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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAAATTTTCGAAGGCCATTCCCATTATGTTATGCAAGTCACTTTCAACCCCAAAGACACCAATACTTTTGCTAGTGCATCCCTTGACCGTACCATAAAAgtaagattagtcttcaacttttaagttacaccttcttctttcattcccaatttcccattatgagaagcttaacatttgttttcctgtatctacatcttttcttacctag

Basic information

species Arabidopsis thaliana
transcript AT1G79990.5
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 6
TCAAATTTTCGAAGGCCATTCCCATTATGTTATGCAAGTCACTTTCAACCCCAAAGACACCAATACTTTTGCTAGTGCATCCCTTGACCGTACCATAAAAgtaaga---ttagtcttcaacttttaagttacaccttcttctttcattcccaatttcccattatgagaagcttaacatt-tgttttcctgtatctacatcttttcttacctag
|||||| ||||| || ||||| || ||||||||||||||||| || ||||| ||||| |||||||||||||||||||| || ||||| || ||  |||| ||  |    || ||     || |||   |  ||  |  || || |||| | ||  |  | |  |  | |  | ||  |  ||   |  | ||  | ||               
TCAAATCTTCGAGGGGCATTCTCACTATGTTATGCAAGTCACATTTAACCCGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAGgtttgcgattttgttccttacatttgcttggca--tagtttttgcatttctaacatttcttggtctggatttgaatgtggtgcccttatttaatttcag--------------

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GRMZM2G443953_T01 (Zea mays), 5'ss of exon 7
TCAAATTTTCGAAGGCCATTCCCATTATGTTATGCAAGTCACTTTCAACCCCAAAGACACCAATACTTTTGCTAGTGCATCCCTTGACCGTACCATAAAAgtaagattagtcttcaacttttaagttacaccttcttctttcattcccaatttcccattatgagaagcttaacatttgttttcctgtatctacatcttttcttacctag
||||||||| || ||||| || || ||||| ||||||||||| || |||||||||||||| ||||||||||||||||| || ||||| |||||  |||| |||     |    |    ||||   |||    |  |   || ||| |   ||| ||  | ||  |  ||||||      ||| || ||  |  |  || |         
TCAAATTTTTGAGGGCCACTCTCACTATGTCATGCAAGTCACATTTAACCCCAAAGACACAAATACTTTTGCTAGTGCTTCTCTTGATCGTACTGTAAAGgtatacccatatgttttattttgttttaatgataatgtattaatttctcgttttcctctttgctagccttaacgagcaattttctttacttgaaatttctag-------

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GRMZM2G141587_T01 (Zea mays), 5'ss of exon 6
TCAAATTTTCGAAGGCCATTCCCATTATGTTATGCAAGTCACTTTCAACCCCAAAGACACCAATACTTTTGCTAGTGCATCCCTTGACCGTACCATAAAAgtaagattagtcttcaacttttaagttacaccttcttctttcatt-cccaatttcccattatgagaagcttaacatttgttttcctgtatctacatcttttcttacctag
|||||| |||||||| ||||| || ||||| |||||||| || || ||||| ||||| ||||| || ||||||||||| ||||| || || || ||||| ||  |  || |||     ||  |||||     |  |       ||     ||||  | | || ||    || | | ||   |     ||||   || | |   || |   
TCAAATATTCGAAGGGCATTCTCACTATGTGATGCAAGTTACATTTAACCCAAAAGATACCAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgtttgtgtaatctctgctttaaaagttctggttggtcacaatgttgtattatttgtcgtcattagctttttcatagtttgatggtgatatcctaatttctgtctatcag-

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 6
TCAAATTTTCGAAGGCCATTCCCATTATGTTATGCAAGTCACTTTCAACCCCAAAGACACCAATACTTTTGCTAGTGCATCCCTTGACCGTACCATAAAAgtaagattagtcttcaacttttaagttacaccttcttctttcattcccaatttcccattatgagaagcttaacatttgttttcctgtatctacatcttttcttacctag
 || || || ||||||||||| |||||||| |||||||| || || || ||||||||||| || || |||||||||||||| ||||| || || ||||| |||  |||| | |||          ||   |||  || |||| |     ||    |||||    |    |    ||   ||| | |                       
CCAGATATTTGAAGGCCATTCTCATTATGTCATGCAAGTAACATTTAATCCCAAAGACACAAACACCTTTGCTAGTGCATCTCTTGATCGGACAATAAAGgtagaatta-tgttc----------ttgttcctggttgtttcctatgatataatgcattaatgcacctgttgtcttctcttttcag-----------------------

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 6
TCAAATTTTCGAAGGCCATTCCCATTATGTTATGCAAGTCACTTTCAACCCCAAAGACACCAATACTTTTGCTAGTGCATCCCTTGACCGTACCATAAAAgtaagattagtcttcaacttttaagttacaccttcttctttcattcccaatttcccattatgagaagct--taacatttgttttcctgtatc--tacatcttttcttacctag------
 || || || ||||| ||||| |||||||| |||||||| || || || ||||||||||| || || ||||| |||||||| ||||| || || ||||| ||   ||||   |     |  |   |      |  || ||  |     ||      |  | || || ||   | | | || | |  || ||   | || || || | | ||        
CCAGATATTTGAAGGTCATTCTCATTATGTCATGCAAGTAACATTTAATCCCAAAGACACAAACACCTTTGCAAGTGCATCTCTTGATCGGACAATAAAGgtgtaattatgttcttgttcctggat---gtttcttttttaaaaaaaaaaaaaagtaaaaagaaaaactatgatcctatgatataatgcattgatgcaactgttatcatctcttttcag

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 6
TCAAATTTTCGAAGGCCATTCCCATTATGTTATGCAAGTCACTTTCAACCCCAAAGACACCAATACTTTTGCTAGTGCATCCCTTGACCGTACCATAAAAgtaagattag--tcttcaacttttaagttac-accttcttctttcattcccaatttcccattatgagaagcttaacatttgttttcctgtatctac-atcttttcttacctag
||| || || || ||||| || |||||||| |||||||| || || || || ||||| ||||| ||||||||||||||||| || || || ||||| || ||| |||  |  | |||   |   || ||   | || | | |||  || |||||||  | | || |  ||  | |   |  | ||  ||     |  || | | |||  | ||
TCAGATCTTTGAGGGCCACTCTCATTATGTGATGCAAGTGACATTTAATCCAAAAGATACCAACACTTTTGCTAGTGCATCTCTGGATCGCACCATTAAGgtatgatctggattttctgttggcaacttgttaactgcattttt--ttaccaattttgcttcatca--agtatgagtgtgctatttatgctctgatgatatctccttttccag

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: PP1S79_180V6.2 (Physcomitrella patens), 5'ss of exon 6
TCAAATTTTCGAAGGCCATTCCCATTATGTTATGCAAGTCACTTTCAACCCCAAAGACACCAATACTTTTGCTAGTGCATCCCTTGACCGTACCATAAAAgtaagattagtcttcaacttttaagttacaccttcttctttcattcccaatttcccattatgagaagcttaacatttgttttcctgtatctacatcttttct---tacctag--------------------------------------------------------------------------------------
||||||||||||||| || || |||||||| |||||||| || || || |||||||||| ||| || ||||| ||||| ||  | || || ||  | || || || | |    |    |     |||  |  ||  |     |||  |  | |   | ||| | ||  |   |||  | || | | |    | | |||| |    ||   |                                                                                       
TCAAATTTTCGAAGGGCACTCTCATTATGTCATGCAAGTAACGTTTAATCCCAAAGACAGCAACACCTTTGCAAGTGCTTCTTTGGATCGAACTGTGAAGgtgaggt-accagttggttccgtcgtt-tatttttctgcagtattagctgtcttgaaatattacaaaat---catagggttccttatgctaatagctttaccccatattcaagcaacgaagttcaactgatgtaagattgtcttccaagacaatagaacaaaacgatggcttaattgtatggactgtctttttaacag

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|164181299|gb|ES085031.1|ES085031
EST:     CCAAAGACACCAATACTTTTGCTAGTGCATCCCTTGACCGTACCATAAAA                         ATATGGAATCTTGGCTCTCCGGATCCAAATTTTACTTTG
genomic: CCAAAGACACCAATACTTTTGCTAGTGCATCCCTTGACCGTACCATAAAAgtaagattag ... tcttacctagATATGGAATCTTGGCTCTCCGGATCCAAATTTTACTTTG