTAATTTGATTGTGGGACTGAATGACACCATA

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|124763839|gb|EH853969.1|EH853969
EST:     CAAGGACATGAG                         GGAGTTTAAGGAGAAGAACAAAGTGGATAAGTTGGTTGTGTTATGGACTGC
genomic: CAAGGACATGAGgtatatagtc ... atatttttagGGAGTTTAAGGAGAAGAACAAAGTGGATAAGTTGGTTGTGTTATGGACTGC
EST: gi|86066777|gb|DR362534.1|DR362534
EST:     ATCAAAGGTACCAAGAAGGAACAAGTTGATCACATCATCAAGGACATGAG                         GGAGTTTAAGGAGAAGAACAAAGTGGATAAGTTGGTTGTGTTATGGACTGC
genomic: ATCAAAGGTACCAAGAAGGAACAAGTTGATCACATCATCAAGGACATGAGgtatatagtc ... atatttttagGGAGTTTAAGGAGAAGAACAAAGTGGATAAGTTGGTTGTGTTATGGACTGC
EST: gi|116396086|gb|EG438678.1|EG438678
EST:     ATCAAAGGTACCAAGAAGGAACAAGTTGATCACATCATCAAGGACATGAG                         GGAGTTTAAGGAGAAGAACAAAGTGGATAAGTTGGTTGTGTTATGGACTGC
genomic: ATCAAAGGTACCAAGAAGGAACAAGTTGATCACATCATCAAGGACATGAGgtatatagtc ... atatttttagGGAGTTTAAGGAGAAGAACAAAGTGGATAAGTTGGTTGTGTTATGGACTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacatagcaaaattagttagttagttagtgtattgatgtgtttgaatatttttagGGAGTTTAAGGAGAAGAACAAAGTGGATAAGTTGGTTGTGTTATGGACTGCAAACACAGAGCGTTATAGCAATGTGATTGTAGGACTTAACGATACGACG
                              tattgat  putative branch site (score: 3)
                                              tattttt  putative PPT
                                      tgtttgaatattttta  TA-rich tract