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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCTGCAACATATCTTGCTTGATATTCCAAGTCTTGCTTTCTTCACCACCTATGCTCTTCTGGTTCTTTTCTGGGCTGAAATTTATTATCAGgtagtttctaatgagtatctatgggtttctttttttgtcaatgcttctttggttttgatattttacttaacactcttttgattggacag

Basic information

species Arabidopsis thaliana
transcript AT2G02180.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G02180.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os03g02850.2 (Oryza sativa), 5'ss of exon 4
ATTCTGCAACATATCTTGCTTGATATTCCAAGTCTTGCTTTCTTCACCACCTATGCTCTTCTGGTTCTTTTCTGGGCTGAAATTTATTATCAGgt-agtttctaatgagtatctatgggtttctttttttgtcaatgcttctttggttttgatattttact-taacactcttttgattggacag
 |  | |||||| |  |  ||||| ||||  | ||||| |||||||| |||||||||||  | || || ||||||||||| ||||| |||||||| |||||    ||  ||| | | |||||  |    ||     |  | |||| | |   |  || |   |  || |  || |         
GTATTTCAACATGTGCTCATTGATTTTCCGGGGCTTGCATTCTTCACAACCTATGCTCTGTTAGTGCTCTTCTGGGCTGAGATTTACTATCAGgttagttttacttggatatattttggttttgtcccatgg----gtgtttttgttctcattggttcatgatggcatttgttag---------

upper sequence: AT2G02180.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G003076_T02 (Zea mays), 5'ss of exon 4
ATTCTGCAACATATCTTGCTTGATATTCCAAGTCTTGCTTTCTTCACCACCTATGCTCTTCTGGTTCTTTTCTGGGCTGAAATTTATTATCAGgtagtttctaatgagtatctatgggtttc--tttttttgtcaatgcttctttggttttgatattttacttaacactcttttgattggacag
||  | |||||| |  | || ||||| ||  | ||||| |||||||| || ||||| ||| | || || ||||||||||| ||||||||||||||| ||  |  ||  | | | |||   ||  || ||||||||||| |  | ||  | | | |||||  ||     ||| | |         
ATAATACAACATGTGCTTCTGGATATGCCCGGGCTTGCATTCTTCACGACATATGCACTTTTAGTGCTCTTCTGGGCTGAGATTTATTATCAGgtatttctttttgtctctgt-tggacctctattgttttgtcaatgttgttgtgcctctta-atttttgttcctgttctctag---------

upper sequence: AT2G02180.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G426306_T01 (Zea mays), 5'ss of exon 5
ATTCTGCAACATATCTTGCTTGATATTCCAAGTCTTGCTTTCTTCACCACCTATGCTCTTCTGGTTCTTTTCTGGGCTGAAATTTATTATCAGgtagtttctaatgagtat-ctatgggtttctttttttgtcaatgcttctttggttttgatattttacttaacactcttttgattggacag
||  | |||||| |  | || ||||| ||  | ||||| |||||||| || ||||| ||| | || || ||||||||||| ||||||||||||||| || ||  |   | |  ||    | | || ||||||||||| |  | ||  | | | |||||  ||     ||| | |         
ATAATACAACATGTGCTTCTGGATATGCCCGGGCTTGCATTCTTCACGACATATGCACTTTTAGTGCTCTTCTGGGCTGAGATTTATTATCAGgtatttccttttatctctgttagacctctattgttttgtcaatgttgttgtgcctctta-atttttgttcctgttctctag---------

upper sequence: AT2G02180.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G174286_T03 (Zea mays), 5'ss of exon 5
ATTCTGCAACATATCTTGCTTGATATTCCAAGTCTTGCTTTCTTCACCACCTATGCTCTTCTGGTTCTTTTCTGGGCTGAAATTTATTATCAGgtagtttctaatgagtatctatgggtttcttt----ttttgtcaatgcttctttggttttgatattttacttaacactcttttgattggacag
||  | || ||| |  | || ||||| ||  | ||||| |||||||| || ||||| ||||| || || |||||||| || |||||||||||||||  |  |  ||  | |  || |   ||| |    |||||| |||| |  |  | || | | |||||  || |   ||| | |         
ATAATACAGCATGTGCTTCTAGATATGCCTGGGCTTGCATTCTTCACAACATATGCACTTCTAGTGCTCTTCTGGGCAGAGATTTATTATCAGgtacctcgttttgtctctg-atagacctctctattgttttgttaatgttgttgcgcttctta-atttttgttcatgttctgtag---------

upper sequence: AT2G02180.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA07G28990.1 (Glycine max), 5'ss of exon 4
ATTCTGCAACATATCTTGCTTGATATTCCAAGTCTTGCTTTCTTCACCACCTATGCTCTTCTGGTTCTTTTCTGGGCTGAAATTTATTATCAGgtagtttctaatgagtatctatgggtttcttttt--ttgtcaatgcttctttggttttgatattttacttaacactcttt--tgattggacag----------------------------------------
||| | ||||| |||||||||||  | || |||||||||||||| || || ||||| ||| |||| || ||||||||||| ||||||||||||| |  ||  | |     |  ||  | ||||   |  |||      || || || ||||  | ||  |  ||      |||  |||||||                                            
ATTGTTCAACACATCTTGCTTGACGTGCCGAGTCTTGCTTTCTTTACAACATATGCACTTTTGGTCCTGTTCTGGGCTGAGATTTATTATCAGgcaagtttgatttgtggtgcatttgcttctacatggttggtttgcctcctgtgattttcttcttccaggtagtgtgttttgctgattggttttgatgggctgattactgcctcggtgttaaatgctttttcag

upper sequence: AT2G02180.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA08G09640.1 (Glycine max), 5'ss of exon 4
ATTCTGCAACATATCTTGCTTGATATTCCAAGTCTTGCTTTCTTCACCACCTATGCTCTTCTGGTTCTTTTCTGGGCTGAAATTTATTATCAGgtagtttc------taatgagtatctatgggtttctttttttgtcaatgcttctttggttttgatattttacttaacactcttttgattggacag-----------------------
||| | ||||||||||| ||||| || || |||||||||||||| || || ||||| ||  |||| || ||||||||||| |||||||| |||| |  |||      |  |   | |  ||    |  |||| || | ||||  | |  | | ||| ||||||  |   |    || ||| |  |                          
ATTGTCCAACATATCTTACTTGACATGCCTAGTCTTGCTTTCTTTACAACTTATGCGCTGTTGGTACTGTTCTGGGCTGAGATTTATTACCAGgcaagttcattctgtggtatatgtacatttactatttttctttttaatgagtatgggatattgctattttggt-ggcctgattatgagtttatgactttgatgctacatgttttgcag

upper sequence: AT2G02180.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA05G26630.2 (Glycine max), 5'ss of exon 4
ATTCTGCAACATATCTTGCTTGATATTCCAAGTCTTGCTTTCTTCACCACCTATGCTCTTCTGGTTCTTTTCTGGGCTGAAATTTATTATCAGgt------agtttctaatgagtatctatgggtttctttttttgtcaat----gcttctttggttttgatattttacttaacactcttttgattggacag-----------
||| | ||||||||||| ||||| || || |||||||||||||| || || ||||| ||  |||| || ||||||||||| |||||||| ||||       | ||  |  ||  | | ||  | |||  |||||  | |      | |  |    ||||| |    |  |||  ||| |  || |  |  |            
ATTGTCCAACATATCTTACTTGACATGCCTAGTCTTGCTTTCTTTACAACTTATGCACTGTTGGTACTGTTCTGGGCTGAGATTTATTACCAGgcaagttgaattcgtggtgcatttttactgtttttctttttaattagcttgggatgttgctattttggtggcctgattatgactttgatgctacgttacctgtttggcag

upper sequence: AT2G02180.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA20G01360.1 (Glycine max), 5'ss of exon 4
ATTCTGCAACATATCTTGCTTGATATTCCAAGTCTTGCTTTCTTCACCACCTATGCTCTTCTGGTTCTTTTCTGGGCTGAAATTTATTATCAGgtagtttctaatgagtatctatgggtttcttttt--ttgtcaatgcttctttggttttgatattttacttaa---cactcttttgattggacag----------------------------------------
||| | ||||| |||||||||||  | || |||||||||||||| || || ||||| ||| |||| || ||||||||||| |||||||| |||| |  ||  | |     |  ||  | ||||   |  |||      || || || ||||  ||||  |    |      | |  |||||||                                            
ATTGTTCAACACATCTTGCTTGACGTGCCGAGTCTTGCTTTCTTTACAACATATGCACTTTTGGTCCTGTTCTGGGCTGAGATTTATTACCAGgcaagtttgatttgtggtgcatttgcttctacatggttggtttgcctcctgtgattttcttattccatggcagtgtgttttgctgattggttttgatgggctgattactgcctcggtgttaaatgcttttgcag

upper sequence: AT2G02180.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA02G19410.1 (Glycine max), 5'ss of exon 4
ATTCTGCAACATATCTTGCTTGATATTCCAAGTCTTGCTTTCTTCACCACCTATGCTCTTCTGGTTCTTTTCTGGGCTGAAATTTATTATCAGg------tagtttctaatgagta----tctatgggtttctttttttgtcaatgcttctttggttt--tgatattttacttaac--actc-ttttgattggacag------------------------------
||| | ||||| ||||||||||| ||  | |||||||||||||| || || ||||| ||| |||| || |||| |||||| |||||||| ||||      |  ||| |  ||  |     ||||   | ||  |||     | ||| || |||  ||   ||  | | |  ||  |  | |  ||||||| ||  |                               
ATTGTTCAACACATCTTGCTTGACATGTCGAGTCTTGCTTTCTTTACAACATATGCACTTTTGgtcctgttctaggctgagatttattaccaggctagtttgatttgtggtgcatttgcttctacatggttggtttgcctcctatgatttttttcttccatggcagtgtgttttgctgattggttttgatgggctaattaccacctcggtgttaaatgcttttgcag

upper sequence: AT2G02180.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv01s0010g01740.t01 (Vitis vinifera), 5'ss of exon 4
ATTCTGCAACATATCTTGCTTGATATTCCAAGTCTTGCTTTCTTCACCACCTATGCTCTTCTGGTTCTTTTCTGGGCTGAAATTTATTATCAGgtagtttctaatgagtatctatgggtttctttttttgtcaatgcttctttggttttgatattttacttaacactcttttgattggacag
||| | ||||||||||| |||||||| |||||||||||||||||||| |||||||||||| ||||  | |||||||| ||||| || ||||||||      ||   |  |  ||||||| |   | ||| |  ||| || | | ||| | |  ||   || |  | | | |  |   |||||
ATTATCCAACATATCTTACTTGATATGCCAAGTCTTGCTTTCTTCACAACCTATGCTCTTTTGGTATTGTTCTGGGCAGAAATATACTATCAGgt------taggcataacttatgggtcttactcttt-tgtatgtttgtattgttatta-gttcgtctcattattttctcaacatgacag

upper sequence: AT2G02180.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S295_28V6.1 (Physcomitrella patens), 5'ss of exon 4
ATTCTGCAACATATCTTGCTTGATATTCCAAGTCTTGCTTTCTTCACCACCTATGCTCTTCTGGTTCTTTTCTGGGCTGAAATTTATTATCAGgtagtttctaatgagtatctatgggtttctttttttgtcaatgcttctttggttttgatattttacttaacactcttttgattggacag------------------------------------------------------------------
||  |||||||  |  |  | ||| | ||  |  |   ||||||||| || ||| |||||||||| ||||||||||||||||| ||| | ||||||   |     | |  ||| |   || |   |  |  | ||||| ||   ||| | | |  |  || || |   | |  |||  |  |                                                                  
ATATTGCAACACGTTCTTTTGGATCTGCCGGGCATAATTTTCTTCACAACATATACTCTTCTGGTGCTTTTCTGGGCTGAAATCTATCACCAGgtaaggttgggagtggctctcttcatt-caactggtagctatgctgcta-agttctcacaaatggctgaa-atgttctgaattctatggagttgagtgcacccatgtaacagacgacatgcgagatttattgtgcggatttttctgtgatttcag

upper sequence: AT2G02180.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S237_67V6.1 (Physcomitrella patens), 5'ss of exon 4
ATTCTGCAACATATCTTGCTTGATATTCCAAGTCTTGCTTTCTTCACCACCTATGCTCTTCTGGTTCTTTTCTGGGCTGAAATTTATTATCAGgta-----------gtttctaatgagt--atctatgggtttcttttt---ttgtcaatgcttctttggttttgatattttacttaacactcttttgat-----tggacag-------------------------------------------
||  | || ||  |  |  | ||  | ||  |  ||   || |||||||| ||| ||||||||||  | |||||||||||||||||| | |||||             |||||  | | |   |    || | |  || |   || |||        | |  | |||||  || |  | |   || ||| |     ||| |                                             
ATATTACAGCACGTTCTTTTGGACCTGCCGGGCATTTTGTTTTTCACCACATATACTCTTCTGGTGTTGTTCTGGGCTGAAATTTATCACCAGgtgcgtatgttaggatttctcttcatttagttagcggctgtgcttctaacttttcagaagggagtagagtatgataagttgcgcatcgtgctgttgttccttgtggccgataagattcggggattgattgtgagatatatgttgccatttcag

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|19877197|gb|AU238028.1|AU238028
EST:     TCACCACCTATGCTCTTCTGGTTCTTTTCTGGGCTGAAATTTATTATCAG                         GCGCGTGCAGTATCGACTGATGGACTCAGGCCAAGCTTCTTCACAATTAAT
genomic: TCACCACCTATGCTCTTCTGGTTCTTTTCTGGGCTGAAATTTATTATCAGgtagtttcta ... gattggacagGCGCGTGCAGTATCGACTGATGGACTCAGGCCAAGCTTCTTCACAATTAAT