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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGATGCAAACTCCTGAAACTTTGGCGCGACCAGAAAATCCAAATCCAAAGTGGCCTGTGCCAAAGGATCTTATTGAGTTACAGCCTTCATATAAGCAGgtagatatgcgtataaaccatcttataagttaacgacttggttcctggaatggtatactcaaatgcattacttcattattcag

Basic information

species Arabidopsis thaliana
transcript AT3G54460.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G54460.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os01g72310.1 (Oryza sativa), 5'ss of exon 3
TGAGATGCAAACTCCTGAAACTTTGGCGCGACCAGAAAATCCAAATCCAAAGTGGCCTGTGCCAAAGGATCTTATTGAGTTACAGCCTTCATATAAGCAGgtagatatgcgtataaaccatcttataagttaacgacttggttcctggaatgg-------tatactcaaatgca---ttacttcattattcag
||||||||| ||||||||||||   || || |||||||||||||| ||||| ||||| ||||| || || || |||||||| ||||||||||||||||||||   ||   || |      |  |   | || |  | |   ||  || | | |       | |    |||| ||   || |    ||||  ||
TGAGATGCAGACTCCTGAAACTCGTGCACGGCCAGAAAATCCAAACCCAAAATGGCCAGTGCCCAAAGACCTAATTGAGTTGCAGCCTTCATATAAGCAGgtcagtacttgtgtgctatgttatgctacttcatcattcttttgttgcagttgaaaagattgtctctaaatacaaatttcccatcttatgtag

upper sequence: AT3G54460.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G379804_T01 (Zea mays), 5'ss of exon 2
TGAGATGCAAACTCCTGAAACTTTGGCGCGACCAGAAAATCCAAATCCAAAGTGGCCTGTGCCAAAGGATCTTATTGAGTTACAGCCTTCATATAAGCAGgtagatatgcgtataaaccatcttataagttaacgacttg---gttcctggaatggtatactcaaatgcattacttcattattcag
|||||||||  ||||||| |||   ||  | |||||||||||||| ||||||||||| ||||| |||||||| ||||| || || ||||||||||||||||||  |    ||   | |      ||   |   |   |||   | |  || ||    ||  ||  |    || |    ||  | ||
TGAGATGCAGTCTCCTGAGACTCGTGCAAGGCCAGAAAATCCAAACCCAAAGTGGCCAGTGCCTAAGGATCTAATTGAATTGCAACCTTCATATAAGCAGgtacgtgcttgtgctatcttgtccatttttatcccctttgtgtgctattgaaaataaattttctgaaattttgcaat-ttccttag

upper sequence: AT3G54460.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA11G21600.1 (Glycine max), 5'ss of exon 3
TGAGATGCAAACTCCTGAAACTTTGGCGCGACCAGAAAATCCAAATCCAAAGTGGCCTGTGCCAAAGGATCTTATTGAGTTACAGCCTTCATATAAGCAGgta-gatatgcgtataaaccatcttataa----gttaacgacttggttcctggaatggtatactcaaatgcattacttcattattcag-------
                        ||| ||||| |||||||| || || ||||||||||| || || |||||||||||| |||| |||||||||||||||| | | |    | | ||  ||  | | |      ||     |    || ||||  ||  || || | ||||| |  || |||||| |        
---------------------AGAGGCCCGACCTGAAAATCCTAAACCGAAGTGGCCTGTACCCAAAGATCTTATTGAGCTACAACCTTCATATAAGCAGGCATGGTTAATGGAGAACTCAgttaacattcatctttttttccctctttctggtttgcaatgctaacatgcaatg-ttgattatttaatacccag

upper sequence: AT3G54460.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA04G28970.1 (Glycine max), 5'ss of exon 4
-------------------------------------------------------TGAGATGCAAACTCCTGAAACTTTGGCGCGACCAGAAAATCCAAATCCAAAGTGGCCTGTGCCAAAGGATCTTATTGAGTTACAGCCTTCATATAAGCAGgta-gatatgcgtataaaccatcttataagttaacgacttggttcctggaatggtatactcaaatgcattacttcattattcag
                                                       ||||||||| | |   ||      ||| ||||| |||||||| || || ||||||||||| || || |||||||||||| |||| |||||||||||||||| | | |    | |                                                                      
ATTGTGTTTCTATAGACAATACAAAGTGTACTTATCCTGGCTGCAGTAAATTGTATGAGATGCAGAGTAGAGA------GGCCCGACCTGAAAATCCTAAACCGAAgtggcctgtacccaaagatcttattgagctacaaccttcatataagcaggcatggttaatggag---------------------------------------------------------------------

upper sequence: AT3G54460.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA04G28970.2 (Glycine max), 5'ss of exon 3
------------------------------------------------TGAGATGCAAACTCCTGAAACTTTGGCGCGACCAGAAAATCCAAATCCAAAGTGGCCTGTGCCAAAGGATCTTATTGAGTTACAGCCTTCATATAAGCAGgta-gatatgcgtataaaccatct-----tataagttaacgacttgg-----ttcctggaatggtatactcaaatgcattacttcattattcag-------
                                                ||||||||| | |   ||      ||| ||||| |||||||| || || ||||||||||| || || |||||||||||| |||| |||||||||||||||| | | |    | | ||  || ||     ||  | | | |   ||       || ||||  ||  ||  | | |||||||  || ||| || |        
TTCTATAGACAATACAAAGTGTACTTATCCTGGCTGCAGTAAATTGTATGAGATGCAGAGTAGAGA------GGCCCGACCTGAAAATCCTAAACCGAAGTGGCCTgtacccaaagatcttattgagctacaaccttcatataagcaggcatggttaatggagaactcagctggcattaacattcatctttttttccctctttctggtttgcaatggtaacatgcattg-ttgattgtttaatacccag

upper sequence: AT3G54460.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv13s0067g03330.t01 (Vitis vinifera), 5'ss of exon 4
TGAGATGCAAACTCCTGAAACTTTGGCGCGACCAGAAAATCCAAATCCAAAGTGGCCTGTGCCAAAGGATCTTATTGAGTTACAGCCTTCATATAAGCAGgtagatatgcgtataaaccatcttataagttaacgacttggttcctggaatggtatactcaaatgcattacttcattattcag---------------------
|||||||||  |||||||||  ||  | || ||||||||||| || |||||||||||||| || || || ||||||||||||||||||||||||||||||||| |  |  |||  |   || |  | | | |    ||   ||| |  |||  |     |  |  || |  |  || |||                        
TGAGATGCAGTCTCCTGAAATATTAACCCGTCCAGAAAATCCCAACCCAAAGTGGCCTGTTCCCAAAGACCTTATTGAGTTACAGCCTTCATATAAGCAGgtaaac-taagtactataaatatgttgaatca-tatctattttcttcaaattttcactcctcaaacaatgttctatgatttgatatattgtggtttttatacag

upper sequence: AT3G54460.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S15_94V6.1 (Physcomitrella patens), 5'ss of exon 4
TGAGATGCAAACTCCTGAAACTTTGGCGCGACCAGAAAATCCAAATCCAAAGTGGCCTGTGCCAAAGGATCTTATTGAGTTACAGCCTTCATATAAGCAGgtagatatgcgtataaaccatc--ttataagttaacgacttggttc--ctggaatggtatactcaaatgcattacttcatta-ttcag---------------------------------------------------------------------------------------
  ||||||| | |||||     ||||| || || ||||||||||  ||||||||||| |||||  ||||||| |||||||| ||||| |||||    ||||||   ||     |      |   ||  ||| |  ||      ||      ||||   ||    |    || | |  |     || ||                                                                                       
CAAGATGCAGAGTCCTGCTGAATTGGCTCGTCCTGAAAATCCAACACCAAAGTGGCCCGTGCCGCAGGATCTCATTGAGTTGCAGCCATCATACGCTCAGgtaataatttaggtgcgttgtggatttcaaggttgcggaggcattaaatccgaattacatgtgtactatcacttcgacgacgctttaggtagtttggcatgttacagacgttccatgttcaaatgacttttgtcctctgtcttcttgcatttctgaggctttgattgtgtggcag

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|164076508|gb|ES140419.1|ES140419
EST:     ATCTTATTGAGTTACAGCCTTCATATAAGCAG                         GACGATTGGAATCCTGACTGGCAATCTACGTCCAGCAGTAAAGTCAGTTAT
genomic: ATCTTATTGAGTTACAGCCTTCATATAAGCAGgtagatatgc ... cattattcagGACGATTGGAATCCTGACTGGCAATCTACGTCCAGCAGTAAAGTCAGTTAT